scholarly journals Identification of death-associated protein-like 1 (DAPL1) as a novel prognostic biomarker of breast cancer

2020 ◽  
Author(s):  
Haichao Zhang ◽  
Xin Qu ◽  
Lu Han
Keyword(s):  
Breast Cancer ◽  
Dna Repair ◽  
Survival Data ◽  
Immune Cell ◽  
Excision Repair ◽  
Analysis Data ◽  
Clinical Prognosis ◽  
Free Survival ◽  
Normal Tissues ◽  
M1 Macrophage

Abstract Background: It is meaningful to identify the potential clinical prognosis-associated oncogenes for cases with breast cancer, considering the complicated pathogenesis of breast cancer.Methods: We first utilized the bioinformatics approach to investigate the role of the DAPL1 (death-associated protein-like 1) in breast cancer, based on the available datasets of TCGA and GEO.Results: DAPL1 is lowly expressed in breast cancer tissues compared with the normal tissues. For the breast cancer cases of the TCGA-BRCA cohort, we observed a correlation between lowly expressed DAPL1 gene and poor clinical prognosis of overall survival ( P =0.0028). Based on the survival data of GEO, the low DAPL1 expression was associated with a poor prognosis of distant metastasis free survival ( P =0.0023), and relapse free survival ( P =0.0065). DAPL1 expression was linked to the mutation status or copy number variation o f several genes, such as MAP3K1 , NUP98 , and CCDC59. The infiltration level of immune cells (e.g., M1 macrophage, Follicular B helper T cells, etc.) may be involved in the etiology of breast cancer. Based on the DAPL1 -correlated genes, GSEA, GO, and KEGG analysis data indicated the association between DAPL1 expression and a series of biological issues, such as DNA packaging complex, DNA repair complex, nucleotide excision repair, ubiquitin-like protein binding, and ubiquitin proteasome pathway. We also identified several DAPL1 -associated phosphorylation kinases, such as MAPK, PRKACA, and GSK3B.Conclusions: DAPL1 gene is first identified as a prognosis biomarker of breast cancer, and the underlying molecular mechanism involves protein phosphorylation, immune cell infiltration, and DNA repair or protein ubiquitin-associated cellular pathways.

scholarly journals PECAM-1 is a prognostic-related biomarker and correlated with immune infiltrates in breast cancer

2021 ◽  
Author(s):  
Qingfang Yue ◽  
Fei Wang ◽  
Fei Cao ◽  
Xianglong Duan ◽  
Jun Bai
Keyword(s):  
Breast Cancer ◽  
T Cells ◽  
Invasive Carcinoma ◽  
Immune Cell ◽  
Progression Free Survival ◽  
Immune Gene ◽  
Poor Overall Survival ◽  
Free Survival ◽  
Normal Tissues ◽  
Kaplan Meier

Abstract Background: Breast invasive carcinoma (BRCA) is the primary cause of cancer-associated mortality worldwide. Platelet endothelial cell adhesion molecule 1 (PECAM-1) has been implicated in a number of important biological processes. However, the interrelation between PECAM-1 gene expression, tumor immunity, and prognosis of patients with BRCA is unclear. The current study is aimed to analyze the expression and clinical significance of PECAM-1 in breast cancer and the correlation between PECAM-1 and immune infiltrations. Methods: The differential expressions of PECAM-1 in breast cancer tissues and normal tissues were evaluated via exploring TIMER, Oncomine and UALCAN databases; the relationship within expression level of PECAM-1 and outcome of breast patients was evaluated via Kaplan-Meier plotter and PrognoScan; the methylation of PECAM-1 were investigated through the MethSurv platform; the correlation between PECAM-1 and tumor immune cell infiltration was further investigated by TIMER and GEPIA databases; the correlation between PECAM-1 and gene makers of immune infiltration were checked using TIMER and GEPIA. Results: There were significant differences in PECAM-1 expression levels between breast invasive carcinoma tissues and adjacent normal tissues. Low PECAM-1 expression was significantly related to poor overall survival, progression-free survival and distant metastasis free survival in patients with breast cancer. In DNA methylation level, PECAM-1 hypermethylation in three CpG sites (cg20830094, cg00427260 and cg00879592) showed poor survival in breast cancer. PECAM-1 expression exhibited significantly positive correlations with the levels of infiltrated B cell, CD4+T cells, CD8+ T cells, neutrophils, macrophages, and dendritic cells in breast cancer. Furthermore, PECAM-1 expression is positively correlated with multiple immune gene makers in breast cancer.Conclusion: The expression of PECAM-1 can serves as a prognostic biomarker in breast invasive carcinoma and is correlated with immune infiltrates.

