A novel immune-related long noncoding RNA (lncRNA) pair model to predict the prognosis of triple-negative breast cancer
Original Article

A novel immune-related long noncoding RNA (lncRNA) pair model to predict the prognosis of triple-negative breast cancer

Jing-Ying Li1, Chen-Ji Hu1, Hui Peng1, En-Qiang Chen2

1Department of Pharmacy, West China Hospital, Sichuan University, Chengdu, China; 2Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China

Contributions: (I) Conception and design: JY Li, CJ Hu; (II) Administrative support: EQ Chen; (III) Provision of study materials or patients: JY Li; (IV) Collection and assembly of data: H Peng; (V) Data analysis and interpretation: JY Li, EQ Chen; (VI) Manuscript writing: All authors; (VII) Final approval of manuscript: All authors.

Correspondence to: En-Qiang Chen, PhD. Center of Infectious Diseases, West China Hospital, Sichuan University, No. 37, Guoxue Lane, Wuhou District, Chengdu 610041. Email: chenenqiang1983@hotmail.com.

Background: Breast cancer (BC) is the most prevalent cancer type and is the principal cause of cancer-related death in women. Anti-programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) immunotherapy has shown promising effects in metastatic triple-negative breast cancer (TNBC), but the potential factors affecting its efficacy have not been elucidated. Immune-related long noncoding RNAs (irlncRNAs) have been reported to be involved in immune escape to influence the carcinogenic process through the PD-1/PD-L1 signaling pathway. Therefore, exploring the potential regulatory mechanism of irlncRNAs in PD-1/PD-L1 immunotherapy in TNBC is of great importance.

Methods: We retrieved transcriptome profiling data from The Cancer Genome Atlas (TCGA) and identified differentially expressed irlncRNA (DEirlncRNA) pairs. Least absolute shrinkage and selection operator (LASSO) regression analysis was performed to construct a risk assessment model.

Results: Receiver operating characteristic (ROC) curve analysis indicated that the risk model may serve as a potential prediction tool in TNBC patients. Clinical stage and risk score were proved to be independent prognostic predictors by univariate and multivariate Cox regression analyses. Subsequently, we investigated the correlation between the risk model and tumor-infiltrating immune cells and immune checkpoints. Finally, we identified USP30-AS1 through the StarBase and Multi Experiment Matrix (MEM) databases, predicted the potential target genes of USP30-AS1, and then discovered that these target genes were closely associated with immune responses.

Conclusions: Our study constructed a risk assessment model by irlncRNA pairs regardless of expression levels, which contributed to predicting the efficacy of immunotherapy in TNBC. Furthermore, the lncRNA USP30-AS1 in the model was positively correlated with the expression of PD-L1 and provided a potential therapeutic target for TNBC.

Keywords: Breast cancer (BC); immune-related long noncoding RNAs (irlncRNAs); The Cancer Genome Atlas (TCGA); triple-negative breast cancer (TNBC)


Submitted Oct 24, 2023. Accepted for publication Feb 08, 2024. Published online Mar 11, 2024.

doi: 10.21037/tcr-23-1975


Highlight box

Key findings

• Our study constructed a risk assessment model by immune-related long noncoding RNA (irlncRNA) pairs regardless of expression levels, which contributed to predicting the efficacy of immunotherapy in triple-negative breast cancer (TNBC).

What is known and what is new?

• Previous studies have revealed that TNBC is critically related to the expression of programmed cell death ligand 1 (PD-L1) in the tumor microenvironment.

• We investigated the correlation between the risk model and tumor-infiltrating immune cells and immune checkpoints. Finally, we identified USP30-AS1 through the StarBase and Multi Experiment Matrix databases, predicted the potential target genes of USP30-AS1, and then discovered that these target genes were closely associated with immune responses.

What is the implication, and what should change now?

