Zhang Xue Qin, Li Li
Department of Gynecology and Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, People's Republic of China.
Key Laboratory of Early Prevention and Treatment for Regional High Frequency Tumor, Ministry of Education, Nanning, Guangxi, People's Republic of China.
Int J Gen Med. 2021 Oct 16;14:6825-6838. doi: 10.2147/IJGM.S330256. eCollection 2021.
Vacuolar protein sorting-associated protein 13A (VPS13A) has been shown to be associated with rhabdomyosarcoma, gastric cancer and ovarian cancer, but the pan cancer analysis of VPS13A is still lacking, and the bioinformatics function of VPS13A has not been studied yet.
We used TCGA and GEO databases to investigate the distribution, expression and prognosis of VPS13A in 33 tumors for the first time. We used TIMER2, ULCAN databases to obtain the expression differences of VPS13A in tumor tissues and corresponding normal tissues, and further obtain the gene expression in different pathological stages of tumors from the GEPIA database. Mutation types and survival analysis of VPS13A were obtained from cBioPortal database. The relationship between VPS13A and immune infiltration was explored using TIMER2. We used the String website to obtain VPS13A binding proteins and draw the protein-protein interaction network map. JVENN was used for cross analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) were used for gene enrichment analysis.
VPS13A is highly expressed in most tumors, and gene expression is associated with prognosis in patients with tumors. The expression level of VPS13A was correlated with the infiltration depth of CD8+T cells in DLBC, LUAD, SKCM and TGCT, and was correlated with carcinoma-associated fibroblasts in BRCA, CESC, LIHC and THYM. Compared with normal tissue, VPS13A methylation levels were higher in some primary tumors. KEGG gene enrichment indicates that VPS13A is involved in RNA degradation, autophagy, cell senescence, cell cycle, apoptosis and other pathways.
VPS13A is closely related to the occurrence and progression of tumors and can be used as a biomarker for tumor screening and diagnosis. The level of VPS13A expression and the presence of mutations affect the prognosis of patients with certain cancers, which can be determined by early genetic testing.
液泡蛋白分选相关蛋白13A（VPS13A）已被证明与横纹肌肉瘤、胃癌和卵巢癌有关，但尚未对VPS13A进行泛癌分析，其生物信息学功能也尚未得到研究。
我们首次使用TCGA和GEO数据库研究VPS13A在33种肿瘤中的分布、表达及预后情况。利用TIMER2、ULCAN数据库获取VPS13A在肿瘤组织及相应正常组织中的表达差异，并从GEPIA数据库进一步获取肿瘤不同病理阶段的基因表达情况。从cBioPortal数据库获取VPS13A的突变类型及生存分析结果。利用TIMER2探索VPS13A与免疫浸润的关系。我们通过String网站获取VPS13A结合蛋白并绘制蛋白质-蛋白质相互作用网络图。使用JVENN进行交叉分析，运用京都基因与基因组百科全书（KEGG）和基因本体论（GO）进行基因富集分析。
VPS13A在大多数肿瘤中高表达，且基因表达与肿瘤患者的预后相关。VPS13A的表达水平与弥漫性大B细胞淋巴瘤（DLBC）、肺腺癌（LUAD）、皮肤黑色素瘤（SKCM）和睾丸生殖细胞肿瘤（TGCT）中CD8 + T细胞的浸润深度相关，与乳腺癌（BRCA）、子宫颈癌（CESC）、肝癌（LIHC）和胸腺瘤（THYM）中的癌相关成纤维细胞相关。与正常组织相比，VPS13A在一些原发性肿瘤中的甲基化水平更高。KEGG基因富集表明VPS13A参与RNA降解、自噬、细胞衰老、细胞周期、凋亡等途径。
VPS13A与肿瘤的发生发展密切相关，可作为肿瘤筛查和诊断的生物标志物。VPS13A的表达水平及突变情况影响某些癌症患者的预后，可通过早期基因检测来确定。
