Breast cancer is considered as a major human health problem with the highest incidence among cancers and an increased mortality rate1. Therefore, elucidating molecular mechanisms underlying different BC subtypes is inevitable for choosing effective treatment methods and improving the prognosis of patients. Here we found 13 core and 12 subtype-specific DEGs associated with prognosis in BC, potentially indicating the clinical application of these DEGs.
C9orf116, also known as PIERCE1, was discovered to be involved in the cell cycle process in mice24. C9orf116 was found to induce cell proliferation in rat liver cell line BRL-3A25. Moreover, C9orf116 ablation inhibited cell growth in KRAS-mutant non-small cell lung cancer (NSCLC), which might have therapeutic potential in KRAS-mutant NSCLC26. However, the role of C9orf116 in BC is unclear at present. Our analysis showed that C9orf116 was specifically up-regulated in the Luminal A subtype, and this high expression predicted better OS in the Luminal A subtype BC.
We revealed that FAM13A and RASIP1 expressions were specifically down-regulated in the Luminal B subtypes. Also, elevated expression of FAM13A and RASIP1 was correlated with shorter OS in the Luminal B subtype. FAM13A single-nucleotide polymorphism (SNP) rs1059122 was found to be associated with BC risk in the Chinese female population27. It has been demonstrated that RASIP1 is essential for blood vessel formation and angiogenesis28. RASIP1 was identified to play a role in NSCLC metastasis29, whereas its role in BC is unclear.
In the selected specific DEGs for TNBC subtype BC, expression of PDE7A, TM4SF1, COTL1, and AREG was notably associated with prognosis. We found that PDE7A was specifically up-regulated in TNBC. It has been demonstrated that inhibition of PDE3, PDE4, PDE7, or PDE8 suppresses migration in triple-negative MDA-MB-231 cells through stimulating cyclic adenosine monophosphate (cAMP) signaling pathway30. We revealed that high mRNA expression of PDE7A significantly conferred longer OS. Also, we observed that the PDE7A gene was altered in 14% of BC patients. Several lines of evidence indicate that TM4SF1 functions as an oncogene in various cancers31–33. Fan et al. reported that TM4SF1 implicates in BC cell migration and invasion34. Interestingly, the TM4SF1 expression level was identified to be obviously high in the TNBC subtype compared to the other subtypes31,34, which is in conformance with our findings. We identified that elevated expression of TM4SF1 was significantly associated with shorter OS in TNBC patients. COTL1 was reported to suppress BC cell growth35, while in a recent study, COTL1 was identified to be up-regulated in BC tissues, promoting cell migration and tumor metastasis36. We observed that COLT1 was specifically highly expressed in TNBC, and its overexpression conferred longer OS in TNBC patients. It was demonstrated that knock-down of AREG in SUM-149 cells, a TNBC cell line, inhibited cellular invasion in BC37. We found that the expression level of AREG was specifically down-regulated in TNBC tissues. Moreover, we identified that overexpression of AREG was related to the shorter OS in TNBC patients.
In the selected specific DEGs for HER2 subtype BC, expression of GSR, HOTAIR, DAPK2, PLEKHG4, and POU6F1 was notably associated with prognosis. GSR encodes glutathione reductase, providing a protective role against oxidative stress38. GSR was reported to be a potential biomarker that could predict response to treatment in primary ER+ ductal breast carcinoma39. Copy number loss of GSR was identified in primary lung adenocarcinoma and squamous cell carcinoma40. Our results showed that GSR was specifically highly expressed in the HER2 subtype. Also, overexpression of GSR was associated with better OS in the HER2 subtype. Compared to normal breast tissues, overexpression of Long noncoding RNA HOTAIR has been detected in BC tissues and cells41–44. A growing body of evidence indicates that HOTAIR might display a role in cell proliferation, migration, invasion, metastasis, and apoptosis in BC44–47. We revealed that HOTAIR expression was specifically up-regulated in the HER2 subtype, which was notably correlated with worse OS in the HER2 subtype. DAPK2, a pro-apoptotic protein, was suppressed in BC cells by miR-520h, which protected BC cells from drug-induced apoptosis48. We found that DAPK2 was specifically down-regulated in the HER2 subtype. Moreover, we observed that enhanced expression of DAPK2 conferred favorable OS in the HER2 subtype. PLEKHG4, also known as FLJ00068, was identified to play an essential role in skeletal muscle and adipocytes49,50, while its role in tumors is unknown. Our results showed that PLEKHG4 was specifically down-regulated in the HER2 subtype. We found that elevated expression of PLEKHG4 was related to poor OS. POU6F1, a transcription factor, was indicated to play a role in stem cell proliferation in HER2 positive BC tissues51. We revealed that POU6F1 was specifically down-regulated in the HER2 subtype. Additionally, we found that overexpression of POU6F1 predicted a shorter OS in the HER2 subtype.
