Parkinson’s disease (PD), familial and sporadic, is the second most common human neurodegenerative disease after Alzheimer’s disease with almost 90,000 people in the USA diagnosed each year, and a 2019 world-wide prevalence rate of 8.5 million individuals that is increasing (1). PD pathology is age-related and characterised by progressive degeneration of dopaminergic neurons in the substantia nigra and other brainstem nuclei, with accumulation of tau and alpha-synuclein deposits (Lewy body inclusions) throughout the peripheral and central nervous systems (2–5). Essential differential observations accompanying PD subtypes include loss of dopamine, bradykinesia (movement disorders), rigidity, tremor and a range of non-motor symptoms such as cognitive impairment and sleep disturbance (6, 7). The primary and secondary causes of PD may involve genetic, environmental, metabolic and immunological factors with various non-neurological features and varying overlap with age-related autoimmune diseases such as multiple sclerosis, amyotrophic lateral sclerosis, thyroid diseases and rheumatoid myalgia (3, 8–11). In regard to the effect of the environment and immunogenetics, Braak et al. (12) postulated that an unknown viral or bacterial infection in the neurons of the gut and/or nasal cavity initiated the onset of sporadic PD with specific alpha-synuclein spreading and eventual Lewy body formation and glial neuroinflammatory activation. Considerable preclinical, clinical and laboratory evidence supports Braak’s hypothesis of PD progression, although the specific mechanisms, stages and pathways still have to be elucidated (13, 14). Recent animal in vitro studies and human neuropathological examinations suggest that neuronal antigen presentation may have a role in PD and other neurodegenerative disorders (15).

Although the aetiology of sporadic PD remains unknown, the immune system has an important role in this disease (3, 8–11). The protective effect of nonsteroidal anti-inflammatory drugs in animal models and epidemiological studies underscores the role of neuroinflammation in PD (16). Large numbers of microglia expressing human leucocyte antigen (HLA)-DR have been detected in the brain of PD patients, particularly in areas of maximal neurodegeneration (15, 17). Leucine-rich repeat kinase 2 (LRRK2), a risk gene of PD, is highly expressed in microglia, monocytes and other immune cells (18), and has been reported to be associated with an increasing risk of Crohn’s disease, an inflammatory bowel disease and other autoimmune diseases (19–21). Alpha-synuclein specific T cell reactivity is associated with HLA-DRB1*15:01 and -DRB5*01:01 (22, 23), and with preclinical and early PD (24, 25), and the infiltration of CD4+ lymphocytes into the brain contributes to neurodegeneration in a mouse model of PD (15, 26). At least 90 genetic loci have been associated with PD risk in genome-wide association studies (GWAS), including the HLA-DRA, -DRB, and -DQ genes within the Major Histocompatibility Complex (MHC) class II region on the short arm of chromosome 6 at 6p21.3 (27, 28).

HLA class I and class II molecules are polymorphic cell-membrane-bound glycoproteins that present antigens to circulating CD8+ and CD4+ T-lymphocytes, and regulate the innate and adaptive immune responses including autoimmunity, infectious diseases and transplantation outcomes (29–31). The MHC or HLA genomic region encodes at least 160 genes within ~ 3 to 4 MB including three distinct structural regions designated as class I, class II and class III. Of the 32 HLA genes, the classical HLA class I genes, HLA-A, -B and -C, and the classical HLA class II genes, HLA-DR, -DQ and -DP, are characterised by an extraordinary large number of polymorphisms, whereas the non-classical HLA class I genes, such as HLA-E, -F and -G, are differentiated by their tissue-specific expression and limited polymorphism (32, 33). Several GWASs have shown an association between the HLA locus and the risk of PD especially involving the HLA class II gene SNPs of HLA-DQA1, -DQA2, -DQB1, -DRB1, and -DRB5 (27, 34–36).

