Table_4_Regulatory SVA retrotransposons and classical HLA genotyped-transcripts associated with Parkinson’s disease.xlsx

IntroductionParkinson’s disease (PD) is a neurodegenerative and polygenic disorder characterised by the progressive loss of neural dopamine and onset of movement disorders. We previously described eight SINE-VNTR-Alu (SVA) retrotransposon-insertion-polymorphisms (RIPs) located and expressed within the Human Leucocyte Antigen (HLA) genomic region of chromosome 6 that modulate the differential co-expression of 71 different genes including the HLA classical class I and class II genes in a Parkinson’s Progression Markers Initiative (PPMI) cohort.
Aims and methodsIn the present study, we (1) reanalysed the PPMI genomic and transcriptomic sequencing data obtained from whole blood of 1521 individuals (867 cases and 654 controls) to infer the genotypes of the transcripts expressed by eight classical HLA class I and class II genes as well as DRA and the DRB3/4/5 haplotypes, and (2) examined the statistical differences between three different PD subgroups (cases) and healthy controls (HC) for the HLA and SVA transcribed genotypes and inferred haplotypes.
ResultsSignificant differences for 57 expressed HLA alleles (21 HLA class I and 36 HLA class II alleles) up to the three-field resolution and four of eight expressed SVA were detected at p<0.05 by the Fisher’s exact test within one or other of three different PD subgroups (750 individuals with PD, 57 prodromes, 60 individuals who had scans without evidence of dopamine deficits [SWEDD]), when compared against a group of 654 HCs within the PPMI cohort and when not corrected by the Bonferroni test for multiple comparisons. Fourteen of 20 significant alleles were unique to the PD-HC comparison, whereas 31 of the 57 alleles overlapped between two or more different subgroup comparisons. Only the expressed HLA-DRA*01:01:01 and -DQA1*03:01:01 protective alleles (PD v HC), the -DQA1*03:03:01 risk (HC v Prodrome) or protective allele (PD v Prodrome), the -DRA*01:01:02 and -DRB4*01:03:02 risk alleles (SWEDD v HC), and the NR_SVA_381 present genotype (PD v HC) at a 5% homozygous insertion frequency near HLA-DPA1, were significant (Pc<0.1) after Bonferroni corrections. The homologous NR_SVA_381 insertion significantly decreased the transcription levels of HLA-DPA1 and HLA-DPB1 in the PPMI cohort and its presence as a homozygous genotype is a risk factor (Pc=0.012) for PD. The most frequent NR_SVA_381 insertion haplotype in the PPMI cohort was NR_SVA_381/DPA1*02/DPB1*01 (3.7%). Although HLA C*07/B*07/DRB5*01/DRB1*15/DQB1*06 was the most frequent HLA 5-loci phased-haplotype (n, 76) in the PPMI cohort, the NR_SVA_381 insertion was present in only six of them (8%).
ConclusionsThese data suggest that expressed SVA and HLA gene alleles in circulating white blood cells are coordinated differentially in the regulation of immune responses and the long-term onset and progression of PD, the mechanisms of which have yet to be elucidated.

引言：帕金森病（Parkinson’s disease, PD）是一种神经退行性多基因疾病，以神经多巴胺进行性丢失与运动障碍起病为特征。本团队此前曾报道，位于6号染色体人类白细胞抗原（Human Leucocyte Antigen, HLA）基因组区域内的8个SINE-VNTR-Alu（SINE-VNTR-Alu, SVA）反转录转座子插入多态性（retrotransposon-insertion-polymorphisms, RIPs）可在帕金森病进展标志物倡议（Parkinson’s Progression Markers Initiative, PPMI）队列中，调控包括经典HLA I类与II类基因在内的71个不同基因的差异共表达。

研究目的与方法：本研究（1）重新分析了来自1521名受试者（867名病例、654名对照）全血的PPMI基因组与转录组测序数据，以推断8个经典HLA I类、II类基因以及DRA与DRB3/4/5单倍型所表达转录本的基因型；（2）检验了HLA与SVA转录基因型及推断的单倍型在3个PD亚组（病例）与健康对照（healthy controls, HC）之间的统计学差异。

结果：在未对多重比较进行Bonferroni校正的情况下，通过Fisher精确检验，在3个PD亚组（750名确诊PD患者、57名前驱期患者、60名无多巴胺缺损证据的扫描受试者[scans without evidence of dopamine deficits, SWEDD]）中的任一亚组与PPMI队列中的654名健康对照相比时，57个表达的HLA等位基因（21个HLA I类等位基因与36个HLA II类等位基因，分辨率达三位域）以及8个表达的SVA中的4个均存在显著差异（p<0.05）。其中20个显著等位基因中有14个仅在PD与HC的比较中存在，而57个等位基因中有31个在两个或更多亚组比较中存在重叠。经Bonferroni校正后，仅以下等位基因与基因型仍具有统计学显著性（Pc<0.1）：（PD vs HC组中）表达的HLA-DRA*01:01:01与-DQA1*03:01:01保护性等位基因；（HC vs 前驱期组、PD vs 前驱期组中）-DQA1*03:03:01风险或保护性等位基因；（SWEDD vs HC组中）-DRA*01:01:02与-DRB4*01:03:02风险等位基因；以及（PD vs HC组中）位于HLA-DPA1附近、纯合插入频率为5%的NR_SVA_381存在基因型。同源的NR_SVA_381插入在PPMI队列中可显著降低HLA-DPA1与HLA-DPB1的转录水平，且该基因型以纯合状态存在时是PD的风险因素（Pc=0.012）。PPMI队列中最常见的NR_SVA_381插入单倍型为NR_SVA_381/DPA1*02/DPB1*01（占比3.7%）。尽管HLA C*07/B*07/DRB5*01/DRB1*15/DQB1*06是PPMI队列中最常见的HLA 5位点定相单倍型（n=76），但其中仅6例（8%）携带NR_SVA_381插入。

结论：本研究数据表明，循环白细胞中表达的SVA与HLA基因等位基因在免疫应答调控以及PD的长期起病与进展过程中存在差异性协同调控作用，其具体机制尚待阐明。