泛凋亡基因PRKAR1B中rs71518324与非综合征型唇腭裂风险相关

doi:10.13591/j.cnki.kqyx.2025.07.002

摘要/Abstract

摘要：

目的确认泛凋亡是否参与非综合征型唇腭裂(non-syndromic cleft lip with or without cleft palate,NSCL/P)的发生并寻找其中的关键遗传变异和基因。方法首先收集两阶段人群进行全基因组关联分析(genome-wide association study,GWAS)以确定单核苷酸多态性(single-nucleotide polymorphism,SNP)与NSCL/P的相关性。接着选取泛凋亡基因集并提取SNPs,在一阶段人群中进行质控和基于基因的关联分析以筛选候选SNPs,二阶段样本作为验证。Haploreg、RegulomeDB、ATAC测序的功能注释结合基于连锁不平衡的聚集进一步鉴定关键功能遗传变异和风险基因。最后运用表达数量性状位点(expression quantitative trait loci,eQTL)分析、RNA测序、单细胞测序和蛋白质互作分析预测位点和基因的调控效应。结果 rs71518324与NSCL/P的发病风险相关(P_meta<0.001),所在区域富集了大量活性功能元件标志物。rs71518324对PRKAR1B基因的eQTL效应显著(P<0.001)。在RNA测序中PRKAR1B在颅颌面的表达随胚胎发育而增加。在单细胞RNA测序中识别了5个细胞簇,PRKAR1B主要定位于外胚层。结论泛凋亡相关基因PRKAR1B中的rs71518324与NSCL/P风险显著相关。

关键词: 唇腭裂, 全基因组关联分析, 泛凋亡

Abstract:

Objective To confirm whether PANoptosis is involved in the occurrence and development of non-syndromic cleft lip with or without cleft palate (NSCL/P) and identify key genetic variations and genes involved. Methods Firstly, a two-stage population was collected for genome-wide association study (GWAS) to determine the correlation between single nucleotide polymorphisms (SNPs) and NSCL/P. Next, the PANoptosis gene set was selected and SNPs were extracted to conduct quality control and gene-based association analysis in the stage Ⅰ population to screen candidate SNPs, and the stage Ⅱ samples were used as validation. The functional annotation of Haploreg, RegulomeDB, and ATAC sequencing combined with linkage disequilibrium-based clumping further identified the key functional SNP and risk gene. Finally, expression quantitative trait loci (eQTL) analysis, RNA sequencing, single-cell sequencing, and protein-protein interaction analysis were used to predict the regulatory effects of the locus and gene. Results rs71518324 was associated with the risk of NSCL/P (P_meta<0.001), and the surrounding region was enriched with a large number of active functional element markers. The eQTL effect of rs71518324 on PRKAR1B gene was significant (P<0.001). The expression of PRKAR1B in RNA sequencing generally increased over time. Five cell clusters were identified in single-cell RNA sequencing, with PRKAR1B mainly localized to the ectoderm. Conclusion rs71518324 in PRKAR1B, a PANoptosis related gene, is significantly associated with NSCL/P risk.

Key words: cleft lip, GWAS, PANoptosis

中图分类号:

R783.5

高越, 潘永初. 泛凋亡基因PRKAR1B中rs71518324与非综合征型唇腭裂风险相关[J]. 口腔医学, 2025, 45(7): 488-494.

GAO Yue, PAN Yongchu. rs71518324 in PRKAR1B was associated with the risk of non-syndromic cleft lip with or without cleft palate[J]. Stomatology, 2025, 45(7): 488-494.

图/表 7

表1

图1

表2

表3

PRKAR1B上的rs71518324与NSCL/P风险之间的关联"

染色体	SNP	Ref/Alt^a	基因	数据批次	MAF^b (病例/对照)	OR^c (95%置信区间)	P	$P m e t a d$
7	rs71518324	C/G	PRKAR1B	一阶段	0.15/0.11	1.42 (1.12~1.71)	0.020	<0.001
7	rs71518324	C/G	PRKAR1B	二阶段	0.16/0.13	1.37 (1.15~1.59)	0.005	<0.001

表3

表4

图2

图3

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队列阶段	组别	例数	年龄 ($\bar{x}±s$)/岁	性别n(%)
队列阶段	组别	例数	年龄 ($\bar{x}±s$)/岁	男	女
一阶段	病例组	504	1.51±0.51	308(61.11)	196(38.89)
一阶段	对照组	455	0.00±0.00	236(51.87)	219(48.13)
二阶段	病例组	565	4.53±6.92	374(66.19)	191(33.81)
二阶段	对照组	1 269	10.71±2.43	428(33.73)	841(66.27)
总计	病例组	1 069	3.10±8.31	682(63.80)	387(36.20)
总计	对照组	1 724	7.88±4.82	664(38.51)	1 060(61.49)

基因名称	染色体	起始位置	结束位置	SNP数量	Z^a	P^b	类别
CLSPN	1	36185819	36235568	46	2.77	0.003	细胞凋亡
TGFBR3	1	92145902	92371892	543	1.89	0.029	细胞凋亡
NTRK1	1	156785432	156851642	75	2.65	0.004	细胞凋亡
BCL2L11	2	111876955	111926024	72	2.77	0.003	细胞凋亡
MYD88	3	38179969	38184513	1	2.28	0.011	细胞凋亡
ARHGAP10	4	148653214	148993931	430	1.74	0.041	细胞凋亡
IRF2	4	185308867	185395734	216	2.07	0.019	细胞焦亡
UNC5A	5	176237478	176307897	46	2.22	0.013	细胞凋亡
PRKAR1B	7	588834	767287	318	2.06	0.020	细胞凋亡
CDKN2A	9	21967751	21995300	23	1.76	0.040	细胞凋亡
CAMK2G	10	75572259	75634343	85	1.71	0.044	坏死性凋亡
CHUK	10	101948055	101989376	71	2.17	0.015	细胞凋亡
MGMT	10	131265448	131566271	680	2.15	0.016	细胞凋亡
CASP5	11	104864962	104893895	30	1.68	0.047	细胞焦亡
CCND2	12	4382938	4414516	66	2.18	0.015	细胞凋亡
KRT18	12	53342655	53346685	4	1.92	0.027	细胞凋亡
ITGA5	12	54789045	54813244	4	2.23	0.013	细胞凋亡
HMGB1	13	31032884	31191734	224	1.82	0.035	坏死性凋亡
IRF9	14	24630262	24635774	4	2.00	0.023	坏死性凋亡
LGALS3	14	55590828	55612126	55	1.78	0.037	细胞凋亡
PSMA3	14	58711549	58738730	23	1.98	0.024	细胞凋亡
HSP90AA1	14	102547075	102606036	47	2.17	0.015	坏死性凋亡
BCL2L10	15	52401460	52404972	10	2.23	0.013	细胞凋亡
CYLD	16	50775961	50835846	51	1.73	0.042	细胞凋亡
MMP2	16	55423612	55540603	389	2.86	0.002	细胞凋亡
ALOX15	17	4534197	4545589	6	1.77	0.038	坏死性凋亡
PLA2G4C	19	48551100	48614074	194	2.03	0.021	坏死性凋亡
PSMF1	20	1093906	1160596	96	1.71	0.043	细胞凋亡
SPATA2	20	48519928	48532080	34	1.99	0.023	坏死性凋亡

SNP	Haploreg^a						RegulomeDB^b
SNP	启动子组蛋白标志	增强子组蛋白标志	DNase	转录因子结合	eQTL	基因组成分	得分	级别
rs71518324	3种组织	7种组织	6种组织	6个基序	11个命中	内含子	0.79	2b