scholarly journals Transcriptional expressions of SCNs family correlates with overall survival in patients with breast cancer

2022 ◽  
Author(s):  
Wenxing Peng ◽  
Xiujin Shi ◽  
Yifan Wang ◽  
Huanyu Qiao ◽  
Yang Lin
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Mrna Expression ◽  
Protein Complexes ◽  
Her2 Positive ◽  
Kaplan Meier ◽  
Nav Channels ◽  
The Relationship ◽  
Kaplan Meier Plotter ◽  
Α Subunits

Introduction: Voltage-gated sodium (Nav) channels encoded by SCNs are heteromeric protein complexes containing pore-forming α subunits together with non-pore-forming β subunits. Methods: To analyze the expression of SCNs in the samples of different types of breast cancer (BC) patients and the relationship between the expression of α and β subunits and the prognosis of in BC patients, the study investigated the roles of SCNs in the prognosis of BC using ONCOMINE, UALCAN, Kaplan-Meier Plotter, GEPIA, Metascape, LinkedOmics databases. The study analyzed significant changes of SCNs expression and prognosis in transcription level between BC and normal samples, and association of mRNA expression of distinct SCNs family members with prognosis in overall BC patients and HER2-positive/HER2-negative subgroups, respectively. Moreover, we predicted functions and pathways of the mutations in SCNs and their neighbor genes in BC patients by GO/KEGG and GSEA analysis. Results: The results showed that transcriptional and proteinic expressions of 9 SCNs were downregulated in patients with BC, including SCN1A~4A, 7A, 9A and SCN2B~4B. low expressions of 11 SCNs members were found to be significantly associated with poorer overall survival (OS) in BC patients (P＜0.01), including SCN2A, 3A, 5A, 7A, 9A~11A and SCN1B~4B. Moreover, prognostic value of mRNA expression of SCNs could only be seen in HER2-negative BC patients when we performed subgroup analysis. Conclusions: These results indicated that SCNs could be prognostic biomarkers for survivals of BC patients. Some medicines that regulate SCNs might provide new targets for BC treatment.

scholarly journals Transcriptional Expressions of SCNs Family Correlates With Overall Survival in Patients With Breast Cancer

2021 ◽  
Author(s):  
Wenxing Peng ◽  
Xiujin Shi ◽  
Yi Zhang ◽  
Honglei Zhao ◽  
Yunnan Zhang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Prognostic Value ◽  
Protein Complexes ◽  
Invasion And Metastasis ◽  
Cellular Processes ◽  
Metastatic Cells ◽  
Kaplan Meier ◽  
Nav Channels ◽  
Kaplan Meier Plotter ◽  
Α Subunits

Abstract Background: Voltage-gated sodium (Nav) channels encoded by SCNs are heteromeric protein complexes containing pore-forming α subunits together with non-pore-forming β subunits. Ion channels play an important role in the regulation of many cellular processes during normal physiology, and increasingly recognized for their contribution to pathophysiology, including cancers. Numerous studies in the last years have reported the expression of SCNs in metastatic cells of many cancers and their upregulation have been evident in promoting migration, invasion and metastasis, whereas it remains unclear whether distinct SCNs family members play an important role in the development and progression of BC. Results: The study investigated the roles of SCNs in the prognosis of BC using ONCOMINE, UALCAN, Kaplan-Meier Plotter, GEPIA, Metascape, LinkedOmics databases. The results showed that transcriptional and proteinic expressions of 9 SCNs were downregulated in patients with BC, including SCN1A~4A, 7A, 9A and SCN2B~4B. low expressions of 11 SCNs members were found to be significantly associated with poorer overall survival (OS) in BC patients (P＜0.01), including SCN2A, 3A, 5A, 7A, 9A~11A and SCN1B~4B. Moreover, prognostic value of mRNA expression of SCNs could only be seen in HER2-negative BC patients when we performed subgroup analysis. Conclusions: These results indicated that SCNs could be prognostic biomarkers for survivals of BC patients. Some medicines that regulate SCNs might provide new targets for BC treatment.

scholarly journals Paclitaxel Promotes Tumor-Infiltrating Macrophages in Breast Cancer