• Our study constructed a risk assessment model by irlncRNA pairs regardless of expression levels, which contributed to predicting the efficacy of immunotherapy in TNBC. Furthermore, the lncRNA USP30-AS1 in the model was positively correlated with the expression of PD-L1 and provided a potential therapeutic target for TNBC.


Introduction

Breast cancer (BC) is the most commonly diagnosed cancer in females worldwide and is classified into different molecular subtypes, including luminal A, luminal B, human epidermal growth factor receptor-2 (HER-2) overexpression and triple-negative breast cancer (TNBC) (1,2). TNBC is characterized by a lack of estrogen receptor (ER), progesterone receptor (PR), and HER2 expression, representing approximately 15–20% of BC cases (3,4). At present, comprehensive mode therapy combining local therapy (surgery, radiotherapy) with systemic therapy (endocrine therapy, chemotherapy, etc.) is a relatively mature treatment method for BC (5,6). However, chemotherapy promotes cancer heterogeneity of tumor cells, which could result in chemoresistance and cancer development (4,5,7). TNBC is characterized by significant biological heterogeneity. Despite its advances in neoadjuvant and adjuvant therapies, overall TNBC is associated with a higher risk of relapse and disease progression and poorer outcomes (8).

The development of immunotherapeutic drugs has revolutionized the field of clinical oncology. Immune checkpoint inhibitors (ICIs) are currently available to induce durable immune responses and potential long-term benefits in different tumor types, including lung cancer, hepatocellular carcinoma, melanoma, and renal cell carcinoma (9-12). However, BC, as a “cold” cancer, is considered poorly immunogenic and immunotherapy is not a priority option (13). There is growing evidence that TNBC exhibits the strongest immunogenicity in BC (14). Compared to other subtypes, TNBC has been shown to have a higher proportion of tumor infiltrating lymphocytes (TILs) (15), a relatively high tumor mutational burden (TMB) (16) and PD-L1 expression (17). PD-L1 expression has been found in approximately 20% of TNBCs, and several clinical trials have shown that antibodies against the programmed cell death protein 1/programmed cell death ligand 1 (PD-1/PD-L1) pathway could induce immune responses and improve clinical outcomes in TNBC patients (2,18,19). Thus, immunotherapy has emerged as a promising option for the treatment of TNBC and has encouraged the development of additional immunologic agents for the treatment of TNBC patients. However, not all TNBC patients are sensitive to immunotherapy. Given the heterogeneity of TNBC, it is imperative to explore potential mechanisms for regulating the efficacy of immunotherapy in TNBC patients.

Long noncoding RNAs (lncRNAs) play a prominent role in carcinogenesis, such as regulating gene expression, cell differentiation, aggressiveness of cancer cells and their ability to metastasize (20-22). LncRNAs can be transcribed from both protein-coding and noncoding regions of DNA (23). Several lncRNAs have been reported to influence the carcinogenic process and have particular applications in the prediction and diagnosis of different cancers (24). Ma et al. observed that a metabolism-related lncRNA signature was identified that can predict the recurrence-free survival (RFS) of BC patients, and a prognostic nomogram was established that helps guide the individualized treatment of patients at different risks (25). Li et al. observed that four-lncRNA immune prognostic signatures were prognostic biomarkers and could be possible therapeutic targets in TNBC (26).

Immune system disorders play a critical role in the development of various types of cancers (27,28). LncRNAs play crucial roles in the regulation of the immune system. Over the past few years, lncRNAs have emerged as key players in epigenetic regulation in the inhibitory tumor microenvironment (TME) because of their potential role in regulating tumor immunity by directly regulating genes involved in immune activation or suppression (29,30). For example, lncRNA KCNQ1OT1 secreted by tumor cell-derived exosomes regulates PD-L1 ubiquitination via miR-30a-5p/USP22 to promote immune escape in colorectal cancer (31). However, the role of immune-related lncRNAs (irlncRNAs) in regulating malignant progression and the efficacy of immunotherapy in TNBC has rarely been investigated. Exploring the potential mechanism by which lncRNAs regulate PD-L1 expression in TNBC patients is of great significance to identify novel therapeutic targets for TNBC.