Most studies of PD association with HLA class I and class II alleles are limited in scope and power mainly because of small sample numbers and limited resolution of HLA typing methods. Studies with more than 500 PD cases suggest that HLA genes have a role in risk or protection in PD progression. The study by Saiki et al. (37) of a UK study group (528 PD cases and 3430 controls) revealed that HLA-DRB1*03 and -DQB1*05 allele groups were possible PD risk alleles whereas HLA-DRB1*04 and -DQB1*03 might be protective. Wissemann et al. (35) in an analysis of 2843 European PD cases from two separate cohorts including healthy controls found that the HLA class II risk alleles were HLA-DRB1*15:01, -DQA1*01:02 and -DQB1*06:02, and the protective alleles were -DRB1*04:04, -DQA1*03:01, and -DQA1*03:02. They also suggested that HLA-B*07:02 and -C*07:02 are part of an HLA risk haplotype, whereas HLA-B*40:01 and -C*03:04 are protective alleles. Hollenbach et al. (38) in a sequencing and typing analysis of 11 classical HLA loci using 1597 PD and 1606 controls found strong protective effects of HLA-DRB1*04:01 and HLA-DQB1*03:02, but no significant differences between cases and controls for alleles of any class I locus (HLA-A, -B, and -C) or class II loci HLA-DPA1, -DPB1, -DRB3, -DRB4, and -DRB5. They also proposed that HLA susceptibility to PD can be explained by a specific combination of amino acids at positions 70–74 on the HLA-DRB1 molecule referred to as the ‘shared epitope’ (SE) and that the SE in combination with valine at position 11 (11-V) is highly protective in PD, but a risk with the absence of 11-V. More recently, Yu et al. (34) used 13,770 European PD patients in a meta-analysis of multiple cohorts from eight independent sources to confirm that HLA-DRB1*04:01, -DRB1*04:04, -DQA1*03:01 and -DQB1*03:02 were protective. They concluded that the effect of the HLA-DRB1 gene in susceptibility for PD is small and does not merit routine HLA typing in PD. An earlier study of Chinese Han (567 PD cases and 746 controls) indicated that HLA-DRB1*03:01 was a risk allele, whereas HLA-DRB1*04:06 was a protective allele in their study of only HLA-DRB1 alleles (39). More studies of the association between HLA genotypes and PD are needed to understand the role of HLA in the disease processes of PD and how HLA genes and alleles might be interlinked with accompanying autoimmune diseases, especially those that show non-neurological symptoms associated with PD such as sleep disorder and a decrease in HLA-DR expression (40).

Apart from protein coding genes, numerous repeat elements (REs) within the human genome have been associated with PD including SINE-R-VNTR-Alu (SVA) retrotransposon insertion polymorphisms (RIPs), such as a SVA that is inserted in the TAF1 gene that has been associated with the disease X-linked dystonia-parkinsonism, and at least five other SVA inserted within the PD (PARK) gene loci of different chromosomes (41, 42). Recently, expression quantitative trait loci (eQTL) of different SVAs and their effect on the regulation of gene expression were identified and described for a Parkinson’s Progression Markers Initiative (PPMI) cohort using whole genome sequence and transcriptome data obtained from the blood of more than a thousand individuals (43). Also, there are SVAs within the MHC genomic region that are expressed and can regulate the expression of HLA genes (44). At least eighteen SVA polymorphic insertions were mapped previously within the MHC class I, II and III regions, and some were found to be haplotypic or haplospecific for particular HLA gene alleles that varied in frequency between European, Japanese and African American populations (45). For example, the SVA-HF, SVA-HA, and SVA-HC were inserted at a relatively low frequency (<0.2) in European populations and strongly associated with the HLA 7.1 ancestral haplotype, but not with the 8.1 haplotype (46, 47).

A PPMI clinical protocol was established in 2010 to acquire comprehensive longitudinal within-participant clinical, imaging, genomic, transcriptomic and biomarker data for three main cohorts, (1) PD with and without genetic risk variants, (2) prodromes (nonmotor features) at risk of PD, and (3) healthy controls with no neurological disorder and no first degree relative, currently aimed at enrolling 4000 participants at about 50 sites worldwide (48). We associated the regulatory properties of 8 SVA RIPs located within the class I and class II MHC regions of the PPMI cohort with the differential co-expression of 71 genes within and 75 genes outside of the MHC region, including all the classical class I and class II genes (44). A limitation of this SVA-HLA eQTL study was the absence of HLA allelic data to associate with the SVA genotypes and for stratifying the statistical differences between PD, prodromes and healthy controls within the PPMI cohort.

