Identification and validation of endocrine resistance-related and immune-related long non-coding RNA (lncRNA) signatures for predicting endocrinotherapy response and prognosis in breast cancer

Background: Endocrine resistance remains a major challenge in breast cancer (BRCA). Increasing evidence has revealed that long non-coding RNA (lncRNA) are closely implicated in tumorigenesis, drug resistance, and the immune-related pathways of cancer. However, the immune-related lncRNA remains to be thoroughly investigated in predicting the endocrine therapeutic response and prognosis of BRCA.

Methods: Based on the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA) databases, and calculating the correlation of lncRNAs with immune-related genes obtained from ImmPort and InnateDB databases, we finally obtained endocrine resistance-related and immune-related long non-coding RNAs (ERIR-lncRNAs). Univariate Cox and least absolute shrinkage and selection operator (LASSO) Cox regression were performed to screen prognosis-associated ERIR-lncRNAs and establish signatures, using 2 separate datasets from GEO for external validation. Principal component analysis (PCA), Kaplan-Meier analysis, receiver operating characteristic (ROC) curves, and multivariate Cox regression were performed to demonstrate the robustness and predictability of the signature. We investigated tumor immune infiltration and tumor mutation burden (TMB) between high- and low-risk groups, and the role of key lncRNAs in endocrine resistant breast cancer was confirmed by quantitative real-time polymerase chain reaction (qRT-PCR), Cell Counting Kit 8 (CCK 8) and transwell assays.

Results: A total of 781 endocrine resistance related lncRNAs were identified, of which 12 lncRNAs were associated with immunity. Then, three ERIR-lncRNAs with prognostic relevance were screened to successfully construct the risk signature. Compared to sensitive patients, the endocrine resistant patients had higher risk scores in both the training and validation sets (P<0.05). The high-risk group had significantly shorter survival times (P<0.001) with area under the curve (AUC) values of 0.710, 0.649, and 0.672 at 1, 3, and 5 years. Univariate and multivariate Cox regression indicated that our signature was an independent prognostic factor (P<0.001). Through immune infiltration analysis, it was revealed that the high-risk scores were associated with T follicular helper (Tfh) differentiation and exhibited a pro-tumor phenomenon with the Th1/Th2 balance shifting toward Th2. The key lncRNAs promote cell proliferation and migration as confirmed by qRT-PCR, CCK-8 and transwell assays.

Conclusions: The ERIR-lncRNA signature is valuable in predicting endocrine therapeutic response and prognosis of BRCA, revealing a potential relationship between endocrine resistance and TME.