The genetic alteration of BCAT2Understanding that genetic alterations and epigenetic modifications can trigger abnormal gene expression, we began our analysis with BCAT2 alterations across different cancer types using the cBioPortal platform. Our findings revealed a notably high frequency of BCAT2 alterations in adrenocortical carcinoma (4.47%), primarily characterized by gene amplification. This was followed by patients with endometrial cancer exhibiting various alterations including amplification, deep deletion, multiple alterations, and mutations (Fig. 1A).Fig. 1The genetic alteration of BCAT2 in pan-cancer. (A) cBioPortal tool was used to evaluate the genetic alteration of BCAT2. (B) Lollipop diagram presented the alteration sites of BCAT2. (C) RSEM quantized the transcript of BCAT2.To delve deeper into the nature of these alterations, the lollipop diagram (Fig. 1B) of mutations indicated that there existed 59 missenses, 5 splices, 2 truncating sties and 2 fusion sites in the gene structure of BCAT2, with the highest mutation frequency occurred at the missense site E153K. Complementing these findings, we employed RSEM14 for quantitative transcript analysis, revealing that the highest transcript expression of BCAT2 occurred in the amplification group on average (Fig. 1C).The expression analysis of BCAT2 in pan-cancerBuilding on our genetic analysis, we next explored BCAT2 gene expression across various cancer types using the TCGA pan-cancer database. Our results revealed that after multiple testing adjustment, BCAT2 was upregulated in 12 tumor types compared to normal tissues, including BLCA, BRCA, CESC, CHOL, GBM, HNSC, KICH, KIRP, LIHC, PRAD, STAD, and UCEC. Notably, higher BCAT2 expression was observed in HPV-positive HNSC compared to HPV-negative HNSC, and in metastatic SKCM relative to primary SKCM tumors. Conversely, BCAT2 expression was downregulated in COAD, PCPG, and THCA tumors (Fig. 2A).Fig. 2BCAT2 expression profile in pan-cancer. (A) The expression of BCAT2 in normal and tumor tissues from TCGA database. (B) BCAT2 expression in paired normal and tumor tissues from TCGA database. (C) Pan-cancer expression of BCAT2 between tumor tissues from TCGA database and normal tissues from GTEx database. *q-value < 0.05; **q-value < 0.01; ***q-value < 0.001.To strengthen these findings, we examined BCAT2 expression in paired tumor and normal tissues. This analysis indicated elevated BCAT2 levels in BRCA, CHOL, HNSC, KIRP, LIHC, PRAD, and STAD tumors, whereas lower levels were observed in LUAD, READ, and THCA tumors (Fig. 2B).Further validation was achieved by integrating data from both the TCGA and GTEx databases, comparing BCAT2 expression in normal and tumor tissues. This comprehensive comparison showed increased BCAT2 expression in 10 tumor types: BRCA, CHOL, DLBC, GBM, HNSC, KICH, KIRP, LIHC, PRAD, and THYM. In contrast, decreased expression was noted in ACC, ESCA, KIRC, LAML, LGG, LUAD, LUSC, OV, PAAD, PCPG, READ, SKCM, STAD, TGCT, THCA, and UCS compared to their respective normal tissues (Fig. 2C).Combining these analysis, we concluded that BCAT2 is consistently upregulated in BRCA, CHOL, HNSC, KIRP, LIHC, and PRAD tumors, while it is downregulated in THCA tumors. These expression difference between tumor and normal samples further underscored the potential role of BCAT2 as tumor progression biomarker. The upregulation of BCAT2 in multiple cancer types aligns with previous findings on its role in metabolic reprogramming15, where cancer cells rely on BCAA metabolism to support their growth and survival. BCAT2 promotes BCAA uptake and sustains BCAA catabolism, providing essential nutrients and energy for tumor progression. This suggests that these tumors may depend heavily on BCAA metabolism for their advancement16. However, the mechanism underlying BCAT2 downregulation in THCA tumors has not been well characterized, and its potential role in thyroid cancer progression remains to be verified, indicating a need for further investigation.The protein abundance of BCAT2Having investigated the genetic alterations and gene expression of BCAT2, we next proceeded to analyze its protein abundance across various tissues. The distribution of BCAT2 protein abundance was