In the current study, we identified differentially expressed irlncRNAs (DEirlncRNAs) in TNBC samples according to public transcriptome profiling data and corresponding clinical data of TNBC patients. Then, we utilized a novel modelling method to construct a risk assessment model, which applied lncRNA pairs and did not require precise expression levels. We further investigated the correlation between the risk model and the tumor immune microenvironment. Finally, we predicted the target genes and performed functional annotation to explore the potential mechanisms. We present this article in accordance with the TRIPOD reporting checklist (available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1975/rc).


Methods

Gene expression profiles and clinical data

The independent data included in this study were downloaded from a public database. The data of 146 TNBC samples and corresponding clinical information were obtained from The Cancer Genome Atlas (TCGA, https://portal.gdc.cancer.gov/) database. In addition, the clinical characteristics of all TNBC patients are shown in Table 1. This study was conducted in accordance with the Declaration of Helsinki (as revised in 2013).

Table 1

Clinical baseline of all 146 triple-negative breast cancer patients from TCGA cohort

Variables TCGA cohort (N=146)
N %
Status
   Alive 125 85.62
   Dead 21 14.38
Age (years)
   ≥55 73 50.00
   <55 73 50.00
AJCC-T
   T1 37 25.34
   T2 92 63.01
   T3 13 8.90
   T4 4 2.74
AJCC-N
   N0 96 65.75
   N1 31 21.23
   N2 11 7.53
   N3 8 5.48
AJCC-M
   M0 124 84.93
   M1 1 0.68
   MX 21 14.38
Stage
   Stage I 26 17.81
   Stage II 95 65.07
   Stage III 21 14.38
   Stage IV 1 0.68
   Unknown 3 2.05
Postoperative adjuvant chemotherapy
   Yes 24 16.44
   No 1 0.68
   NA 121 82.88
Neoadjuvant therapy
   Yes 1 0.68
   No 145 99.32

TCGA, The Cancer Genome Atlas; AJCC, American Joint Committee on Cancer.

Identification of differentially expressed irlncRNAs (DEirlncRNAs)

Gene transfer format (GTF) files were retrieved from Ensembl (http://asia.ensembl.org) for annotation. A list of identified immune-related genes was obtained from the ImmPort database (http://www.immport.org) and was used to distinguish irlncRNAs by coexpression analysis. Correlation analysis was performed between immune-related genes and lncRNAs. LncRNAs with immune gene correlation coefficients greater than 0.4 and P values less than 0.001 were selected as irlncRNAs. The “Limma” package was used for differentially expressed analysis among irlncRNAs to identify DEirlncRNAs. False discovery rate (FDR) <0.05 and |log2 fold change (FC)| >1 were set as the standard to select DEirlncRNAs for further analysis.

Pairing DEirlncRNAs

The matching process of DEirlncRNA pairs was as follows: one lncRNA pair included two genes (A and B); if the expression level of A was larger than that of B, the score was 1; otherwise, the score was 0. Next, DEirlncRNA pairs with constant values (0 or 1) were removed from all individual datasets included in the meta-dataset, and the remaining DEirlncRNA pairs were considered candidate DEirlncRNA pairs. Additionally, only samples with a 0.2–0.8 pair ratio, defined as the total pair value, were included.

Construction of a prognostic risk model

Univariate Cox regression analysis was performed to identify prognostic irlncRNA pairs. Least absolute shrinkage and selection operator (LASSO) regression analysis was performed with 10-fold cross validation and a P value of 0.01. Then, multivariate Cox regression analysis was utilized to calculate the coefficients (βi) of selected lncRNA pairs. A risk assessment model was constructed using βi and lncRNA expression levels to calculate the risk score of each patient. The risk score was calculated as follows: risk score = ∑βi * Expi. The TNBC patients in the TCGA cohort were stratified into two categories, namely low-risk and high-risk, based on the risk score calculated using the median value. The 2-, 3-, and 5-year ROC curves were plotted to estimate the predictive efficacy of the model. The R packages used in these steps included “survival”, “survminer”, “glmnet”, and “survivalROC”.

