Analysis of LAGEs Family Gene Signature and Prognostic Relevance in Breast Cancer

Abstract

Breast cancer (BRCA) is one of the most complex diseases and involves several biological processes. Members of the L-antigen (LAGE) family participate in the development of various cancers, but their expressions and prognostic values in breast cancer remain to be clarified. High-throughput methods for exploring disease progression mechanisms might play a pivotal role in the improvement of novel therapeutics. Therefore, gene expression profiles and clinical data of LAGE family members were acquired from the cBioportal database, followed by verification using the Oncomine and The Cancer Genome Atlas (TCGA) databases. In addition, the Kaplan-Meier method was applied to explore correlations between expressions of LAGE family members and prognoses of breast cancer patients. MetaCore, GlueGo, and GluePedia were used to comprehensively study the transcript expression signatures of LAGEs and their co-expressed genes together with LAGE-related signal transduction pathways in BRCA. The result indicated that higher LAGE3 messenger (m)RNA expressions were observed in BRCA tissues than in normal tissues, and they were also associated with the stage of BRCA patients. Kaplan-Meier plots showed that overexpression of LAGE1, LAGE2A, LAGE2B, and LAGE3 were highly correlated to poor survival in most types of breast cancer. Significant associations of LAGE family genes were correlated with the cell cycle, focal adhesion, and extracellular matrix (ECM) receptor interactions as indicated by functional enrichment analyses. Collectively, LAGE family members’ gene expression levels were related to adverse clinicopathological factors and prognoses of BRCA patients; therefore, LAGEs have the potential to serve as prognosticators of BRCA patients.

Identification of Dipeptidyl Peptidase (DPP) Family Genes in Clinical Breast Cancer Patients via an Integrated Bioinformatics Approach

“…The CCLE is comprised of many human cancer cell lines ( n = 1457) with large numbers of unique datasets ( n = 136,488). Gene expression levels were retrieved using an RNA sequencing method in 60 breast cancer cell lines and the data were plotted with default settings as we previously described [ 34 , 35 , 36 , 37 ].…”

Multidimensional Analysis of the Role of Charged Multivesicular Body Protein 7 in Pan-Cancer

“…The Human Protein Atlas provides immunohistochemical evidence of differential expression of CHMP7 in normal and tumor tissues at the pathological level. [28][29][30] R software (version 3.6.3) was employed to further explore the correlation between CHMP7 expression levels and clinicopathological features.…”

Potential Therapeutic and Prognostic Values of LSM Family Genes in Breast Cancer

“…A heatmap of expression levels of 1222 BRCA patients was also performed using the "DESeq2" package to illustrate differences between the two phenotypes: "normal" and "tumor". We selected the top 10% of genes, ranked by the log2[fold change (FC) expression values], with |logFC| > 1.5 set as the threshold [50][51][52][53][54].…”