initially examined (Fig. 3A). Notably, high BCAT2 expression was observed in a broad range of tissues, with particularly elevated levels in the adrenal gland, bladder, nerve, ovary, and prostate, whereas blood exhibited lower expression.Fig. 3The protein expression level of BCAT2 in pan-cancer. (A) The protein level of BCAT2 in normal tissues from GTEx database. (B,C) The protein expression of BCAT2 in tumor and normal tissues from HPA database. (D) BCAT2 location in the substructure of cells obtained from from UniProt database. (E) Interaction relationship of BCAT2 protein.Further analysis using the Human Protein Atlas (HPA) database revealed that BCAT2 expression was highest in colorectal cancer, prostate cancer, breast cancer, endometrial cancer, and ovarian cancer (Fig. 3B). This widespread expression pattern was also consistent across various tissues, with the exception of bone marrow, caudate, cerebellum, hippocampus, skeletal muscle, smooth muscle, and adipose tissues, where BCAT2 was not expressed (Fig. 3C), suggesting that its function is more relevant in specific tissue environments and less critical in others, particularly those with lower proliferative activity.Exploring the subcellular localization of BCAT2 through the UniProt database, we found its presence in both the mitochondrion and nucleoplasm (Fig. 3D). This subcellular localization suggests roles in both energy metabolism and nuclear processes. The presence of BCAT2 in the mitochondria suggests its role in enhancing the utilization of BCAA, which directly supports mitochondrial respiration by providing crucial metabolites for energy production16. In the nucleoplasm, BCAT2 participates in regulatory processes that influence gene expression or nuclear signaling pathways, potentially linking metabolic status to nuclear functions involved in tumor cell proliferation and survival17,18.Finally, our analysis of the protein-protein interaction (PPI) network indicated that BCAT2 interacts with multiple metabolic proteins, such as GCLC and BCK (Fig. 3E). These interactions highlight the potential involvement of BCAT2 in key metabolic pathways, further supporting its role in cancer metabolism and progression.The correlation of BCAT2 with pan-cancer prognosisAfter conducting an in-depth bioinformatics analysis of BCAT2, we further analyzed the significance of BCAT2 in pan-cancer clinical prognosis. Initially, we scrutinized the BCAT2 gene expression across different stages of tumors, guided by WHO cancer staging criteria. BCAT2 exhibited decreased expression in later stages of BLCA (P = 0.009, Fig. 4A), in contrast to increased expression in advanced stages of UVM and HNSC (P = 0.035 and 0.040 respectively, Fig. 4B,D). For THCA tumors, a unique expression pattern was observed: BCAT2 gene expression levels increased in stage II (P = 0.009) but decreased in advanced stages (P = 0.004 and 0.008 respectively, Fig. 4C). After adjusting the p-values, we still observed a significant expression pattern indicating progression in both THCA and HNSC. Additionally, we fitted a linear regression for UVM, revealing a significant increasing linear trend (P = 0.0044), indicating that as the tumor progressed, BCAT2 expression steadily increased.Fig. 4Variations in BCAT2 expression across different stages. *P < 0.05; **P < 0.01; ***P < 0.001; ns: non-significant.We then aimed to elucidate the relationship between BCAT2 gene expression and the survival of cancer patients, after leveraging significant findings from prior research and using available data from relevant databases. The top three quartiles of BCAT2 gene expression were defined high expression category19. The divergence in survival outcomes across different cancers suggests that BCAT2 may play contrasting roles, either as a pro-survival factor or as a driver of tumor progression, depending on the cancer type. For instance, the association between high BCAT2 expression and better OS in KIRP and PAAD could indicate that BCAT2 supports metabolic processes that sustain tumor homeostasis without driving aggressive tumor behavior. In contrast, poorer OS in GBMLGG, LGG, and UVM patients with high BCAT2 expression suggests that BCAT2 may contribute to a more aggressive tumor