Evaluation of the constructed risk model

To verify the predictive value of the cut-off point, Kaplan-Meier analysis was performed to compare the difference in survival in the high- or low-risk groups. The Chi-square test was conducted to investigate the association between the model and clinicopathologic characteristics, and a band diagram was plotted to show the results. Univariate and multivariate Cox regression analyses between the risk score and clinicopathological characteristics were performed to determine whether the ability of the model to predict overall survival (OS) was independent. Box diagrams show the differences in the risk score among different groups of these clinicopathological characteristics by the Wilcoxon signed-rank test. The R packages used in these steps are “survival”, “survminer”, “ggpubr”, and “ComplexHeatmap”.

Investigation of tumor-infiltrating immune cells and immune checkpoint molecules

We further investigated the association between the risk and immune status using XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT-ABS, and CIBERSORT. The results were shown in a lollipop diagram generated by the R “ggplot2” package with P<0.05. The correlation between the risk score and the expression levels of immune checkpoint-related genes was exhibited in violin plots using the “ggpubr” package.

Correlation between the risk model and drug sensitivity

We calculated the half-maximal inhibitory concentration (IC50) of commonly administered chemotherapeutic drugs for TNBC in the TCGA database. The differences in the IC50 of imatinib, erlotinib, bexarotene, methotrexate and camptothecin between the high- and low-risk groups were compared using the R packages “pRRophetic” and “ggplot2”.

Target gene prediction and gene enrichment analysis

We utilized the StarBase and Multi Experiment Matrix (MEM) databases to identify potential lncRNAs in the three lncRNA pairs, and USP30-AS1 was selected. We performed coexpression analysis to predict the potential target genes of USP30-AS1 and calculated Spearman’s rank correlation coefficients. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses were performed for functional annotation. “Pathview” was used to pathway-based data integration and visualization (32,33).

Statistical analysis

The Chi-square test was used to compare clinical variables. Kaplan-Meier analysis was performed to compare the difference in survival between different patient groups. The correlation was determined by Spearman correlation analysis. Survival status was analysed by Cox regression analysis. P<0.05 was considered statistically significant.


Results

Identification of DEirlncRNAs

We downloaded the transcriptome profiling data of 146 cases of TNBC patients in the TCGA dataset. The expression matrix of immune-related mRNA was obtained from the ImmPort database and was used to identify irlncRNAs by coexpression analysis. The patients were divided into a high-expression group and a low-expression group based on the median cut-off value of PD-L1 expression. A total of 58 DEirlncRNAs were identified (Figure 1A), among which 52 irlncRNAs were upregulated in the high-PD-L1 group, and 6 irlncRNAs (AC007991.2, BCL2L1-AS1, DTNB-AS1, LINC00582, LINC01781, LINC02446) were upregulated in the low-PD-L1 group (|log2FC| >1, FDR <0.05) (Figure 1B). These results indicated that irlncRNAs may be potential regulators of PD-L1 expression in TNBC patients.

Figure 1 Identification of DEirlncRNAs in TCGA dataset. (A) Gene expression levels of DEirlncRNAs in the TCGA dataset; (B) volcano plot of DEirlncRNAs. The red dots represent up-regulated DEirlncRNAs, the green dots represent down-regulated DEirlncRNAs and the black dots represent irlncRNAs whose FDR >0.05 or |log2FC| <1; (C) forest map of ten DEirlncRNA pairs identified by univariate Cox regression analysis. FDR, false discovery rate; FC, fold change; CI, confidence interval; DEirlncRNAs, differentially expressed immune-related long noncoding RNAs; TCGA, The Cancer Genome Atlas.