A Pan-Cancer Analysis of the Tumorigenic Role of Yin-Yang1 (YY1) in Human Tumors

2021 ◽  
Author(s):  
Ke-Hao Pan ◽  
Nai-Peng Shi ◽  
Yi-Fan Liu ◽  
Ya-Li Wang ◽  
Ming Chen
Keyword(s):  
Survival Data ◽  
Immune Cell ◽  
High Expression ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Clinical Prognosis ◽  
Free Survival ◽  
Cancer Data ◽  
Pan Cancer

Abstract Background: Yin-yang1 (YY1) is a nuclear transcription factor possessing dual transcriptional activity, which has different expression in a variety of tumor tissues. However, it remains unclear that the role of YY1 in most tumors and its association with immune cell infiltration.Methods: The expression of YY1 was analyzed in pan-cancer data which were downloaded from The Cancer Genome Atlas (TCGA) database. The clinical survival data downloading from TCGA was used to analyze the effect of YY1 on clinical prognosis. We had access to the R package “clusterProfiler” to make the enrichment analysis of YY1. The score of the immune cell infiltration of TCGA samples was downloaded from published articles and the correlation between YY1 expression and the immune cell infiltration was analyzed.Results: YY1 had a high expression in 25 tumors and strongly associated with clinical stage. In most tumor types, the over-expression of YY1 was connected to the worse prognostic indicator, such as overall survival(OS), progression-free survival (PFS), disease-specific survival(DSS) and disease-free survival (DFS). Moreover, the expression of YY1 had a correlation with tumor mutation burden(TMB). Nearly all of immune-related genes had co-expression with YY1 and almost all genes had positive correlation with YY1 in all types of tumors. It's worth noting that the expression levels of B cells and T cells were lower in the group with high YY1 expression. In addition, 22 m6A methylation-related cells were co-expressed with YY1, such as METTL3, YTHDC1, FTO and so on. Conclusions: Our study leads to a suggestion that YY1 may be a marker of bad prognosis and high expression of YY1 may lead to immune infiltration and be connected to m6A methylation.

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>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 CDCA3 Is a Novel Prognostic Biomarker Associated with Immune Infiltration in Hepatocellular Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-19
Author(s):  
Zhihuai Wang ◽  
Shuai Chen ◽  
Gaochao Wang ◽  
Sun Li ◽  
Xihu Qin
Keyword(s):  
Hepatocellular Carcinoma ◽  
T Cells ◽  
Immune Cell ◽  
Disease Free Survival ◽  
In Silico Analysis ◽  
Gene Markers ◽  
Free Survival ◽  
Immune Infiltration ◽  
Normal Tissues ◽  
Tumor Tissues

Cell division cycle-associated protein-3 (CDCA3) contributes to the regulation of the cell cycle. CDCA3 plays an important role in the carcinogenesis of various cancers; however, the association between CDCA3 expression, prognosis of patients, and immune infiltration in the tumor microenvironment is still unknown. Here, we demonstrated that CDCA3 was differentially expressed between the tumor tissues and corresponding normal tissues using in silico analysis in the ONCOMINE and Tumor Immune Estimation Resource (TIMER) databases. We analyzed the relationship between the expression of CDCA3 and prognosis of patients with hepatocellular carcinoma (HCC) using the Kaplan–Meier plotter database and Gene Expression Profiling Interactive Analysis (GEPIA). Furthermore, we determined the prognostic value of CDCA3 expression using univariate and multivariate analyses. We observed that CDCA3 expression closely correlated with immune infiltration and gene markers of infiltrating immune cells in the TIMER database. CDCA3 was highly expressed in the tumor tissues than in the adjacent normal tissues in various cancers, including HCC. Increased expression of CDCA3 was accompanied by poorer overall survival (OS), relapse-free survival (RFS), progression-free survival (PFS), and disease-specific survival (DSS). The correlation between CDCA3 expression and OS and disease-free survival (DFS) was also studied using GEPIA. CDCA3 expression was associated with the levels of immune cell infiltration and was positively correlated with tumor purity. Moreover, CDCA3 expression was associated with gene markers such as PD-1, CTLA4, LAG3, and TIM-3 from exhausted T cells, CD3D, CD3E, and CD2 from T cells, and TGFB1 and CCR8 located on the surface of Tregs. Thus, we demonstrated that CDCA3 may be a potential target and biomarker for the management and diagnosis of HCC.