phenotype in these cancer types, possibly through enhanced BCAA metabolism and cell proliferation (Fig. 5).Fig. 5BCAT2 gene expression and the overall survival of pan-cancer patients. (A–E) The correlation between BCAT2 expression and OS of indicated cancer patients was discovered using data from TCGA database.Delving deeper, univariate Cox regression analysis using TCGA data linked high BCAT2 expression with decreased OS in LGG, PCPG, and UVM patients, but a favorable OS in BLCA, BRCA, KIRP, and PAAD cases (Fig. 6A). Disease-specific survival (DSS) analysis classified high BCAT2 expression as a protective biomarker for BLCA, KIRP, and PAAD, and as a risk marker for LGG, PCPG, PRAD, THCA, THYM, and UVM (Fig. 6B). Disease-free interval (DFI) assessments, defined as time from treatment completion to disease recurrence or death, showed BCAT2 acting as a contributor in DLBC, LGG, PCPG, and UVM and as an inhibitor in BLCA, KIRP, and PAAD (Fig. 6C). Additionally, BCAT2 was established as a protective factor for KIRP patients in progression-free interval (PFI), defined as time from the start of treatment to disease progression or death, reflecting treatment effectiveness, analysis (Fig. 6D).Fig. 6Cox regression analysis of BCAT2. (A–D) The univariate Cox regression of BCAT2 for the OS, DSS, DFI and PFI in TCGA pan-cancer patients was presented by forest maps. After adjusting for p-values, we still observe significant correlations between OS and BCAT2 expression in KIRP, LGG, PAAD, and UVM. For DSS, significant correlations are found in KIRP, LGG, PAAD, PCPG, THCA, THYM, and UVM. No significant correlations were observed for DFI, while for PFI, significant associations remain for LGG, KIRP, PAAD, PCPG, and UVM.Overall, these findings highlight a complex, cancer-type-specific role for BCAT2, underscoring the need for a deeper understanding of its mechanisms in different cancer types. Further studies are necessary to explore the biological underpinnings of these associations, particularly the metabolic and signaling pathways that BCAT2 regulates in distinct tumor environments. Understanding these mechanisms will be crucial for developing targeted therapies that could modulate BCAT2 activity in a context-dependent manner.Analysis of BCAT2 and immune cell infiltrationBuilding on our previous investigations, we conducted a correlation analysis using the TIMER2 database to evaluate the association between BCAT2 expression and immune cell infiltration across various cancer types. Our analysis revealed diverse interactions between BCAT2 expression and different subsets of immune cells.Fig. 7Immune infiltration analysis of BCAT2. (A) The expression of BCAT2 was correlated with CD4+ T cell infiltration by analyzing on TIMER2 database. (B) The correlation between BCAT2 expression and the infiltration of CD8+ T cells on TIMER2 database. (C) BCAT2 expression was associated to Treg cells infiltration in pan-cancer using data from TIMER2 database. *P < 0.05; **P < 0.01; ***P < 0.001.Specifically, BCAT2 expression positively correlated with naïve CD4+ T cells in BLCA, SKCM, and THCA; with both CD4+ T cells and CD4+ Th cells in HNSC; and with CD4+ Th cells in LGG, SARC, and READ. Conversely, a negative correlation was observed with non-regulatory CD4+ T cells in GBM; with CD4+ Th cells in BLCA and TGCT; and with CD4+ memory cells in BRCA, KIRC, and THCA (Fig. 7A). Regarding CD8+ T cells, BCAT2 expression exhibited a significant positive correlation in CESC, HNSC-HPV(+), and UVM. However, negative correlations were identified in BRCA, KIRC, KIRP, PCPG, SKCM, and THYM (Fig. 7B). In the context of Treg cells, BCAT2 expression was positively associated with Treg cells in HNSC-HPV(+), LUAD, and TGCT, but negatively correlated with Treg cells in KIRP and THCA (Fig. 7C).These findings underscore the complex role of BCAT2 in modulating the immune microenvironment across different cancer types. By influencing the infiltration and activity of various immune cell subsets, BCAT2 may play a pivotal role in tumor immunity and progression. This highlights the importance of further investigating the mechanisms of BCAT2 in immune regulation to better understand its potential as a therapeutic target in cancer.