Construction of DEirlncRNA pairs and a risk assessment model

We established 1,145 DEirlncRNA pairs and performed univariate Cox regression analysis. Ten DEirlncRNA pairs with prognostic significance were identified (Figure 1C). LASSO and multivariate Cox regression analyses were applied to identify three lncRNA pairs (Table 2) and establish a risk assessment model based on the transcriptome profiling data of the above DEirlncRNAs (Figure 2A,2B). The optimal cut-off value of the 5-year ROC curve was identified as 1.058 (Figure 2C). Time-dependent ROC curve analysis was applied to illustrate the sensitivity and specificity of the prediction model, with the area under the curve (AUC) reaching 0.680 at 2 years, 0.795 at 3 years, and 0.795 at 5 years (Figure 2D). Figure 2E displayed three lncRNA pairs.

Table 2

Three lncRNA pairs for the establishment of the risk assessment model

DEirlncRNAs Coef HR HR.95 L HR.95 H P value
USP30-AS1|SERPINB9P1 −0.91874 0.399023 0.150387 1.058732 0.064989
AL731567.1|AC004585.1 1.145169 3.142973 1.265462 7.806065 0.013617
AC110995.1|AC007991.2 1.436283 4.205038 1.383095 12.78462 0.011354

LncRNA, long noncoding RNA; DEirlncRNAs, differentially expressed immune-related lncRNAs; Coef, coefficient; HR, hazard ratio; 95L, 95% lower; 95 H, 95% higher.

Figure 2 Construction of a risk assessment model based on DEirlncRNA pairs. (A,B) Three lncRNA pairs for establishing the risk model were identified by the least absolute shrinkage and selection operator Cox regression; (C) the optimal cut-off value was identified according to the maximum inflection point; (D) the 2-, 3-, and 5-year receiver operating characteristic curves for evaluating the sensitivity and specificity of the prediction model; (E) a 3-pair risk assessment model was established by multivariate Cox regression analysis. AUC, area under the curve; CI, confidence interval; DEirlncRNAs, differentially expressed immune-related long noncoding RNAs.

Evaluation of independent prognostic value and correlation between clinical factors and the risk model

To further verify the prognostic ability of the risk model, we calculated the risk scores of the 140 patients with TNBC in the TCGA cohort. The patients were divided into a high-risk and a low-risk group based on the identified cut-off point, of which 55 cases were in the high-risk group, and 91 cases were in the low-risk group. The Kaplan-Meier survival curve indicated that patients in the high-risk group were more likely to exhibit a worse prognosis than those in the low-risk group (P=0.029) (Figure 3A). Univariate and multivariate Cox regression analyses of the risk model were performed to determine whether the prognostic ability of the model was independent. The results of univariate Cox regression analysis showed that clinical stage [hazard ratio (HR) =11.268, 95% CI: 4.680–27.127, P<0.001], T stage (HR =3.413, 95% CI: 1.839–6.332, P<0.001), N stage (HR =3.249, 95% CI: 2.097–5.033, P<0.001), and risk score (HR =2.031, 95% CI: 1.255–3.287, P=0.004) were independent predictive factors (Figure 3B). In multivariate Cox regression analysis, clinical stage (HR =13.055, 95% CI: 2.413–70.631, P=0.003) and risk score (HR =2.518, 95% CI: 1.381–4.592, P=0.003) were still independent prognostic predictors (Figure 3C). A Chi-square test was performed to illustrate the relationship between the risk score of TNBC and clinicopathological characteristics (Figure 3D). We further investigated the correlation between age (Figure 3E), T stage (Figure 3F) and risk by the Wilcoxon signed-rank test. The risk score increased as age and T stage increased. These results showed that age and T stage were significantly related to the risk score.