The purpose of our current study was to undertake an analysis of the expression of ten classical class I (HLA-A, -B, -C) and class II (HLA-DRA, -DRB3/4/5 -DRB1, -DQB1, -DQA1, -DPA1, -DPB1) gene alleles in the context of the eight regulatory SVA RIPs expressed within the MHC genomic region ( Figure 1 ) that we had previously studied (44). The main aims of this study were to determine:

Our RNA data analysis confirms that SVAs are eQTLs for classical HLA class I and class II alleles, and suggests that coordinated SVA and HLA gene expression might influence PD onset or progression via the adaptive immune system.

The regulatory effects of eight transcribed SVA RIPs on the differential co-expression of 71 genes within the MHC genomic region including all the classical class I and class II genes of a PPMI cohort were previously identified by eQTL statistical analysis (41, 43, 44). In this study, the same PPMI RNAseq database was reused to genotype the transcripts encoded by classical class I and class II HLA genes in order to determine their frequency and estimate their haplotypic associations with each other and with the eight regulatory MHC SVAs. The arcasHLA software tool (50) was used to impute the genotypes of the transcripts expressed by the class I and class II HLA genes to at least the three-field resolution that included the ancestral allele group, the protein type and the synonymous changes in the coding regions. In a recent comparison of the seven best of 22 genotyping computation tools, arcasHLA was the fastest and among the top three most accurate (99.1% for MHC-I and 98.1% for MHC-II) for genotyping Caucasian American RNA data (56). The PPMI cohort HLA allele frequency and haplotype data confirmed that our cohort was mostly (>95%) Caucasian American or Caucasian European as expected (33, 48). Consequently, we have accepted the high accuracy and reliability of the arcasHLA imputations without resorting to the use of other genotyping tools.

Significant differences were detected at p<0.05 by the Fisher’s exact test for 21 HLA class I alleles and 36 HLA class II alleles transcribed by 10 HLA genes that were different up to the three-field resolution within four subgroups (PD, Prodrome, SWEDD and HC) of the PPMI cohort when not corrected by multiple testing ( Tables 3 – 5 ). Only five alleles, all from the HLA class II region, were significant after the Bonferroni correction; the expressed protective alleles HLA-DRA*01:01:01 and -DQA1*03:01:01 within PD, the risk allele HLA-DQA1*03:03:01 within the Prodrome cohort and the HLA-DRA*01:01:02 and -DRB4*01:03:02 risk alleles in the SWEDD group. Although HLA-DQA1*03:01:01 differs from -DQA1*03:03:01 by a single nucleotide substitution in exon 3 at codon 160 (c548.C<A), the OR calculations showed that the former was a protective allele and the later a risk allele. HLA-DQA1*03:01:01 was more prevalent at 10.2% than -DQA1*03:03 at 5.7% in the PPMI cohort ( Supplementary Table 2 ). The 52 alleles that did not survive the Bonferroni statistical challenge, but had significant differences p<0.05 between the different cases and controls by the Fisher exact test were placed within a statistically marginal zone of ‘possible’ rather than ‘strong’ or ‘definite’ risk or protective effects. This lower level of statistical significance might have been confounded by various factors such as lack of statistical power due to insufficient sample numbers, unreliable disease and aetiological factors, or various comorbidities and other issues not accounted for in our analysis. However, many of the 57 possible protective or susceptibility HLA alleles (p<0.05 or Pc<0.1) were reported previously by others to be statistically significant in PD and various autoimmune disease studies. For example, we confirmed the results of previous studies that HLA-DRA*01, -DRB4*01:03, -DRB5*01, -DQB1*05 and -C*07:01:01 are predisposing alleles and that HLA-DRB1*04:04, -DQA1*03:01, -DQA1*03:02, and -DQB1*03:02, are protective in PD (34–37, 57). The HLA-A*31:01:02, and -B*40:02:01 possible risk alleles in our PD cohort were not reported previously, although they were associated with the development of acquired aplastic anemia (58). Also, we found that the HLA-DRB1*11:02:01 was a minor possible risk allele in the PD, Prodrome and combined cohorts, but not in the SWEDD cohort. This might be the first report to associate HLA-DRB1*11:02:01 as a possible risk allele in PD, although it has been associated with systemic juvenile idiopathic arthritis (59), Graves’ disease (60) and MS (57).

