The expression level and prognostic value of ACSL3 in patients with breast cancer
The transcriptional level of ACSL3 was evaluated from GEPIA. The mRNA expression level of ACSL3 was significantly higher in breast cancer than that in normal tissues (P < 0.05) (Fig.1A). The ACSL3 expression in different tumor types from the TCGA database was also analyzed in GEPIA database. The results showed that mRNA expression was obviously elevated in BRCA (breast invasive carcinoma), CESC (cervical squamous cell carcinoma and endocervical adenocarcinoma), COAD (colon adenocarcinoma), DLBC (lymphoid neoplasm diffuse large B-cell lymphoma), PAAD (pancreatic adenocarcinoma), PRAD (prostate adenocarcinoma), READ (rectum adenocarcinoma), SKCM (skin cutaneous melanoma) and THYM (thymoma) tissues compared with the adjacent normal tissues. In contrast, mRNA expression was downregulated in LAML (acute myeloid leukemia) (Fig.1B). Next, the Kaplan–Meier Plotter was used to examine the prognostic values of the ACSL3 mRNA expression in breast cancer. Elevated mRNA expression of ACSL3 was correlated with a worse prognosis of RFS (Fig 1C, HR =1.14, 95% CI: 1.03–1.28, P=0,015). Next, we explored the correlation between ACSL mRNA expression and overall survival OS. Upregulated ACSL3 mRNA expression level suggested poor OS (Fig 1D, HR =1.26, 95% CI: 1.02–1.56, P=0.033). Next, based on the immunohistochemistry results from Human Protein Atlas database, we examined the expression of ACSL3 protein expression in breast cancer tissues and normal mammary tissues. The results revealed that ACSL3 protein was mainly located to the cell membrane and cytoplasm. Breast cancer tissues showed moderate to high ACSL3 expression, while non-cancerous tissues were detected moderate ACSL3 expression in adipocytes, glandular cells and myoepithelial cells (Fig 1E-F).
Validation of ACSL3 protein expression by IHC
We further evaluated the association between ACSL3 expression and the clinicopathological parameters in breast carcinomas. 297 patients diagnosed with breast carcinomas and underwent surgical excision were included. During the follow-up period, 42 cases have tumor progression (14.1%), contributing to 38 cases of deaths (12.8%). The median survival time was 63 months (varying from 14 to 69 months), and the median age at diagnosis of patients was 55 years (ranging from 27 to 83 years). In the study cohort, 75 (25.3%) were diagnosed as Luminal A subtype, 156 (52.5%) were diagnosed as Luminal B subtype, 23 (7.7%) as HER2-enriched subtype, and 43 (14.5%) as TNBC. A total of 251 cases with low and moderate pathological grade (I-II) and 46 cases of tumors with high pathological grade (III). A total of 179 (60.3%) patients had lymph node metastasis and 118 (39.7%) patients had no lymph node metastasis.
A total of 297 cases of breast cancer tissues were categorized into low and high ACSL3 expression groups. High ACSL3 expression was observed in 52.5% (156/297) of all cases. Immunochemical staining for different scores (0–3) was displayed in Figure 1A-D. Clinicopathologic characteristics are displayed in Table 1. ACSL3 expression was associated with ER expression, PR expression, different molecular subtype, histological grade, lymph node metastasis and tumor-node-metastasis (TNM) stage (P < 0.05). There were no statistically differences between ACSL3 expression and age at diagnosis, tumor size, HER2 expression and Ki67 (P > 0.05).
Relevance between ACSL3 expression and the status of ER, PR, and HER2
Next, we analyzed the results from immunochemical staining and clinicopathologic features of all patients to explore the relevance between ACSL3 protein expression and the status of ER, PR and HER2. Representative images of negative/positive status of ER, PR and HER2 were displayed in Figure 3A. We further combined semi-quantitative methods to calculate the difference. As illustrated in Figure 3B, ACSL3 were significantly upregulated in ER-compared to ER+ breast tumors (P <0.0001). Similar result was found in PR- compared to PR+ breast tumors (P <0.0001). However, no significant differences were found in the HER2 status (P =0.1106) of breast tumors. Collectively,
ASCL3 expression was significantly correlated with the status of hormone receptor.
Correlation between ACSL3 and molecular subtypes of breast carcinoma
We further investigated the relevance of ACSL3 expression and molecular subtypes of breast cancer.
Figure 4A manifested the representative images of ACSL3 immunochemical staining in luminal and TNBC subtypes. Further semi-quantitative analyses revealed that ACSL3 was significantly upregulated in TNBC tissues in comparison of luminal subtypes (P = 0.0034) (Figure 4B). No other significant differences were found within other disparate subtypes. Ultimately, we concluded that ACSL3 was relatively abundant in highly malignant TNBC tissues compared with luminal-subtype tissues.