Figure 3 Prognosis prediction and clinical evaluation of the risk assessment model. (A) Kaplan-Meier survival curve showed that patients in the low-risk group experienced a longer overall survival than patients in the high-risk group; (B) univariate Cox regression analysis of the model; (C) multivariate Cox regression analysis of the model; (D) the strip chart shows the relationship between the risk score and clinicopathological characteristics; (E) age was significantly associated with the risk score; (F) T stage was significantly associated with the risk score. CI, confidence interval; TMB, tumor mutational burden; PD-L1, programmed cell death ligand 1.

The risk model is highly correlated with tumor-infiltrating immune cells and immune checkpoint molecules

Given that irlncRNAs were identified based on the coexpression of immune genes, we investigated whether the prediction model was related to the tumor immune microenvironment. We evaluated the immune infiltration status among the samples using XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT-ABS, and CIBERSORT. A detailed Spearman correlation analysis was performed to study the relationship between the risk score and immune infiltrated cells. The correlation coefficients are shown in a lollipop diagram (Figure 4A) and listed in Table S1. The high-risk group was positively correlated with natural killer (NK) cells, regulatory T cells (Tregs), and M0 macrophages and negatively correlated with other immune infiltrating cells, which indicated that patients in the high-risk group may be insensitive to immunotherapy. Since checkpoint blockade therapy is extensively used in the clinical treatment of BC, we further investigated the relationship between the risk model and the expression levels of immune checkpoint molecules in the TCGA database. The results of violin plots revealed that high risk scores were positively associated with low expression of PD-1, PD-L1, PD-L2, CTLA4, TIM3, and IDO1 (P<0.05) (Figure 4B).

Figure 4 Estimation of tumor-infiltrating immune cells and immune checkpoint molecules. (A) The correlation coefficients are shown in a lollipop diagram. The high-risk group was more positively associated with NK cells, Tregs, and M0 macrophages and negatively correlated with other immune infiltrating cells. (B) Violin plots showing the expression levels of immune checkpoint inhibitor-related genes in the low- and high-risk groups. **, P<0.01; ***, P<0.001. NK, natural killer; Tregs, T regulatory cells.

The risk model may act as a potential predictor of chemotherapeutics

To evaluate the risk model in the clinic for TNBC treatment, we identified the relationship between the risk and the efficacy of commonly administered chemotherapeutic drugs in the TCGA database. The inhibitory concentration (IC50) of chemotherapeutic drugs, including imatinib, erlotinib, bexarotene, methotrexate, and camptothecin, was calculated. The results showed that a high-risk score was related to a lower IC50 of imatinib (P=0.043), erlotinib (P=0.04), and bexarotene (P=0.095) (Figure 5A) and a higher IC50 of methotrexate (P=0.0073) and camptothecin (P=0.039) (Figure 5B), indicating that the risk model may act as a potential predictor of chemotherapeutic drug sensitivity.

Figure 5 The risk model may act as a potential predictor of chemotherapeutic drug sensitivity. (A) A high-risk score was associated with a lower IC50 of imatinib, erlotinib, and bexarotene; (B) a high-risk score was associated with a higher IC50 of methotrexate and camptothecin. IC50, half-maximal inhibitory concentration.