In our study, there was an overall greater number of possible protective alleles than risk alleles at a ratio of 12 to 8 (60%) in the PD group compared to healthy controls, whereas the Prodrome and SWEDD comparisons with HC had more possible risk alleles than protective alleles at ratios of 18 to 2 (90%), and 18 to 5 (78%), respectively. This greater ratio of HLA risk to protective alleles in Prodrome and SWEDD compared to HC might in part explain the gradual or variable progression to PD. Idiopathic, spasmodic and prodromal PD groups have a mixed population of different HLA haplotypes and HLA alleles that carry and present various peptides and antigens to T lymphocytes, which in turn are activated to regulate a diversity of immune responses including inappropriate and harmful autoimmune responses that can cause extensive tissue damage. In this study, we could not discern easily, which are the possible high risk HLA haplotypes that lead to a faster rate of disease onset, and which are protective or low risk HLA alleles that slow down the disease rate. Wissemann et al. (35) on the basis of their study suggested that the 7.1 ancestral haplotype (AH) that consists of the linked HLA alleles B*07:02/C*07:02/DRB5*01/DRB1*15:01/DQA1*01:02/DQB1*06:02 is a PD high risk haplotype and that the C*03:04, DRB1*04:04 and DQA1*03:01 alleles are part of low-risk haplotypes. We found that five of the alleles in the possible high risk 7.1AH were present in the SWEDD-HC comparison, but not in the PD-HC or Prodrome-HC comparisons. DRB1*15:01 was a possible risk allele only in the Combination (all subgroups)-HC comparison. Also, these high-risk alleles were present in the SWEDD group at a frequency of between 14.2% and 18.3% relative to a frequency between 7% and 10.7% in the HC group. The low-risk alleles DRB1*04:04 and DQA1*03:01 were distributed as protective alleles in our PD-HC comparison. In contrast, C*03:04 was a risk allele in the Prodrome-HC, and the SWEDD-HC comparisons. Furthermore, none of the HLA alleles of the frequent Caucasian 8.1AH haplotype: HLA-A*0101/C*0701/B*0801/DRB1*0301/DQA1*0501/DQB1*0201, except for C*0701, were significant in our study groups.

The statistical results for the HLA-DRB1*04 alleles in previous studies of PD suggested both susceptibility (36) and protective associations (34, 35, 37–39). Our results revealed that the HLA-DRB1*04 alleles were significant statistically at the ‘possible’ level (uncorrected Fisher’s exact test, p<0.05) with HLA-DRB1*04:02 and -DRB1*04:04 protective in PD and PPMI ( Table 3 ), whereas HLA-DRB1*04:01 was a possible risk allele in the Prodrome and SWEDD groups, and the PPMI cohort ( Table 5 ). This difference between the PD, Prodrome, and SWEDD groups might reflect that neither the Prodrome, nor SWEDD groups were an established PD with as yet degenerated dopaminergic neurons and large aggregates of alpha-synuclein or tau proteins (48). A recent study by Mignon et al. (61), reported in a preprint, suggested that HLA-DRB1*04 alleles strongly bound to an epitope sequence of tau in neurofibrillary tangles and mediated an adaptive immune response against tau to decrease PD risk. This protective effect of the HLA-DRB1*04 antigen was intermediary with HLA-DRB1*04:01 and HLA-DRB1*04:03, and absent for HLA-DRB1*04:05 (61), which might explain in part the differentiated statistical results that we obtained for the HLA-DRB1*04 alleles in the PPMI cohort ( Tables 3 – 5 ). In contrast, HLA-DRB1*04:01 might transport alpha-synuclein to the cell surface of T-cells (62) to become a risk factor for individuals in the Prodrome and SWEDD groups ( Table 5 ). According to Hollenbach et al. (38), HLA-DRB1*04:01 is part of the protective Caucasian haplotype DRB1*04:01/DQA1*03:01/DQB1*03:02 and that, along with DRB1*01:01, has the ‘shared epitope’ (SE) with the amino acid motif Q/RK/RRAA at positions 70–74 in combination with valine at position 11 (11-V) that are highly protective in PD. In our study, HLA-DRB1*01:02 was a possible protective allele within the combined cohort-healthy controls comparison.