In the selected core DEGs for BC, expression of IFI6, UBE2S, AK5, C2orf40, CNN1, HOXA5, NTRK2, PAMR1, PROS1, SCARA5, SDPR, TGFBR3, and TSHZ2 was notably associated with prognosis. IFI6, also known as 6-16, is an antiapoptotic protein that enhances the metastatic potential of BC cells via mtROS52. Notably, high expression of IFI6 was remarkably associated with shorter OS in ER+ BC patients53. Also, we observed that IFI6 was up-regulated in BC patients, and its high expression was associated with poor OS. UBE2S was reported to be highly expressed in BC tissues and associated with BC cell migration and invasion54. Similarly, we observed up-regulation of UBE2S in BC tissues, which was significantly correlated with worse OS. AK5 induces proliferation and autophagy and inhibits apoptosis in gastric cancer. Also, AK5 was suggested as a potential prognostic marker as well as a therapeutic target for gastric cancer55. AK5 was down-regulated in colorectal cancer due to hypermethylation, and it is involved in cell migration and invasion in colorectal cancer56. In a previous study, AK5 was indicated to be aberrantly hypermethylated in BC cells57. We identified that all four BC subtypes displayed lower expression of AK5 than normal breast tissues. Moreover, we observed that an increased level of AK5 predicted better OS in BC. The role of AK5 in the development and progression of BC needs further exploration.
It has been demonstrated that HOXA5 mRNA and protein expression was remarkably decreased in the BC tissues and cells58–61. Until now, few studies have reported the tumor-suppressive function of HOXA5 in inducing apoptosis in BC cells through p53-dependent and caspase-dependent pathways58,59. Teo et al. indicated that loss of HOXA5 in mammary cells leads to reduced CDH1 and CD24 expression and consequently results in loss of epithelial phenotypes, enhanced stemness, and acquisition of invasion and migration characteristics62. Consistent with previous findings, we observed remarkably decreased HOXA5 mRNA in the BC tissues compared to normal breast tissues. Moreover, we identified that overexpression of HOXA5 conferred better OS in BC.
In line with our findings, CNN1 was identified to be down-regulated in BC tissues and cells compared to normal breast tissues and cells, and it was suggested as a potential gene involved in BC development63,64. Wang et al. clarified that overexpression of CNN1 suppressed proliferation, migration, and invasion of BC cells and promoted cell apoptosis63. Our findings also showed that high expression of CNN1 conferred better OS in BC patients. Accumulating evidence has shown that C2orf40, also known as ECRG4, expression was down-regulated in BC tissues and cells64–67, confirming our results. Additionally, Lu et al. found that promoter hypermethylation leads to a decrease in the expression of C2orf40 in BC. They also indicated that C2orf40 overexpression inhibits cell proliferation, migration, and invasion in BC cells by blocking cell cycle progression at the M phase through inhibiting UBE2C expression, a mitosis-regulating gene. According to the abovementioned findings, C2orf40 was proposed as a tumor suppressor gene in BC66. Notably, higher expression of C2orf40 was identified to be associated with better OS67, which is in conformance with our findings. NTRK2 has been reported to be involved in the mechanism underlying invasive breast cancer68. In line with our results, it was demonstrated that high expression of NTRK2 was notably related to better OS. Therefore, it was supposed to be a candidate prognostic marker of OS in BC68,69.
PAMR1 expression was reported to be frequently lost in BC tissues and cell lines70,71. In line with these findings, we observed down-regulation of PAMR1 in BC patients compared to normal breast tissues. Additionally, we showed that up-regulation of PAMR1 in BC patients was notably correlated with longer OS. PROS1 acts as a ligand of the TAM receptors. Abnormally high expression of PROS1 has been reported to be involved in tumorigenesis and the development of human cancers, including oral squamous cell carcinoma, glioblastoma, papillary thyroid carcinoma, prostate, and colorectal cancer72–76. According to the available literature, PROS1 expression and prognostic significance in BC are still unknown. In the current study, we identified that PROS1 expression was decreased in the BC patients compared to normal samples. In addition, we found that high expression of PROS1 was notably associated with longer OS. It was reported that down-regulation of SCARA5 is implicated in BC tumorigenesis via promoter methylation77. Similarly, You et al. revealed that BC tissues displayed lower SCARA5 expression than para-carcinoma tissues and significantly exhibited a correlation with histological grade, tumor size, and lymph node metastasis78. In line with these findings, we identified that SCARA5 expression was significantly decreased in BC tissues and that conferred worse OS in BC cohorts.
SDPR, also known as CAVIN2, is reported to be down-regulated in BC tissues and cell lines79–85, and its expression level correlated with the tumor stage84. It was previously demonstrated that decreased level of SDPR was remarkably associated with poor OS83,84, RFS, and DMFS81, representing the prognostic potential of SDPR in BC81,84. Dong et al. found a reduction in TGFBR3 expression during BC progression and determined that decreased expression of TGFBR3 was associated with unfavorable RFS. They provided evidence that loss of TGFBR3 expression induces BC invasion and metastasis86. He et al. also reported that low expression of TGFBR3 was associated with a worse OS87, which is in line with our finding. TSHZ2 was proposed to act as a tumor suppressor in BC88, and lower expression of TSHZ2 leads to mammary tumorigenesis89. We observed significant down-regulation of TSHZ2 in the four subtypes of BC patients compared to the normal breast samples that was corrrelated with worse OS.
In summary, we conducted bioinformatics analysis to identify key core and specific genes among the BC subtypes and evaluate their potential prognostic values. Although further experimental studies are required to validate our findings, the current study provides a new perspective into the molecular characteristics of each subtype of BC and might help to select precision prognostic biomarkers in different BC subtypes in the future.