2020 ◽  
Vol 19 ◽  
pp. 153303382094582
Author(s):  
Jun Shen ◽  
Cong Chen ◽  
Zhaoqing Li ◽  
Shufang Hu
Keyword(s):  
Breast Cancer ◽  
Progression Free Survival ◽  
Cancer Prognosis ◽  
Migration And Invasion ◽  
P Value ◽  
Free Survival ◽  
Kaplan Meier ◽  
The Relationship ◽  
Kaplan Meier Plotter ◽  
Paclitaxel Treatment

Objective: Breast cancer remains the most threatening triggers of cancer death in women. Drug resistance inevitably leads to the weakness of treatment for breast cancer. Macrophages, as one of the most abundant immune cells in tumor immune-infiltrating microenvironment, involves in cell survival, migration, and invasion of breast cancer. Methods: In this study, we compared the proportions of macrophages in patients with breast cancer with and without paclitaxel treatment, and investigated the targeted genes associated with macrophages for paclitaxel response. To explore the relationship between drug-related genes and breast cancer prognosis, survival analysis based on the drug-related genes were performed by website of Kaplan-Meier plotter with the threshold of significant P value < .05. Results: Compared to the normal samples, we revealed that paclitaxel significantly enhanced the ratio of macrophages in the tumor microenvironment. Furthermore, the expression of 3 drug-related genes (IFT46, PEX11A, and TMEM223) were significantly negatively associated with the proportions of macrophages. And it is worth to notice that PEX11A and TMEM223 were associated with better progression-free survival outcomes of patients with breast cancer. Moreover, PEX11A was associated with longer overall survival time of breast cancer. Conclusion: Taken all together, all the findings support to gain a better understanding to the development of more effective therapies targeted with paclitaxel.

scholarly journals PER1 Is a Prognostic Biomarker and Correlated With Immune Infiltrates in Ovarian Cancer

2021 ◽  
Vol 12 ◽  
Author(s):  
Mali Chen ◽  
Lili Zhang ◽  
Xiaolong Liu ◽  
Zhen Ma ◽  
Ling Lv
Keyword(s):  
Ovarian Cancer ◽  
Overall Survival ◽  
Transcription Factors ◽  
Prognostic Biomarker ◽  
Poor Overall Survival ◽  
Immune Infiltration ◽  
Kaplan Meier ◽  
Stage 1 ◽  
The Relationship ◽  
Kaplan Meier Plotter

Background: Period circadian protein homolog 1 (PER1) is an important component of the biorhythm molecular oscillation system and plays an important part in the development and progression of mammalian cancer. However, the correlations of PER1 with prognosis and tumor-infiltrating lymphocytes in ovarian cancer (OV) remain unclear.Methods: The Oncomine and TIMER databases were used to examine the expression of PER1 in OV. Kaplan–Meier Plotter and PrognoScan were used to evaluate the relationship between PER1 and prognosis. Kaplan–Meier Plotter was used to analyze the relationships between PER1 and clinicopathological features of OV patients. The relationship between PER1 expression and immune infiltration in OV was investigated using the TIMER database and CIBERSORT algorithm. The STRING database was used to analyze PER1-related protein functional groups, the GeneMANIA online tool was used to analyze gene groups with similar functions to those of PER1, and Network Analyst was used to identify transcription factors that regulate PER1. The correlation between PER1 and immunoinvasion of OV was analyzed using TIMER. Finally, quantitative real-time polymerase chain reaction (qRT-PCR) was performed to detect PER1 expression.Results: PER1 was differentially expressed in different cancer tissues, and its expression in various OV subtypes was lower than that in normal ovarian tissue. OV patients with low PER1 expression had a reduced overall survival rate. Decreased PER1 expression in stage 1 and stage 1+2 OV patients was related to poor prognosis, while increased PER1 expression in stage 3+4 patients and TP53 mutation were related to poor overall survival and progression-free survival. We identified eight genes whose expression was strongly correlated with that of PER1, as well as four transcription factors that regulate PER1. In OV, PER1 expression levels were positively correlated with infiltration levels of cells including neutrophils, regulatory T cells, and M2 macrophages, and closely related to a variety of immune markers. Reduced expression of PER1 was significantly associated with poor overall survival.Conclusion: These findings suggest that PER1 could be used as a prognostic biomarker to determine prognosis and immune infiltration in OV patients.