Four possible HLA risk alleles, HLA-DRB5*01:01, -DRB1*04:01, -DRB1*15:01, and -DQB1*03:01, are of particular interest because they have been associated with alpha-synuclein specific T cell reactivity in patients with PD (23–25). In this regard, Ozono et al. (62) showed experimentally that HLA class II molecules with the DRB5*01:01 allele captured and transported conformationally abnormal alpha-synuclein extracellularly, whereas HLA-DRB1*04:01 transported normal alpha-synuclein to the cell surface to present to circulating CD4-positive T cells, but did not translocate structurally abnormal alpha-synuclein. Moreover, alpha-synuclein32-46 peptide immunisation of mice that expressed HLA-DRB1*15:01 triggered intestinal inflammation, enteric neurodegeneration, constipation, and weight loss (22), suggesting a critical role for alpha-synuclein autoimmunity in HLA-DRB1*15:01 carriers in the combined PPMI cohort ( Supplementary Table 4 ). The findings by Garretti et al. (22) are consistent with the hypothesis that alpha-synuclein-mediated pathology can originate in the enteric neural system and proceed into the brain via the vagus nerve (12, 52). In this context, Braak’s hypothesis (12) connects the onset of PD to the alleles HLA-DRB1*15:01, -DRB1*04:02:01, -DQA1*03, and -DQB1*03:02:01 that are associated with Crohn’s disease, colitis or celiac disease (63–65), and that we found were significant (p<0.05) in the PPMI cohort ( Tables 3 – 5 ; Supplementary Table 4 ). The question remains whether the CD4+ T lymphocytes that recognise and interact with the presented HLA class II bound alpha-synuclein antigens might in turn trigger cytotoxic CD8+ T lymphocytes and antibody producing B-lymphocytes to attack and destroy neurons that display HLA-bound alpha-synuclein antigen at the cell surface in the peripheral and central nervous systems. A dysfunctional blood brain barrier in PD patients can lead to increased levels of alpha-synuclein, autoantibodies against alpha-synuclein, and infiltrating T cells in the CSF and plasma (66). Consequently, more information is required about what subgroups of autoreactive T and B lymphocytes and other self-antigens beside alpha-synuclein might be generated by the adaptive immune system in PD pathogenesis.

Eight SVA eQTLs expressed within the MHC region were inferred to differentially modulate the transcription levels of classical class I and class II HLA genes within the PPMI cohort (43, 44). In the present study, four of the eight regulatory SVA-RIPs, R_SVA_25, NR_SVA_380, R_SVA_85 and NR_SVA_381, are significant (p<0.05) by the Fisher’s exact test within the different PPMI subgroups, but only the SVA_381 PP genotype is significant (Pc<0.1) after Bonferroni corrections for multiple testing ( Table 6 ). SVA_381 PP is a significant (p<0.05) risk in the PD-HC, Prodrome-HC and combination-HC comparisons, but not significant (p>0.05) in the SWEDD-HC comparison. This result might be related to the observation that the homologous NR_SVA_381 insertion (PP) is associated significantly with a decrease in the transcription levels of HLA-DPA1 (p=0.037) and HLA-DPB1 (p=0.001) in the PPMI cohort ( Figure 4 ). The suppressed transcription rate might result in a reduced level of HLA-DPA1 and -DPB1 antigen presentation to the circulating CD4+ helper cells. Previously, NR_SVA_381 was inferred to modulate only the allelic expression of the HLA-DPA1, -DPB1 and -B genes, whereas R_SVA_85 only modulates the HLA-DPA1 and -DPB1 genes (44). Thus, R_SVA_85 and NR_SVA_381 might have opposing regulatory effects on the HLA-DPA1, and -DPB1 gene expression that together could have a small, but significant effect in some PD and Prodrome cases ( Figures 3 , 4 ).