Target gene prediction and functional analysis of USP30-AS1

Among the selected DEirlncRNAs, USP30-AS1 was identified through StarBase, the MEM database and the expression matrix of irlncRNAs. We predicted the potential target genes of USP30-AS1 in the risk model and identified 941 target genes (correlation coefficients ≥0.4, P<0.05), the top 100 of which are shown in Table S2. The genes encoding PD-1 (PDCD1) and PD-L1 (CD274) were included. Spearman’s rank correlation coefficient revealed that the expression of PD-L1 (Figure 6A) and PD-1 (Figure 6B) had a significant positive correlation with the expression of USP30-AS1 (P<0.001). To identify the potential biological functions and pathways of target genes of USP30-AS1, we further performed GO analysis (Figure 6C) and KEGG pathway analysis (Figure 6D). Based on GO analysis, the target genes were significantly correlated with cytokine binding, receptor binding, cytokine activity, and several immune-related biological processes. The results of the KEGG pathway analysis revealed that the most relevant pathway for target genes was the cytokine-cytokine receptor interaction. We further generated a KEGG view of the cytokine-cytokine receptor interaction (Figure 7) and found that most genes in this pathway were positively regulated by USP30-AS1. It can be assumed that USP30-AS1 may play an important role in the immune responses of TNBC.

Figure 6 Target gene prediction and functional annotation of USP30-AS1. CD274 (A) and PDCD1 (B) were identified as target genes of USP30-AS1; results of GO (C) and KEGG (D) analyses in The Cancer Genome Atlas dataset. Cor, correlation; GO, Gene Ontology; KEGG, Kyoto Encyclopedia of Genes and Genomes. CCR, CC chemokine receptor; MHC, major histocompatibility complex; NF, nuclear factor.
Figure 7 A KEGG view of the cytokine-cytokine receptor interaction. Most genes in the cytokine-cytokine receptor interaction pathway were positively regulated by USP30-AS1 (32,33). KEGG, Kyoto Encyclopedia of Genes and Genomes; IL, interleukin; TNF, tumor necrosis factor; TGF-β, tumor growth factor β.

Discussion

Key findings, comparison with similar researches and explanations of findings

Previous studies have revealed that TNBC is critically related to the expression of PD-L1 in the TME (15,17). Furthermore, accumulating data have shown that PD-1/PD-L1 inhibitors are able to induce durable clinical responses in some TNBC patients (34). The KEYNOTE-355 trial suggested that pembrolizumab (an anti-PD-1 antibody)-chemotherapy showed a significant and clinically meaningful improvement in progression-free survival (PFS) versus placebo-chemotherapy among patients with metastatic TNBC (mTNBC) (35). The IMpassion130 trial revealed that atezolizumab (an anti-PD-L1 antibody) plus nab-paclitaxel significantly improved PFS and median OS in patients with mTNBC, especially for PD-L1-positive patients (36). However, the IMpassion 131 trial revealed that the combination of atezolizumab and paclitaxel did not improve PFS nor OS compared with paclitaxel alone, suggesting that the specific mechanisms of anti-PD-1/PD-L1 immunotherapies for mTNBC still need to be further explored (36,37).

In the present study, we used the cyclic single pairing method (38) and 0 or 1 matrix to verify the signatures of lncRNA pairs to predict the prognosis of TNBC. Therefore, only pairs with high or low expression need to be detected without examining the specific expression value of each lncRNA. Ten pairs with prognostic values were identified by univariate Cox regression analysis. Some lncRNAs of the ten pairs have been reported to be critically involved in tumorigenesis, such as USP30-AS1 (39-41), HLA-DQB1-AS1 (42,43), and MIR155HG (44-46). Based on the LASSO regression analysis, we constructed a risk assessment model composed of three DEirlncRNA pairs (USP30-AS1|SERPINB9P1, AL731567.1|AC004585.1, AC110995.1|AC007991.2). We further plotted ROC curves for 2, 3 and 5 years, and the model exhibited remarkable prognostic validity. The patients were divided into a high-risk and a low-risk group according to the identified cut-off point. The results of the survival analysis showed that the survival probability of the high-risk group was lower than that of the low-risk group. The results of univariate and multivariate Cox proportional hazard regression analyses showed that clinical stage and risk score were independent predictive factors for TNBC. In addition, age and T stage were significantly related to the risk score. The risk score increased as age and T stage increased. The highest increase in the risk score was found in patients with the T4 stage, which was much higher compared to patients with the T1-T3 stage. The results of the T1, T2 and T3 stages exhibited no significant difference, which may result from the limited samples of patients with low stages.