scholarly journals MEX3A and MEX3B as Potential Prognostic Indicators in Stomach Adenocarcinoma

2021 ◽  
Author(s):  
Junwei Zou ◽  
Yong Huang ◽  
Zhaoying Wu ◽  
Hao Xie ◽  
Rongsheng Wang ◽  
...  
Keyword(s):  
Overall Survival ◽  
Rna Splicing ◽  
Rna Binding ◽  
The Cancer Genome Atlas ◽  
Prognostic Indicators ◽  
Kaplan Meier ◽  
Cancer Genome Atlas ◽  
Stomach Adenocarcinoma ◽  
Tumor Pathogenesis ◽  
Kaplan Meier Plotter

Abstract Stomach adenocarcinoma(STAD) is one of the deadliest cancers in the world. The expression levels of family members of mex-3 RNA that bound MEX3A (member A) and MEX3B (member B) were high expressions in different cancers and interconnected to deficient prognosis. The present research assessed the potential regarding the expression of MEX3A and MEX3B in STAD by analysing the facts of STAD (viz. The Cancer Genome Atlas). TCGA, MEX3A and MEX3B in the cancers were analyzed using TIMER2.0, Kaplan Meier Plotter, and cBioPortal. The data was visualized using version 4.0.3 of R. We found MEX3A and MEX3B had various expressions regarding major cancer and relevant common tissues. Especially, high expression of MEX3A and MEX3B had relationships with the OS (namely overall survival) with deficiency and RFS (viz. relapse-free survival) concerning STAD. The expressions of MEX3B had correlations to T stage with P being 0.012 and to the race with P being 0.049. MEX3B was highly expressed in T3 and T4 stages, and was highly expressed in the white race. MEX3A mutation had a better survival without diseases, with P being 0.0205. However, the situation was different with non-overall survival, with P being 0.194, in comparison with the patients who did not have MEX3A change. MEX3A and MEX3B on tumor pathogenesis might be related to "RNA splicing" and "spliceosomal complex" and "single-stranded RNA binding". We further investigated the association between MEX3A and MEX3B and immune cells. The mast cells of the most connections to MEX3A (R=-0.300, P<0.001) and the NK cells were positively correlation with MEX3B (R=0.590, P<0.001). It showed that they might be potential prognostic molecular biomarkers in patients with STAD.

scholarly journals Identification of Flap Endonuclease 1 With Diagnostic and Prognostic Value in Breast Cancer

2021 ◽  
Vol 11 ◽  
Author(s):  
Min Wu ◽  
Pan Zhang ◽  
Penghui Wang ◽  
Zhen Fang ◽  
Yaqin Zhu
Keyword(s):  
Breast Cancer ◽  
Prognostic Marker ◽  
Prognostic Value ◽  
Diagnostic Value ◽  
Roc Curve Analysis ◽  
Free Survival ◽  
Flap Endonuclease 1 ◽  
Normal Tissues ◽  
Kaplan Meier ◽  
Kaplan Meier Plotter

ObjectiveThis study aims to identify the potential value of flap endonuclease 1 (FEN1) as a diagnostic and prognostic marker for breast cancer (BC).MethodsELISA was used to measure serum FEN1 levels and ECLIA for CA153 and CEA levels. Receiver operating characteristic (ROC) curve analysis was used to evaluate the diagnostic value. Oncomine and UALCAN databases were used to analyze the differences in FEN1 mRNA and protein expressions. Kaplan-Meier Plotter database was then used to assess the prognostic value.ResultsBioinformatics analysis showed that the FEN1 mRNA and protein levels were significantly higher in BC tissues than in normal tissues. FEN1 was detected in culture medium of BC cell lines and serum FEN1 concentrations were significantly increased in BC patients than in cancer-free individuals. Besides, FEN1 exhibited higher diagnostic accuracy (AUC values&gt;0.800) than CA153 and CEA for distinguishing BC patients, especially early BC, from the healthy and benign groups, or individually. Additionally, serum FEN1 levels were significantly associated with the stage (P=0.001) and lymph invasion (P=0.016), and serum FEN1 levels were increased with the development of BC. Furthermore, serum FEN1 levels were significantly decreased in post-operative patients than in pre-operative patients (P=0.016). Based on the Kaplan-Meier Plotter database, the survival analysis indicated that FEN1 overexpression was associated with poor prognoses for overall survival (OS), relapse-free survival (RFS), and distant metastasis-free survival (DMFS) in BC patients.ConclusionFEN1 might be a novel diagnostic and prognostic marker for BC.