The total absence of R_SVA_85 (genotype AA) is a minor risk factor for the Prodrome cohort ( Table 6 ), which suggests that its presence (genotype PP) might be protective. A possible protective role is supported by its presence in four significant protective haplotypes ( Figure 2 ). Although R_SVA_85 significantly increased (p=0.023) the transcription of HLA-DPB1, its presence (PP) had no significant statistical effect (p>0.05) on the levels of HLA-DPA1 transcription ( Figure 4 ). Therefore, the protective effect of the presence of R_SVA_85 in PD or in the Prodrome cohort might be diluted out in a statistical analysis because of its overall high frequency (82.9%) in the PPMI cohort and strong association with many different HLA-DPA1 alleles ( Table 7 ; Figure 3 ). Although the R_SVA_85 and NR_SVA_381 loci are separated from each other by 1.7 kb in an intergenic region between the HLA-DOA and HLA-DPA1 genes ( Figure 1 ), they are together only at a low frequency of 1.6% ( Figure 3 ). The effects of R_SVA_85 and NR_SVA_381 on the gene expression of HLA-DPA1 and -DPB1 genes ( Figure 4 ), either separately or together, is of interest also for unrelated hematopoietic cell transplantation because the level of expression of HLA-DP in the recipient is an important prognostic indicator of donor-anti-host recognition and for evaluating the risk of graft-versus-host disease (67, 68).

Of the two other SVA-RIPs that had minor significance (p<0.05), R_SVA_25 modulates the transcription of all the HLA class I genes and HLA-DRB5, -DRB1 and -DQB1, whereas NR_SVA_380 modulates the transcription of the HLA-C, HLA-DRB1 and the two HLA-DQ genes (44). R_SVA_25 is inserted 23.4 kb telomeric of HLA-C, occurs at low frequency (8.6%), but upregulates the expression of 88.2% of the C*07:02:01 risk alleles and 92% of the B*07:02:01 risk alleles ( Table 7 ) in the SWEDD-HC comparison ( Table 4 ). SVA_380 AA is a minor risk genotype in the SWEDD-HC comparison, while SVA_380 PA is protective in the PD-HC comparison as well as in the SWEDD-HC comparison ( Table 6 ). NR_SVA_380, inserted between DRB5 and DRB6, up-regulates 93.8% of DRB1*01:01:01 and 100% of DRB1*10:01:01 neutral alleles ( Table 7 ).

Our previous study was unable to discern whether SVA_24, SVA_380 or SVA_27 modulated the expression of HLA-DQA1 protective or risk alleles (44). The present study revealed that of the 110 HLA-DQA1*03:03:01 risk alleles in the PPMI cohort, 31 (28.2%) were associated with SVA_24, none with SVA_380, and none with SVA_27. Similarly, of 147 DQA1*03:01:01 protective alleles, 35 (23.7%) were associated with SVA_24, none with SVA_380, and none with SVA_27. Although SVA_24 is located near HLA-A within the alpha block of the MHC class I region and located 2.7 Mb from the HLA-DQA1 locus, it appears to regulate the expression levels of the two most statistically significant (Pc<0.1) HLA class II alleles, HLA-DQA1*03:01:01 and -DQA1*03:03:01, detected in our study ( Tables 3 , 5 , respectively). If this is the case, then the statistical significance of SVA_24 transcription and regulation of HLA alleles in PD was not detected probably because it is associated more strongly with transcription modulation of the HLA-A3, -A11 and -A30 neutral alleles ( Table 7 ). None of the other transcribed SVA RIPs were associated with the significant HLA-DQA1*03 alleles.

