Analysis of SKA1 gene expression in clear cell renal cell carcinoma and its clinical significance based on bioinformatics database

doi:10.3760/cma.j.cn371439-20200113-00085

Abstract

Abstract:

Objective To investigate the expression of spindle and kinetochore-associated complex subunit 1 (SKA1) gene in clear cell renal cell carcinoma (ccRCC) and its clinical significance. Methods The venous blood samples of 76 preoperative patients with ccRCC and 24 healthy subjects were collected from the Affiliated Tumor Hospital of Xinjiang Medical University from January 2018 to December 2018. The level of SKA1 in whole blood was detected by real-time fluorescence quantitative PCR, and the relationship between SKA1 level and clinicopathological characteristics was analyzed. SKA1 data were retrieved from Oncomine (v4.5), The Human Protein Atlas (THPA) gene databases, The Cancer Genome Atlas (TCGA) databasec (cBioportal) and Gene Expression Omnibus (GEO). The Kaplan-Meier method was used to perform patients' survival analysis based on cBioportal ccRCC data, and the survival rates were compared by log-rank method. The relationship between SKA1 expression level and clinicopathological characteristics was analyzed by χ² test. Receiver operating characteristic (ROC) curve was used to evaluate the diagnostic value of SKA1 mRNA in ccRCC, and enrichment analysis of SKA1 gene was carried out using KOBAS 3.0 online tool. Results Two studies on the expression level of SKA1 mRNA in ccRCC were retrieved from Oncomine (v4.5) database, and there were 38 samples. The results showed that SKA1 mRNA was highly expressed in ccRCC tissues. Further detection showed that the expression level of SKA1 mRNA in ccRCC tissues was significantly higher than that in normal renal tissues [-2.21(-3.56,-1.59) vs. -3.41(-4.55,-1.65)], and there was a statistically significant difference (Z=2.282, P=0.022). The analysis of THPA online website showed that SKA1 protein showed obvious moderate staining in ccRCC tissues, while weakly positive or no expression in normal renal tissues. SKA1 was mainly located in the plasma membrane, which was consistent with the results of mRNA analysis. The results of cBioportal showed that the expression level of SKA1 was significantly correlated with AJCC staging (χ²=21.352, P<0.001), T staging (χ²=19.967, P<0.001), N staging (χ²=11.323, P=0.003) and M staging (χ²=27.248, P<0.001). The relative level of SKA1 in peripheral blood of 76 patients with ccRCC was 0.301±0.147, and 0.162±0.052 in healthy subjects, with a statistically significant difference (t=7.360, P<0.001). The level of SKA1 was correlated with AJCC staging (t=2.445, P=0.017) and lymph node metastasis (t=2.242, P=0.028). The results were consistent with tissue analysis in cBioportal database. Survival analysis showed that in cBioportal database, the expression level of SKA1 mRNA was related to the overall survival rate and disease free survival rate of patients with ccRCC (χ²=22.440, P<0.001; χ²=23.830, P<0.001). In GEO database, the expression level of SKA1 mRNA was not related to the overall survival rate of patients with ccRCC (χ²=0.241, P=0.632). The results of ROC analysis in cBioportal database showed that when the cut-off value was -0.944, the sensitivity and specificity of SKA1 mRNA in the diagnosis of ccRCC were 100% and 98.7%. The area under the ROC curve (AUC) was 0.991 (95%CI: 0.972-1.000). The results of ROC analysis of 76 patients with ccRCC showed that when the cut-off value was 0.235, the sensitivity and specificity of peripheral blood SKA1 in the diagnosis of ccRCC were 75.0% and 95.8%, and the AUC was 0.837 (95%CI: 0.761-0.914). KOBAS enrichment analysis showed that SKA1 high expression samples were enriched in gene sets such as chromosomal centromeres, microtubule polymerization and depolymerization regulation and mitotic spindle check-up points. Conclusion SKA1 is highly expressed in ccRCC tissues, which is obviously related to the prognosis of patients. It can be used as a diagnostic indicator and potential therapeutic target for ccRCC.