scholarly journals APOBEC3-Mediated RNA Editing in Breast Cancer is Associated with Heightened Immune Activity and Improved Survival

2019 ◽  
Vol 20 (22) ◽  
pp. 5621 ◽  
Author(s):  
Mariko Asaoka ◽  
Takashi Ishikawa ◽  
Kazuaki Takabe ◽  
Santosh K. Patnaik
Keyword(s):  
Breast Cancer ◽  
T Cell ◽  
Rna Editing ◽  
Cell Receptor ◽  
Cytolytic Activity ◽  
Sequencing Data ◽  
Immune Activity ◽  
Normal Tissues ◽  
Gene Sets ◽  
M1 Macrophage

APOBEC3 enzymes contribute significantly to DNA mutagenesis in cancer. These enzymes are also capable of converting C bases at specific positions of RNAs to U. However, the prevalence and significance of this C-to-U RNA editing in any cancer is currently unknown. We developed a bioinformatics workflow to determine RNA editing levels at known APOBEC3-mediated RNA editing sites using exome and mRNA sequencing data of 1040 breast cancer tumors. Although reliable editing determinations were limited due to sequencing depth, editing was observed in both tumor and adjacent normal tissues. For 440 sites (411 genes), editing was determinable for ≥5 tumors, with editing occurring in 0.6%–100% of tumors (mean 20%, SD 14%) at an average level of 0.6%–20% (mean 7%, SD 4%). Compared to tumors with low RNA editing, editing-high tumors had enriched expression of immune-related gene sets, and higher T cell and M1 macrophage infiltration, B and T cell receptor diversity, and immune cytolytic activity. Concordant with this, patients with increased RNA editing in tumors had better disease- and progression-free survivals (hazard ratio = 1.67–1.75, p < 0.05). Our study identifies that APOBEC3-mediated RNA editing occurs in breast cancer tumors and is positively associated with elevated immune activity and improved survival.

scholarly journals Bioinformatics identification of CCL8/21 as potential prognostic biomarkers in breast cancer microenvironment

2020 ◽  
Vol 40 (11) ◽  
Author(s):  
Bowen Chen ◽  
Shuyuan Zhang ◽  
Qiuyu Li ◽  
Shiting Wu ◽  
Han He ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Data ◽  
Triple Negative ◽  
Immune Escape ◽  
Lymphocyte Activation ◽  
Prognostic Biomarkers ◽  
Bioinformatics Analyses ◽  
Tumor Immune Escape ◽  
Normal Tissues ◽  
Cc Chemokines

Abstract Background: Breast cancer (BC) is the most common malignancy among females worldwide. The tumor microenvironment usually prevents effective lymphocyte activation and infiltration, and suppresses infiltrating effector cells, leading to a failure of the host to reject the tumor. CC chemokines play a significant role in inflammation and infection. Methods: In our study, we analyzed the expression and survival data of CC chemokines in patients with BC using several bioinformatics analyses tools. Results: The mRNA expression of CCL2/3/4/5/7/8/11/17/19/20/22 was remarkably increased while CCL14/21/23/28 was significantly down-regulated in BC tissues compared with normal tissues. Methylation could down-regulate expression of CCL2/5/15/17/19/20/22/23/24/25/26/27 in BC. Low expression of CCL3/4/23 was found to be associated with drug resistance in BC. Results from Kaplan–Meier plotter and BC Gene-Expression Miner v4.2 (bcGenExMiner) v4.2 demonstrated that BC patients with high CCL8 and low CCL19/21/22 expression were more likely to have a worse prognosis. CCL8 expression was significantly up-regulated in BC tissues compared with normal tissues. High CCL8 expression was significantly correlated with negative PR, negative ER, positive nodal status, triple-negative BC subtype, basal-like BC subtype, triple-negative and basal-like BC subtype and high grades. CCL21 was down-regulated in BC, while high levels of CCL21 was associated with negative PR, triple-negative subtype, basal-like subtype and low tumor grade. Functional analysis demonstrated that CCL8 and CCL21 were involved in carcinogenesis, tumor immune escape and chemoresistance in BC. Conclusion: Integrative bioinformatics analysis demonstrated CCL8/21 as potential prognostic biomarkers in BC microenvironment.

