Exploration of the immune-related signature and immune infiltration analysis for breast ductal and lobular carcinoma

Abstract

Background: In this study, we aimed to explore the tumour associated immune signature of breast cancer (BC) and conduct integrative analyses with immune infiltrates in BC.Methods: We downloaded the transcriptome profiling and clinical data of BC from The Cancer Genome Atlas (TCGA) database. The list of immune-related signatures was from the Innate database. The limma package was utilized to conduct the normalization, and we screened the differential immune signatures in BC.A univariate Cox regression model and the LASSO method were used to find the hub prognostic immune genes. The TAIG risk model was calculated based on the multivariate Cox regression results, and a receiver operating characteristic (ROC) curve was generated to assess the predictive power of TAIG. Moreover, we also conducted a correlation analysis between TAIG and the clinical characteristics. Additionally, we utilized the METABRIC cohort as the validation data set. The TIMER database is a comprehensive resource for performing systematic analyses of immune infiltrates across various malignancies. We evaluated the associations of immune signatures with several immune cells based on TIMER. Furthermore, we used the CIBERSORT algorithm to determine the fractions of immune cells in each sample and compared the differential distributions of immune infiltrates between two TAIG groups using the Wilcoxon rank-sum test.Results: A total of 1,178 samples were obtained from the TCGA-BRCA database, but only 1,045 breast tumour samples were matched with complete transcriptome expression data. Meanwhile, we collected a total of 1,094 BC patients from the METABRIC cohort. We found a list of 1,399 differential immune signatures associated with survival, and functional analysis revealed that these genes participated in cytokine-cytokine receptor interactions, Th1 and Th2 cell differentiation and the JAK-STAT signalling pathway. The TAIG risk model was established from the multivariate Cox analysis, and we observed that high TAIG levels correlated with poor survival outcomes based on Kaplan-Meier analysis. The Kruskal-Wallis test suggested that high TAIG levels correlated with high AJCC-TNM stages and advanced pathological stages (P<0.01). We validated the well robustness of TAIG in METABRIC cohort and 5-year AUC reached up to 0.829. Moreover, we further uncovered the associations of hub immune signatures with immune cells and calculated the immune cell fractions in specific tumour samples based on gene signature expression. Last, we used the Wilcoxon ranksum test to compare the differential immune density in the two groups and found that several immune cells had a significantly lower infiltrating density in the high TAIG groups, including CD8 + T cells (P=0.031), memory resting CD4 + T cells (P=0.026), M0 macrophages (P=0.023), and M2 macrophages (P=0.048). Conclusions:In summary, we explored the immune signature of BC and constructed a TAIG risk model to predict prognosis. Moreover, we integrated the identified immune signature with tumour-infiltrating immune cell...

Identification of a Metabolism-Related Signature for the Prediction of Survival in Endometrial Cancer Patients

“…In another study, lower immune and stromal scores are also found in high grade and invasive subtypes ( 10 ). The metastatic foci with the least amount of immune cells infiltration represents the worst immune microenvironment and the immune escape is most likely to occur ( 56 ). In breast cancer, CD8+ T cells, CD4+ T cells, M0 and M2 macrophages showed lower infiltrating concentration in the high tumor-associated immune genes groups, which suggested an adverse association between them ( 56 ).…”

“…The metastatic foci with the least amount of immune cells infiltration represents the worst immune microenvironment and the immune escape is most likely to occur ( 56 ). In breast cancer, CD8+ T cells, CD4+ T cells, M0 and M2 macrophages showed lower infiltrating concentration in the high tumor-associated immune genes groups, which suggested an adverse association between them ( 56 ). Similar to above, the results suggested that the immune cells have a significantly lower infiltrating density in the high-risk group.…”

Significance of hub genes and immune cell infiltration identified by bioinformatics analysis in pelvic organ prolapse

“…The CIBERSORT algorithm can be employed to evaluate immune cell infiltration in tissues based on gene expression datasets. Recently, abundant researches have used this algorithm to explore the function of immune cells in diseases ( Lin et al, 2020 ), breast ductal and lobular carcinoma ( Zhang et al, 2019 ), osteoarthritis ( Cai et al, 2020 ), and high-grade serous ovarian cancer ( Liu et al, 2020 ). Our study found hub genes and immune cells highly related to POP occurrence by analyzing POP expression spectrum data in public databases using WGCNA and the CIBERSORT algorithm, providing novel ideas and methods for the treatment of POP.…”

Identification of an Individualized Immune-Related Prognostic Risk Score in Lung Squamous Cell Cancer

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