Key words: Kidney neoplasms, Prognosis, Computational biology, SKA1

Han Jing, Yuan Shuai, Pu Yan, Liu Huibin. Analysis of SKA1 gene expression in clear cell renal cell carcinoma and its clinical significance based on bioinformatics database[J]. Journal of International Oncology, 2020, 47(10): 598-605.

Figures/Tables 11

References 15

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临床病理特征	例数	SKA1基因表达		χ²值	P值
临床病理特征	例数	高表达 (n=216)	低表达 (n=216)	χ²值	P值
性别
男	286	152(70.4)	134(62.0)	3.352	0.067
女	146	64(29.6)	82(38.0)
年龄(岁)
<59	205	108(50.0)	97(44.9)	1.123	0.289
≥59	227	108(50.0)	119(55.1)
Fuhrman分级
G1+G2	211	107(49.5)	104(48.1)
G3+G4	217	109(50.5)	108(50.0)	3.758	0.184
Gx	4	0(0.0)	4(1.9)
AJCC分期
Ⅰ~Ⅱ	278	116(53.7)	162(75.0)	21.352	<0.001
Ⅲ~Ⅳ	154	100(46.3)	54(25.0)
T分期
T₁	231	96(44.4)	135(62.5)
T₂	60	28(13.0)	32(14.8)	19.967	<0.001
T₃	138	90(41.7)	48(22.2)
T₄	3	2(0.9)	1(0.5)
N分期
N₀	193	107(49.5)	86(39.8)
N₁	12	10(4.6)	2(1.0)	11.323	0.003
N_x	227	99(45.9)	128(59.2)
M分期
M₀	353	174(80.6)	179(82.9)
M₁	53	39(18.1)	14(6.5)	27.248	<0.001
M_x	26	3(1.3)	23(10.6)

临床病理特征	例数	SKA1相对表达量	t值	P值
性别
男	62	0.309±0.145	0.129	0.898
女	14	0.266±0.154
年龄(岁)
>60	26	0.306±0.145	0.311	0.757
≤60	50	0.296±0.150
肿瘤直径(cm)
≥5.9	23	0.310±0.148	0.598	0.552
<5.9	53	0.293±0.147
AJCC分期
Ⅰ~Ⅱ	52	0.276±0.151	2.445	0.017
Ⅲ~Ⅳ	24	0.354±0.124
Fuhrman分级
G1+G2	50	0.288±0.137	1.159	0.250
G3+G4	26	0.329±0.164
淋巴结转移
有	11	0.286±0.141	2.242	0.028
无	65	0.391±0.151
远端转移
有	70	0.295±0.153	0.988	0.326
无	6	0.358±0.060

数据库	ID	注释	P值
Gene Ontology	GO:0000779	浓缩染色体,着丝粒区域	<0.001
	GO:0031110	微管聚合或解聚的调控	0.001
	GO:0099080	多分子复合物	0.003
	GO:0005856	细胞骨架	0.006
	GO:0031109	微管聚合或解聚	0.006
	GO:0032886	微管生物学过程的调控	0.007
	GO:0043228	非质膜结合细胞器	0.011
	GO:0070507	微管细胞骨架组织的调控	0.011
	GO:0033043	细胞器组织的调控	0.019
	GO:0007010	细胞骨架组织	0.024
	GO:0022402	细胞周期过程	0.035
Reactome	R-HSA-141444	通过MAD2抑制因子增强非着丝粒信号通路	0.002
	R-HSA-141424	着丝粒信号增强	0.002
	R-HSA-69618	有丝分裂纺锤体检查点	0.002
	R-HSA-2500257	姐妹染色单体凝聚力的分解	0.002
	R-HSA-5663220	激活肌动蛋白	0.002
	R-HSA-2467813	姐妹染色单体的分离	0.003
	R-HSA-68882	有丝分裂后期	0.003
	R-HSA-2555396	有丝分裂中期和后期	0.003
	R-HSA-68877	有丝分裂前中期	0.003
	R-HSA-69620	细胞周期检查点	0.005
	R-HSA-195258	效应器	0.006
	R-HSA-68886	M相	0.007
	R-HSA-194315	Rho GTPase 介导的信号通路	0.008
	R-HSA-69278	细胞周期,有丝分裂	0.009
	R-HSA-1640170	细胞周期	0.011