High ACSL3 Protein Predicted Poor Prognosis of Breast Cancer Patients
Hazard ratio (HR) and 95% confidence interval (CI) were used to calculate the prognostic value of ACSL3 expression in patients diagnosed with breast cancer patients. Results from KM plotter analysis manifested that higher ACSL3 protein levels were significantly correlated with poor DFS (P = 0.002; HR = 0.332; 95% CI = 0.163-0.618) and OS (P = 0.002; HR = 0.283; 95% CI = 0.130–0.618) (Figure 5A-B). Higher levels of lymph node metastasis were found to be significantly correlated with poor DFS (P = 0.001; HR = 0.198; 95% CI = 0.078-0.503) and OS (P = 0.001; HR = 0.165; 95% CI = 0.058-0.464) (Figure 5C-D). Results from univariate Cox proportional hazard regression analysis in Table 2 and 3 disclosed that high histological grade, high Ki67 index, high lymph node metastasis and high expression of ACSL3 were significant correlated with worse DFS and OS for breast cancer patients. Further multivariate analysis revealed that high Ki67 index, high lymph node metastasis and ACSL3 high-expression were independent predictors of unfavorable DFS and OS. The relevance between ACSL3 expression and the prognosis in different molecular subtypes of breast cancer was further analyzed. ACSL3 protein expression showed a significant relevance between high ACSL3 expression and shorter OS in Luminal-type patients (P = 0.033; HR = 0.293; 95% CI = 0.094–0.908) (Figure 6A), while no significant correlation was found in HER2-enriched (P = 0.226; HR = 3.025; 95% CI = 0.504–18.143) and TNBC patients (P = 0.073; HR = 0.157; 95% CI = 0.021–1.186) (Figures 6B-C). KM plotter analysis of breast cancer patients with lymph node metastasis was further applied to evaluate the prognostic value of ACSL3 in breast cancer. In the positive lymph node metastasis group, higher ACSL3 protein level was associated with worse DFS [HR = 0.077 (0.018–0.323), P < 0.0001; Figure 7A] and OS [HR = 0.041 (0.006–0.305), P = 0.002; Figure 7B]. However, no relevance was observed in the negative lymph node metastasis group (Figure 7C-D).
Enrichment analysis of ACSL3 functional networks in breast cancer
The Function module of LinkedOmics was implemented to examine mRNA sequencing data from 1097 BRCA patients in the TCGA. As illustrated in Figure 8A, there were 4177 genes represented by dark red dots, displaying a significant positive relevance with ACSL3, while there were 5796 genes, represented by dark green dots, having a significant negative correlation with ACSL3 (false discovery rate [FDR] < 0.001). The top 50 significant genes that were positively and negatively associated with ACSL3 have been manifested in the heat map (Figure 8B-C). AS shown in statistical scatter plots (Figure 8D-F), ACSL3 expression displayed a strong positive relevance with expression of CUL3 (Pearson correlation = 0.4799, p = 4.775e–64), NDUFS1 (Pearson correlation = 0.4578, p = 9.759e–58), and TRIP12 (Pearson correlation =0.4364, p = 4.779e–52).
GO and KEGG analysis of ACSL3‑related co‑expressed genes in breast cancer
Based on these results, we applied significant GO term analysis by gene set enrichment analysis (GSEA). The biological process they participate primarily in cargo loading into vesicle (GO:0035459), Golgi vesicle transport (GO:0048193), protein localization to Golgi apparatus (GO:0034067), endomembrane system organization (GO:0010256), vacuolar transport (GO:0007034). Molecular function analysis showed enrichment in helicase activity (GO:0004386), ubiquitinyl hydrolase activity (GO:0070003), electron transfer activity (GO:0101005), ubiquitin-like protein transferase activity (GO:0019787), ATPase activity (GO:0016887) and double-stranded RNA binding (GO:0003725). Cellular Component analysis showed that genes differentially expressed in correlation with ACSL3 were enriched in the transcription elongation factor complex (GO:0008023), endoplasmic reticulum exit site (GO:0070971), tethering complex (GO:0099023), endoplasmic reticulum tubular network (GO:0071782) and Golgi-associated vesicle (GO:0005798). (Figure 9A–C). KEGG pathway analysis showed enrichment in the ubiquitin-mediated proteolysis (hsa04120), circadian rhythm (hsa04710), fatty acid biosynthesis (hsa00061), propanoate metabolism (hsa00640) and protein processing in endoplasmic reticulum (hsa04141) (Figure 9D).
Correlation analysis between ACSL3 expression and immune infiltration
The TIMER analysis was performed to comprehensively assess the correlations between ACSL3 expression and a panel of immune infiltrates in human breast cancer. As illustrated in Figure 10, ACSL3 expression was positively correlated with infiltration level of CD8 + T cells (r= 0.219, P=2.79e-12) and macrophages (r= 0.314, P=3.43e-24), while ACSL3 expression was negatively correlated with infiltration level of CD4 + T cells (r= -0.257, P=1.66e-16). No significant correlation with ACSL3 expression was found in B cells and neutrophils. The relationship between ACSL3 expression and immune infiltration was further analyzed according to molarcular subtypes. In both luminal subtypes of breast cancer, ACSL3 displayed the greatest correlation with macrophages (r= 0.31, P=5.80e-13; r= 0.222, P=1.95e-03). Besides, ACSL3 expression was positively correlated with infiltration level of CD8 + T cells (r= 0.288, P=2.43e-11; r= 0.145, P=4.53e-02) and neutrophil (r= 0.19, P=1.40e-05; r= 0.169, P=1.92e-02), while negatively correlated with infiltration level of CD4 + T cells (r=-0.312, P=3.77e-13; r= -0.158, P=2.86e-02) in both luminal subtypes of breast cancer. In HER2-positive breast cancer, ACSL3 showed significant correlation with infiltration level of CD4 + T cells (r=-0.272, p=2.09e-02) and macrophages (r=0.291, p=1.33e-02). In basal-like breast cancer, ACSL3 was significantly correlated with infiltration level of macrophages (r=0.234, p=1.90e-03) and B cell (r=-0.16, p=3.47e-02).