X-box binding protein 1 (XBP1): a potential role in chemotherapy response, clinical pathologic features, non-inflamed tumour microenvironment for breast cancer

Abstract

X-box binding protein 1 (XBP1) is mainly expressed in breast cancer (BC) in human cancers. Its tumorigenesis and favourable prognosis are contradictory, and its essential role in chemotherapeutic response and immunosuppression is unknown in BC. The study firstly identified XBP1 who received neoadjuvant chemotherapy (NAC) from GSE25055 and GSE24460. Associations between XBP1 expression and clinicopathological characteristics was investigated using Oncomine, TCGA, UALCAN and bc-GenExMiner. The prognostic value of XBP1 was assessed using the Kaplan-Meier Plotter, bc-GenExMiner, GSE25055, and GSE25056. Furthermore, we systematically correlated XBP1 and immunological characteristics in the BC tumour microenvironment (TME) using TISIDB, TIMER, GSE25055, GSE25056 and TCGA dataset. Finally, an essential role of XBP1 in chemotherapy response was evaluated based on GSE25055, GSE25065, GSE24460, GSE5846, ROC Plotter and CELL databases. Furthermore, XBP1 mRNA expression levels were obviously highest in BC among human cancers and were significantly related to a good prognosis. In addition, XBP1 mRNA and protein levels were higher in the luminal subtype than in normal tissues and basal-like subtype, which might be attributed to membrane transport-related processes. Apart from BC, negative immunological correlations of XBP1 were not observed in other malignancies. XBP1 might shape the non-inflamed TME in BC. Finally, XBP1 expression was higher in chemo-resistive than chemo-sensitive cases, it had a predictive value and could independently predict chemotherapy response in BC patients receiving NAC. Our study suggests that the essential role of XBP1 in clinical pathologic features, non-inflamed TME, chemotherapy response in BC.

Keywords: Breast cancer; Molecular subtype; Neoadjuvant chemotherapy; Tumour microenvironment; XBP1.

Figure 1. Identification of neoadjuvant chemotherapy related gene cluster and XBP1

(A) Normalization plot of expression profile form GSE24460, the green bar represents the data before normalization, and the red bar represents the normalized data. (B) Volcano plot of DEGs of GSE24460. The red points represent high expression genes, the blue points represent low expression genes, the black points represent genes with no significant difference (FDR<0.05, absolute log FC>3). (C) Normalization plot of expression profile form GSE25055, the green bar represents the data before normalization, and the red bar represents the normalized data. (D) Volcano plot of DEGs of GSE25055, the red points represent high expression genes, the green points represent low expression genes, the black points represent genes with no significant difference (FDR<0.05, absolute log FC>0.5). (E) Venn plot showing 34 genes shared in the intersection of GSE25055 and GSE24460. (F) The functional association network of overlapped genes was analyzed using the STRING database. (G) Heatmap demonstrated the correlation of genes in NAC-related gene cluster.

Figure 2. Overexpression of XBP1 in breast cancer

(A) ONCOMINE; (B) TIMER; (C) GEPIA; (D,E) The mRNA expression of XBP1 was higher in breast cancer tissues than that in healthy tissues or adjacent breast tissues (TCGA); (F) The protien expression of XBP1 was higher in breast cancer tissues than that in healthy tissues (UALCAN); (G) Violin plot of XBP1 expression according to tumour stage (GEPIA). Represent unpaired t-test was performed.

Figure 3. Prognostic value of XBP1 mRNA expression in patients with breast cancer

(A) High XBP1 expression levels were significantly associated with better good prognosis in all BC patients based on Kaplan–Meier Plotter tool. (B) High XBP1 expression levels were significantly associated with better RFS in different molecular subtypes based on Kaplan–Meier Plotter tool. (C) High XBP1 expression levels were significantly associated with better DMFS in different molecular subtypes based on bc-GenExMiner. (D) High XBP1 expression levels were significantly associated with better DRFS in patients underwent neoadjuvant chemotherapy; BC, breast cancer; DMFS, distant metastasis-free survival; RFS, recurrence-free survival.

Figure 4. Co-expression analysis and gene set enrichment analysis in breast cancer using Linkedomics database

(A) Volcano plot showed positive and negative related genes of XBP1 in breast cancer. (B,C) Heatmap of the top 50 positively and negatively correlated genes of XBP1 in breast cancer. (D) Gene set enrichment analysis for all positively and negatively correlated significant genes of XBP1.

Figure 5. The expression of XBP1 in breast cancer with different molecular subtypes in different datasets

(A,B) bc-GenExMiner; (C) TISIDB7; (D) TCGA; (E) UALCAN; (F) Representative images show XBP1 protein expression in different molecular subtypes using tissue microarray slides; (G,H) Tissue microarray slides.

Figure 6. Correlation between XBP1 and immunomodulators based on GSE25055

(A) chemokines; (B) immunostimulators; (C) MHC; (D) Receptors.

Figure 7. XBP1 shapes a non-inflamed TME in BC based on GSE25055

(A) Scores of the 29 immune-related gene sets between high and low XBP1 group. (B) Difference in TumorPurity between high and low XBP1 group. (C) Difference in TME score between high and low XBP1 group. (D) Correlations between XBP1 and the enrichment scores of immunocytes. (E) Correlations between XBP1 and the enrichment scores of inflammatory activation functions.

Figure 8. Correlation between XBP1 and inhibitory immune checkpoints

(A) Correlation between XBP1 and 13 inhibitory immune checkpoints. (B) Correlation between XBP1 and four immune checkpoints (PD-L1, CTLA-4, PD-1 and LAG-3) based on GETx dataset. (C) Correlation between XBP1 and four immune checkpoints (PD-L1, CTLA-4, PD-1 and LAG-3) based on TCGA dataset. The dots represent cancer types or tissue types, red dots represent BC or breast tissue. The Y-axis represents the Pearson correlation, while the X-axis represents -log₁₀P. (D) Differences in the enrichment scores of immunotherapy-predicted pathways between high and low XBP1 groups.

Figure 9. High XBP1 Mrna expression level in chemo-resistive cases

(A–C) NCI-60 cell lines; (D–F) CCLE; (G) GSE25055; (H) GSE25065; (I) Random testing cohort; (J) Entire testing cohort.