scholarly journals Differential expression of the integrator complex subunit 7 in cancers of the breast.

2021 ◽  
Author(s):  
Shahan Mamoor
Keyword(s):  
Breast Cancer ◽  
Differential Expression ◽  
Survival Data ◽  
Normal Breast ◽  
Luminal A ◽  
Gene Encoding ◽  
Significant Differential Expression ◽  
Primary Tumors ◽  
Free Survival ◽  
Microarray Datasets

Breast cancer affects women at relatively high frequency (1). We mined published microarray datasets (2, 3) to determine in an unbiased fashion and at the systems level genes most differentially expressed in the primary tumors of patients with breast cancer. We report here significant differential expression of the gene encoding the integrator complex subunit 7, INTS7, when comparing primary tumors of the breast to the tissue of origin, the normal breast. INTS7 mRNA was present at significantly higher quantities in tumors of the breast as compared to normal breast tissue. Analysis of human survival data revealed that expression of INTS7 in primary tumors of the breast was correlated with distant metastasis-free survival in patients with luminal A and HER2+ type cancers, but contrarily. INTS7 may be of relevance to initiation, maintenance or progression of cancers of the female breast.

scholarly journals Follistatin-like 1 (FSTL1) is a Prognostic Biomarker and Correlated with Immune Cell Infiltration in Gastric Cancer

2020 ◽  
Author(s):  
Li Li ◽  
Shanshan Huang ◽  
Yangyang Yao ◽  
Jun Chen ◽  
Junhe Li ◽  
...  
Keyword(s):  
Gastric Cancer ◽  
Tumor Immunity ◽  
Survival Data ◽  
Immune Cell ◽  
Bioinformatic Analysis ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Western Blot Assay ◽  
Immune Infiltration ◽  
Normal Tissues

Abstract Background: Follistatin-like 1 (FSTL1) plays a central role in the progression of tumor and tumor immunity. However, the effect of FSTL1 on the prognosis and immune infiltration of gastric cancer (GC) remains to be elucidated.Method: The expression of FSTL1 data was analyzed in Oncomine and TIMER databases. Analyses of clinical parameters and survival data were conducted by Kaplan-Meier plotter and immunohistochemistry. Western blot assay and real‐time quantitative PCR (RT-qPCR) was using to analyzed protein and mRNA expression, respectively. The correlations between FSTL1 and cancer immune infiltrates was analyzed by Tumor Immune Estimation Resource (TIME), Gene Expression Profiling Interactive Analysis (GEPIA) and LinkedOmics database.Results: The expression of FSTL1 was significantly higher in GC tissues than in normal tissues, and bioinformatic analysis and Immunohistochemistry (IHC) indicated that high FSTL1 expression significantly correlated with poor prognosis in GC. Moreover, FSTL1 was predicted as an independent prognostic factor in GC patients. Bioinformatics analysis results suggested that FSTL1 mainly involved in tumor progression and tumor immunity. And significant correlations were found between FSTL1 expression and immune cell infiltration in GC.Conclusion: The study effectively revealed useful information about FSTL1 expression, prognostic values, potential functional networks and impact of tumor immune infiltration in GC. In summary, FSTL1 can be used as a biomarker for prognosis and evaluating immune cell infiltration in GC.

scholarly journals Bioinformatics analysis revealing prognostic significance of RRM2 gene in breast cancer

