Dataset Information

A combined hypoxia and immune gene signature for predicting survival and risk stratification in triple-negative breast cancer.

ABSTRACT:

Background

Increasing evidence showed that the clinical significance of the interaction between hypoxia and immune status in tumor microenvironment. However, reliable biomarkers based on the hypoxia and immune status in triple-negative breast cancer (TNBC) have not been well established. This study aimed to explore a gene signature based on the hypoxia and immune status for predicting prognosis, risk stratification, and individual treatment in TNBC.

Methods

Hypoxia-related genes (HRGs) and Immune-related genes (IRGs) were identified using the weighted gene co-expression network analysis (WGCNA) method and the single-sample gene set enrichment analysis (ssGSEA Z-score) with the transcriptomic profiles from Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) cohort. Then, prognostic hypoxia and immune based genes were identified in TNBC patients from the METABRIC (N = 221), The Cancer Genome Atlas (TCGA) (N = 142), and GSE58812 (N = 107) using univariate cox regression model. A robust hypoxia-immune based gene signature for prognosis was constructed using the least absolute shrinkage and selection operator (LASSO) method. Based on the cross-cohort prognostic hypoxia-immune related gene signature, a comprehensive index of hypoxia and immune was developed and two risk groups with distinct hypoxia-immune status were identified. The prognosis value, hypoxia and immune status, and therapeutic response in different risk groups were analyzed. Furthermore, a nomogram was constructed to predict the prognosis for individual patients, and an independent cohort from the gene expression omnibus (GEO) database was used for external validation.

Results

Six cross-cohort prognostic hypoxia-immune related genes were identified to establish the comprehensive index of hypoxia and immune. Then, patients were clustered into high- and low-risk groups based on the hypoxia-immune status. Patients in the high-risk group showed poorer prognoses to their low-risk counterparts, and the nomogram we constructed yielded favorable performance to predict survival and risk stratification. Besides, the high-risk group had a higher expression of hypoxia-related genes and correlated with hypoxia status in tumor microenvironment. The high-risk group had lower fractions of activated immune cells, and exhibited lower expression of immune checkpoint markers. Furthermore, the ratio of complete response (CR) was greatly declined, and the ratio of breast cancer related events were significantly elevated in the high-risk group.

Conclusion

The hypoxia-immune based gene signature we constructed for predicting prognosis was developed and validated, which may contribute to the optimization of risk stratification for prognosis and personalized treatment in TNBC patients.

SUBMITTER: Yang X

PROVIDER: S-EPMC8386525 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:The interaction between hypoxia and immune status has been confirmed in various cancer settings, and corresponding treatments have been investigated. However, reliable biomarkers are needed for individual treatment, so we sought to develop a novel scoring system based on hypoxia and immune status. Prognostic hypoxia-immune status-related signatures of patients with triple-negative breast cancer (TNBC) were identified in The Cancer Genome Atlas (TCGA) (N = 158), Molecular Taxonomy of Breast Cancer International Consortium (METABRIC) (N = 297), and GSE58812 (N = 107). LASSO Cox regression was used for model construction. Hypoxia and immune status expression profiles were analyzed, and infiltrating immune cells were compared. Quantitative real-time PCR (qRT-PCR) was used for validation in the Sun Yat-sen University Cancer Center (SYSUCC) cohort, and immunofluorescence was applied for the detection of hypoxia and immune markers in cancer tissues. Ten cross-cohort prognostic hypoxia-immune signatures were included to construct the comprehensive index of hypoxia and immune (CIHI) in the METABRIC cohort. Two subgroups of patients with distinct hypoxia-immune status conditions were identified using CIHI: hypoxiahigh /immunelow and hypoxialow /immunehigh , with a significantly better overall survival (OS) rate in the latter (P < 0.01). The prognostic value of CIHI was further validated in the TCGA, GSE58812, and SYSUCC cohorts (P < 0.01). Hypoxia-immune signatures were significantly differentially expressed between the two groups, and more active immune responses were observed in the hypoxialow /immunehigh group. Cytotoxic lymphocytes were inversely correlated with CIHI in silico. Differentially expressed CA-IX and stromal PD-L1 were detected between subgroups of the SYSUCC cohort. A hypoxia-immune-based cross-cohort classifier for predicting prognosis was developed and validated, which may guide hypoxia modifier treatment and immunotherapy for TNBC.