SVAs have been inserted and translocated at different times of human evolutionary history (69). Consequently, the MHC SVA are associated more strongly with some HLA allele groups than others and could be used as evolutionary and disease markers (45). For example, R_SVA_27, although present in 11.9% of the PPMI cohort, is associated with all of the HLA-DRB1*15 and -DRB1*16 alleles, but with none of the other 11 HLA-DRB1 allelic lineages ( Table 7 ). We hypothesize that R_SVA_27 was inserted originally into the MHC class II region in a location between HLA-DRB1 and HLA-DQA1 in an ancestor with either HLA-DRB1*15 or -DRB1*16 or a heterozygote individual who had both alleles. R_SVA_27 is associated strongly also with some of the HLA-DQB1*05 or -DQB1*06 lineage alleles ( Table 7 ). Therefore, R_SVA_27 is an unique autoimmune disease marker because its linkage to the DRB1*15:01/DQA1*01:02/DQB1*06:02 haplotype has been associated with multiple sclerosis (38, 70–72), and the R_SVA_27/DRB1*16/DQB*05 haplotype was associated with other autoimmune diseases (73, 74). In the PPMI cohort, R_SVA_27 is associated strongly with HLA-DQA1*01:02 (96%), but weakly or not at all with the other -DQA1*01 field-three alleles such as HLA-DQA1*01:01:01 (0.7%), -DQA1*01:02:01 (58.9%), or -DQA1*01:03:01 (24.4%). These lower percentage associations suggest that HLA-DQA1*01:01:01 was already fully established in the population before R_SVA_27 was inserted, and that HLA-DQA1*01:02:02 emerged probably at a time proximate to the R_SVA_27 insertion event.

This study confirms and extends our previous reports that transcribed SVA elements inserted within the MHC genomic region can modulate certain HLA genes at the transcription level (41, 43, 44), and therefore, might regulate the expression of particular HLA risk and protective alleles, which in turn influence the onset and progression of PD via the immune response. For example, the upregulated or downregulated HLA transcription levels modulated by SVA transcripts could change the levels of foreign or autoreactive self-peptide presentation to CD4+ T helper lymphocytes or cytotoxic CD8+ T lymphocytes and influence the onset, development or progression of PD. In this regard, the SVA and HLA PD risk variants are likely additive causes with a complicated polygenic structure. Stronger statistical and molecular significance might be found in future studies with better stratification and compartmentalisation of the PD co-morbidities associated with autoimmune diseases and other age-related neurological diseases. The coordination of the adaptive and innate immunity by the HLA system in PD is highly complex and still poorly understood (3, 8, 66). The infiltration of peripheral CD4+ and CD8+ lymphocytes and monocytes into the brain across a dysfunctional blood brain barrier however suggests that the adaptive immune system contributes to neurodegeneration at different stages of PD pathogenesis (10, 14, 26, 66). While we limited our analysis to eight SVA within the MHC genomic region, it is noteworthy that there are many SVAs in other genomic regions that are strongly linked to PD (42, 43), including the SVA insertion within the TAF1 gene that is associated with X-linked dystonia parkinsonism (75).

In conclusion, our study of the expressed SVA and HLA genes in circulating white blood cells confirms that the MHC genomic region has an important role in the coordinated regulation of immune responses possibly associated with the long-term onset and progression of PD, the mechanisms of which yet have to be elucidated. MHC SVA RIPs, by down or up regulating the antigen presenting HLA alleles at the proteomic level, might change the amount of risk or protective antigens presented to the CD4+ or CD8+T helper lymphocytes. Thus, co-expression of regulatory SVA RIPs and HLA class I and class II alleles adds another layer of biomolecular complication to the understanding of immune responses associated with PD.

The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.

The studies involving humans were approved by University of Western Australia Human research ethics office. The studies were conducted in accordance with the local legislation and institutional requirements. The participants provided their written informed consent to participate in this study.

JK: Writing – original draft, Methodology, Writing – review & editing, Formal analysis, Conceptualization. SS: Writing – review & editing, Methodology. TS: Writing – review & editing. AP: Data curation, Writing – review & editing. SK: Project administration, Formal analysis, Conceptualization, Writing – review & editing.