scholarly journals The Alterations and Potential Roles of MCMs in Breast Cancer

2021 ◽  
Vol 2021 ◽  
pp. 1-17
Author(s):  
Xinyu Liu ◽  
Ying Liu ◽  
Qiangshan Wang ◽  
Siqi Song ◽  
Lingjun Feng ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Gene Network ◽  
Relapse Free Survival ◽  
Minichromosome Maintenance ◽  
Free Survival ◽  
Oncomine Database ◽  
Kaplan Meier ◽  
Eukaryotic Dna ◽  
Coexpressed Genes ◽  
Kaplan Meier Plotter

The minichromosome maintenance (MCM) protein family plays a key role in eukaryotic DNA replication and has been confirmed to be associated with the occurrence and progression of many tumors. However, the expression levels, functions, and prognostic values of MCMs in breast cancer (BC) have not been clearly and systematically explained. In this article, we studied the transcriptional levels of MCMs in BC based on the Oncomine database. Kaplan-Meier plotter was used to analyze prognostic value of MCMs in human BC patients. Furthermore, we constructed a MCM coexpression gene network and performed functional annotation analysis through DAVID to reveal the functions of MCMs and coexpressed genes. The data showed that the expression of MCM2–8 and MCM10 but not MCM1 and MCM9 was upregulated in BC. Kaplan-Meier plotter analysis revealed that high transcriptional levels of MCM2, MCM4–7, and MCM10 were significantly related to low relapse-free survival (RFS) in BC patients. In contrast, high levels of MCM1 and MCM9 predicted high RFS for BC patients. This study suggests that MCM2, MCM4–7, and MCM10 possess great potential to be valuable prognostic biomarkers for BC and that MCM1 and MCM9 may serve as potential treatment targets for BC patients.

scholarly journals Eight-Gene Metabolic Signature Related with Tumor-Associated Macrophages Predicting Overall Survival for Hepatocellular Carcinoma

2020 ◽  
Author(s):  
Junyu Huo ◽  
Yunjin Zang ◽  
Hongjing Dong ◽  
Xiaoqiang Liu ◽  
Fu He ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Overall Survival ◽  
Survival Analysis ◽  
Risk Score ◽  
Risk Group ◽  
Cancer Genome ◽  
Metabolic Reprogramming ◽  
Tumor Associated Macrophages ◽  
Kaplan Meier ◽  
The Relationship

Abstract Background: In recent years, the relationship between tumor associated macrophages (TAMs) and solid tumors has become a research hotspot. The study aims at exploring the close relationship of TAMs with metabolic reprogramming genes in hepatocellular carcinoma(HCC), in order to provide a new way of treatment for HCC.Materials and methods: The study selected 343 HCC patients with complete survival information(survival time >= 1month) in the Cancer Genome Atlas (TCGA) as the study objects. Kaplan-Meier survival analysis assisted in figuring out the relationship between macrophage infiltration level and overall survival (OS), and Pearson correlation test to identify metabolic reprogramming genes(MRGs) related to tumor macrophage abundance. Lasso regression algorithm were conducted on prognosis related MRGs screened by Univariate Cox regression analysis and Kaplan-Meier survival analysis to construct the riskscore, another independent cohort (including 228 HCC patients) from the International Cancer Genome Consortium (ICGC) were used for external validation regarding the prognostic signature.Results: A risk score composed of 8 metabolic genes can accurately predict the OS of training cohort(TCGA) and testing cohort(ICGC). It is important that the risk score could widely used for people with different clinical characteristics, and is an independent predictor independent of other clinical factors affecting prognosis. As expected, high-risk group exhibited an obviously higher macrophage abundance relative to low-risk group, and the risk score presented a positive relation to the expression level of three commonly used immune checkpoints(PD1,PDL1,CTLA4).Conclusion: Our study constructed and validated a novel eight‑gene signature for predicting HCC patients’ OS, which possibly contributed to making clinical treatment decisions.