Project description:Background: The objective of this study was to evaluate the prognostic value of clinical characteristics in elderly patients with triple-negative breast cancer (TNBC). Methods: The cohort was selected from the Surveillance, Epidemiology, and End Results (SEER) program dating from 2010 to 2015. Univariate and multivariate analyses were performed using a Cox proportional risk regression model, and a nomogram was constructed to predict the 1-, 3-, and 5-year prognoses of elderly patients with TNBC. A concordance index (C-index), calibration curve, and decision curve analysis (DCA) were used to verify the nomogram. Results: The results of the study identified a total of 5,677 patients who were randomly divided 6:4 into a training set (n = 3,422) and a validation set (n = 2,255). The multivariate analysis showed that age, race, grade, TN stage, chemotherapy status, radiotherapy status, and tumor size at diagnosis were independent factors affecting the prognosis of elderly patients with TNBC. Together, the 1 -, 3 -, and 5-year nomograms were made up of 8 variables. For the verification of these results, the C-index of the training set and validation set were 0.757 (95% CI 0.743-0.772) and 0.750 (95% CI 0.742-0.768), respectively. The calibration curve also showed that the actual observation of overall survival (OS) was in good agreement with the prediction of the nomograms. Additionally, the DCA showed that the nomogram had good clinical application value. According to the score of each patient, the risk stratification system of elderly patients with TNBC was further established by perfectly dividing these patients into three groups, namely, low risk, medium risk, and high risk, in all queues. In addition, the results showed that radiotherapy could improve prognosis in the low-risk group (P = 0.00056), but had no significant effect in the medium-risk (P < 0.4) and high-risk groups (P < 0.71). An online web app was built based on the proposed nomogram for convenient clinical use. Conclusion: This study was the first to construct a nomogram and risk stratification system for elderly patients with TNBC. The well-established nomogram and the important findings from our study could guide follow-up management strategies for elderly patients with TNBC and help clinicians improve individual treatment.

Project description:Background and Aims: This research aimed to construct a novel model for predicting overall survival (OS) and surgical benefit in triple-negative breast cancer (TNBC) patients with de novo distant metastasis. Methods: We collected data from the Surveillance, Epidemiology, and End Results (SEER) database for TNBC patients with distant metastasis between 2010 and 2016. Patients were excluded if the data regarding metastatic status, follow-up time, or clinicopathological information were incomplete. Univariate and multivariate analyses were applied to identify significant prognostic parameters. By integrating these variables, a predictive nomogram and risk stratification model were constructed and assessed with C-indexes and calibration curves. Results: A total of 1,737 patients were finally identified. Patients enrolled from 2010 to 2014 were randomly assigned to two cohorts, 918 patients in the training cohort and 306 patients in the validation cohort I, and 513 patients enrolled from 2015 to 2016 were assigned to validation cohort II. Seven clinicopathological factors were included as prognostic variables in the nomogram: age, marital status, T stage, bone metastasis, brain metastasis, liver metastasis, and lung metastasis. The C-indexes were 0.72 [95% confidence interval [CI] 0.68-0.76] in the training cohort, 0.71 (95% CI 0.68-0.74) in validation cohort I and 0.71 (95% CI 0.67-0.75) in validation cohort II. Calibration plots indicated that the nomogram-based predictive outcome had good consistency with the recoded prognosis. A risk stratification model was further generated to accurately differentiate patients into three prognostic groups. In all cohorts, the median overall survival time in the low-, intermediate- and high-risk groups was 17.0 months (95% CI 15.6-18.4), 11.0 months (95% CI 10.0-12.0), and 6.0 months (95% CI 4.7-7.3), respectively. Locoregional surgery improved prognosis in both the low-risk [hazard ratio [HR] 0.49, 95% CI 0.41-0.60, P < 0.0001] and intermediate-risk groups (HR 0.55, 95% CI 0.46-0.67, P < 0.0001), but not in high-risk group (HR 0.73, 95% CI 0.52-1.03, P = 0.068). All stratified groups could prognostically benefit from chemotherapy (low-risk group: HR 0.50, 95% CI 0.35-0.69, P < 0.0001; intermediate-risk group: HR 0.34, 95% CI 0.26-0.44, P < 0.0001; and high-risk group: HR 0.16, 95% CI 0.10-0.25, P < 0.0001). Conclusion: A predictive nomogram and risk stratification model were constructed to assess prognosis in TNBC patients with de novo distant metastasis; these methods may provide additional introspection, integration and improvement for therapeutic decisions and further studies.