2019 ◽  
Vol 39 (4) ◽  
Author(s):  
Wei-xian Chen ◽  
Liang-gen Yang ◽  
Ling-yun Xu ◽  
Lin Cheng ◽  
Qi Qian ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Survival Data ◽  
Bioinformatics Analysis ◽  
Prognostic Significance ◽  
Prognostic Index ◽  
Disease Free Survival ◽  
Cancer Prognosis ◽  
Breast Cancer Patients ◽  
Free Survival ◽  
Metastatic Relapse

Abstract Background: Ribonucleotide reductase M2 subunit (RRM2) plays vital roles in many cellular processes such as cell proliferation, invasiveness, migration, angiogenesis, senescence, and tumorigenesis. However, the prognostic significance of RRM2 gene in breast cancer remains to be investigated. Methods:RRM2 expression was initially evaluated using the Oncomine database. The relevance between RRM2 level and clinical parameters as well as survival data in breast cancer was analyzed using the Kaplan–Meier Plotter, PrognoScan, and Breast Cancer Gene-Expression Miner (bc-GenExMiner) databases. Results:RRM2 was overexpressed in different subtypes of breast cancer patients. Estrogen receptor (ER) and progesterone receptor (PR) were negatively correlated with RRM2 expression. Conversely, the Scarff–Bloom–Richardson (SBR) grade, Nottingham prognostic index (NPI), human epidermal growth factor receptor-2 (HER-2) status, nodal status, basal-like status, and triple-negative status were positively related to RRM2 level in breast cancer samples with respect to normal tissues. Patients with increased RRM2 showed worse overall survival, relapse-free survival, distant metastasis-free survival, disease-specific survival, and disease-free survival. RRM2 also exerted positive effect on metastatic relapse event. Besides, a positive correlation between RRM2 and KIF11 genes was confirmed. Conclusion: Bioinformatics analysis revealed that RRM2 might be used as a predictive biomarker for prognosis of breast cancer. Further studies are needed to more precisely elucidate the value of RRM2 in evaluating breast cancer prognosis.

Randomized trial of observation versus adjuvant therapy with cyclophosphamide, fluorouracil, prednisone with or without tamoxifen following mastectomy in postmenopausal women with node-positive breast cancer.

1988 ◽  
Vol 6 (9) ◽  
pp. 1388-1396 ◽  
Author(s):  
J N Ingle ◽  
L K Everson ◽  
H S Wieand ◽  
J K Martin ◽  
H J Votava ◽  
...  
Keyword(s):  
Breast Cancer ◽  
Adjuvant Therapy ◽  
Postmenopausal Women ◽  
Survival Data ◽  
Observation Time ◽  
Relapse Free Survival ◽  
Free Survival ◽  
Node Positive ◽  
Overall Survival Benefit ◽  
Positive Breast Cancer

Following mastectomy for node-positive breast cancer, 261 postmenopausal women were randomized to observation or adjuvant treatment with cyclophosphamide, fluorouracil, prednisone (CFP) alone or combined with tamoxifen (T). Doses used were: C, 150 mg/m2 intravenously (IV) days 1 to 5; F, 300 mg/m2 IV days 1 to 5; P, 10 mg by mouth 3 times daily on days 1 to 7; and T, 10 mg by mouth 2 times daily. A total of ten courses of treatment, administered every 6 weeks, was planned and T was stopped 6 weeks after the last course of CFP. Two hundred thirty-four patients were fully eligible and evaluable. With a median observation time slightly in excess of 5 years, the proportion of recurrences on each arm were: CFP, 29 of 75 (39%); CFPT, 29 of 71 (41%); and observation, 50 of 88 (57%). Relapse-free survival distributions for both CFP and CFPT were superior to observation (both two-sided P = .01). Considering prognostic factors in covariate analysis revealed two-sided P = .0006 for CFP v observation and P = .0003 for CFPT v observation. No substantial difference was identified between CFP and CFPT. Survival data are not yet mature with 31% dead; and, although slight separations of the curves exist in favor of the treatment arms, no significant differences in survival have been seen. Both adjuvant therapy programs are well tolerated and there were no treatment-related deaths. Further maturation of the data is required to determine if the advantages in relapse-free survival will be translated into any overall survival benefit which must be considered the goal of primary interest.

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