scholarly journals Changes in Overall Survival Over Time for Patients With de Novo Metastatic Breast Cancer

2021 ◽  
Author(s):  
Toshiaki Iwase ◽  
Tushaar Vishal Shrimanker ◽  
Ruben Rodriguez-Bautista ◽  
Onur Sahin ◽  
Anjali James ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Overall Survival ◽  
Metastatic Breast Cancer ◽  
De Novo ◽  
Metastatic Breast ◽  
Locoregional Therapy ◽  
Cancer Center ◽  
Her2 Positive ◽  
Time Periods ◽  
Over Time

The purpose of this study was to determine the change in overall survival (OS) for patients with de novo metastatic breast cancer (dnMBC) over time. We conducted a retrospective cohort study with 1981 patients with dnMBC diagnosed between January 1995 and December 2017 at The University of Texas MD Anderson Cancer Center. OS was measured from the date of diagnosis of dnMBC. OS was compared between patients diagnosed during different time periods: 5-year periods and periods defined according to when key agents were approved for clinical use. The median OS was 3.4 years. The 5- and 10-year OS rates improved over time across both types of time periods. A subgroup analysis showed that OS improved significantly over time for the estrogen-receptor-positive/HER2-positive (ER+/HER2+) subtype, and exhibited a tendency toward improvement over time for the ER-negative (ER-)/HER2+ subtype. Median OS was significantly longer in patients with non-inflammatory breast cancer (P = .02) and in patients with ER+ disease, progesterone-receptor-positive disease, HER2+ disease, lower nuclear grade, locoregional therapy, and metastasis to a single organ (all P &amp;lt;.0001). These findings showed that OS at 5 and 10 years after diagnosis in patients with dnMBC improved over time. The significant improvements in OS over time for the ER+/HER2+ subtype and the tendency toward improvement for ER-/HER2+ subtype suggest the contribution of HER2-targeted therapy to survival.

scholarly journals Nomogram Models Based on Gene Expression in Prediction of Breast Cancer Bone Metastasis

2021 ◽  
Author(s):  
Teng-di Fan ◽  
Di-kai Bei ◽  
Song-wei Li
Keyword(s):  
Breast Cancer ◽  
Gene Expression ◽  
Bone Metastasis ◽  
Gene Signature ◽  
Functional Enrichment ◽  
Training Set ◽  
Hub Genes ◽  
Kaplan Meier ◽  
Patient Prognosis ◽  
Kaplan Meier Plotter

Abstract Objective: To design a weighted co-expression network and build gene expression signature-based nomogram (GESBN) models for predicting the likelihood of bone metastasis in breast cancer (BC) patients. Methods: Dataset GSE124647 was used as a training set, and GSE14020 was taken as a validation set. In the training cohort, limma package in R was adopted to obtain differentially expressed genes (DEGs) between BC non-bone metastasis and bone metastasis patients, which were used for functional enrichment analysis. After weighted co-expression network analysis (WGCNA), univariate Cox regression and Kaplan-Meier plotter analyses were performed to screen potential prognosis-related genes. Then, GESBN models were constructed and evaluated. Further, the expression levels of genes in the models were explored in the training set, which was validated in GSE14020. Finally, the prognostic value of hub genes in BC was explored. Results: A total of 1858 DEGs were obtained. WGCNA result showed that the blue module was most significantly related to bone metastasis and prognosis. After survival analyses, GAJ1, SLC24A3, ITGBL1, and SLC44A1 were subjected to construct a GESBN model for overall survival. While GJA1, IGFBP6, MDFI, ITGFBI, ANXA2, and SLC24A3 were subjected to build a GESBN model for progression-free survival. Kaplan-Meier plotter and receiver operating characteristic analyses presented the reliable prediction ability of the models. Besides, GJA1, IGFBP6, ITGBL1, SLC44A1, and TGFBI expressions were significantly different between the two groups in GSE124647 and GSE14020. The hub genes had a significant impact on patient prognosis. Conclusion: Both the four-gene signature and six-gene signature could accurately predict patient prognosis, which may provide novel treatment insights for BC bone metastasis.

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