Immune checkpoint molecules have been identified as key modulators of the immune response, and their expression is closely related to the level of tumor-infiltrating immune cells, response to immunotherapy, and survival of patients (47). We evaluated the immune infiltration status among the samples using XCELL, TIMER, QUANTISEQ, MCPCOUNTER, EPIC, CIBERSORT-ABS, and CIBERSORT. We further investigated the relationship between the risk score and ICI-related biomarkers in the TCGA database. The results revealed that low risk scores were positively related to high expression of PD-1, PD-L1, PD-L2, CTLA4, TIM3, and IDO1 (P<0.05). Despite progress in understanding the underlying tumor biology, clinical outcomes for TNBC unfortunately remain poor, and chemotherapy is still the mainstay of treatment for TNBC (48-51). Thus, we evaluated the association of risk values with the IC50 of some commonly used chemotherapy agents. We further found that this risk model may be beneficial in helping physicians choose more effective chemotherapy agents.

We identified the lncRNA USP30-AS1 based on the StarBase and MEM databases. USP30-AS1 is an antisense lncRNA that plays a critical role in regulating gene expression at the replication, transcription, and translation levels (52). The function of antisense lncRNAs is not related to the position of encoding genes but to the coexpressed protein-encoding genes. We further predicted potential target genes of USP30-AS1 and discovered that genes encoding PD-1 (PDCD1) and PD-L1 (CD274) were also included, and the expression levels of PD-1 and PD-L1 were positively correlated with USP30-AS1 expression. The results indicated that USP30-AS1 may be involved in the regulation of PD-1 expression. Furthermore, the predicted target genes were used to perform GO analysis and KEGG pathway analysis. A KEGG pathway, cytokine-cytokine receptor interaction, was significantly enriched by the predicted target genes. In addition, most genes in this pathway were positively regulated by USP30-AS1, suggesting that USP30-AS1 was closely associated with the tumor immune response. Therefore, we speculate that USP30-AS1 may serve as a potential target molecule to affect the efficacy of immunotherapy, and the potential mechanism is that it activates the transcription and upregulates the expression of PD-L1 to promote the immune escape of patients with TNBC.

Limitations

However, our study has some limitations. First, our immune-related prognostic features of lncRNA pairs were developed through retrospective studies. Thus, prospective cohort studies are needed to further validate our results. Second, although functional annotation has revealed that lncRNA USP30-AS1 can regulate the expression of PD-L1, in vivo and in vitro experiments are further needed to explore the specific mechanisms.


Conclusions

In conclusion, our study constructed a risk assessment model by immune-related lncRNA pairs regardless of expression levels, which contributed to predicting the efficacy of immunotherapy in TNBC. Furthermore, the lncRNA USP30-AS1 in the model was positively correlated with the expression of PD-L1 and provided a potential therapeutic target for TNBC.


Acknowledgments

This work was supported by National Key Clinical Specialties Construction Program.

Funding: None.


Footnote

Reporting Checklist: The authors have completed the TRIPOD reporting checklist. Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1975/rc

Peer Review File: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1975/prf

Conflicts of Interest: All authors have completed the ICMJE uniform disclosure form (available at https://tcr.amegroups.com/article/view/10.21037/tcr-23-1975/coif). The authors have no conflicts of interest to declare.

Ethical Statement: The authors are accountable for all aspects of the work in ensuring that questions related to the accuracy or integrity of any part of the work are appropriately investigated and resolved. This study was conducted in accordance with the Declaration of Helsinki (as revised in 2013).

Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.


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Cite this article as: Li JY, Hu CJ, Peng H, Chen EQ. A novel immune-related long noncoding RNA (lncRNA) pair model to predict the prognosis of triple-negative breast cancer. Transl Cancer Res 2024;13(3):1252-1267. doi: 10.21037/tcr-23-1975

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