Introduction

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease (ND) effecting approximately 145,000 people in the UK [1]. With an ageing population, it is predicted that the number of PD patients in the UK will increase by 18.1% between 2015 and 2065 [1]. In the US it is predicted that PD cases will increase from 680,000 to 1,238,000 by 2030 [2]. PD primarily affects motor systems of the central nervous system because of the death of dopamine generating cells in the substantia nigra (SN) in the midbrain [3]. The main neuropathologic hallmark of PD is the accumulation of α-synuclein in neurons in the form of Lewy bodies [3].

Alzheimer’s disease (AD) is the most common ND accounting for 60–80% of dementia cases, characterised pathologically by deposits of intracellular tau neurofibrillary tangles and accumulation of extracellular amyloid β (Aβ) plaques in the brain [4]. The most common clinical symptom of AD is gradual progressive memory loss that eventually affects other cognitive functions such as communication and movement. There are currently many promising advances in the understanding of AD, including novel biomarkers [5, 6] and underlying biological mechanisms [7].

There is increasing evidence that PD and AD both have several common characteristics [1: Table S7).

IPA identified 54 affected pathways in PD and 107 pathways in AD, with 27 shared between these two (Additional file 1: Table S3). Interestingly, many of the top pathways in PD were also dysregulated in AD, including Sirtuin Signalling pathway (AD adjusted p-value = 3.39E-04) and 14–3-3-mediated Signalling (AD adjusted p-value = 5.13E-03). The top five pathways identified using DEGs unique to PD were all among the common pathways between AD and PD. In contrast, only two of the top ten pathways identified by AD unique DEGs were also perturbed in PD, i.e., HIPPO Signalling and Sirtuin Signalling pathway. It is interesting that, of the top five perturbed pathways for the 2688 AD unique DEGs, neuroinflammation signalling pathway, complement system and NF-kB signalling were not perturbed in PD.

Discussion

By integrating 126 brain samples from seven microarray gene expression datasets, we identified 1046 DEGs in PD. To our knowledge this is the largest meta-analysis study on microarray SN data about PD. Our approach allows inclusion of all the genes across all datasets included in this study. Only 267 out of the 1046 identified DEGs were included in all datasets. If only the common genes were used for meta-analysis, as applied in other previous gene expression meta-analysis about PD [23], we will have introduced many false negative results. This is because potentially interesting genes would not be identified when they are not common between studies. For instance, out of the top 30 identified DEGs, 14 would not have been identified, including GBE1 [23] and OPA1 [34] which have been associated with PD revealed in previous studies.

The gene YWHAZ, coding for the 14–3-3 zeta protein, was the top DEG and six 14–3-3 family proteins were important hubs in PPIN. Previously 14–3-3 proteins have been implicated in interactions with several proteins associated with PD including α-synuclein, Parkin and LRRK2 [35] and targeting 14–3-3 PPI using small molecules offers a promising strategy for PD and other neurodegenerative diseases [36]. 14–3-3 theta phosphorylation at S232 is observed in human PD brains to be pathogenic and contributes to the neurodegenerative process [37]. In Creutzfeldt-Jakob Disease (CJD) phosphorylation levels of 14–3-3 proteins have been used as a diagnostic biomarker clinically [35]. As we have found dysregulation of various 14–3-3 proteins in the post-mortem brain, further investigation into the potential of 14–3-3 protein dysregulation and phosphorylation levels as PD biomarkers in CSF and plasma is warranted.

Neuroinflammation is a typical part of the aging process [38] and it is accepted that the extent of neuroinflammation is greater in PD and AD patients [39]. We previously identified NF-kB as a TF in AD and LPS, a key regulator of reactive oxygen species (ROS) production, as a potential upstream regulator [7]. All of these can trigger a pro-inflammatory response. In our present study, inflammation pathways and upstream TFs that are pro-inflammatory are not perturbed in PD, suggesting a reduced importance of inflammation in the brain of patients with developed PD in comparison to AD. Degradation of dopamine is a major source of ROS in nigral tissue in PD brains, and late into PD development a lot of the dopamine producing cells are lost, potentially reducing inflammation levels [40]. Previously it has been shown that particular inflammation markers are not present in Parkinson’s disease dementia when compared to AD, suggesting that the neuroinflammatory mechanisms in PD and AD differ [41].

Although the DEGs between the two diseases were significantly overlapped, PD had a higher proportion that are also perturbed in AD. In addition, of the top five pathways perturbed in PD all were also perturbed in AD, however of the top 5 pathways perturbed in AD, only one was in PD. This suggests that processes underlying the two diseases are similar, however this it is more apparent with PD. Interestingly, the shared DEGs between PD and AD are almost always differentially expressed in the same up or down direction between diseases. This suggests that these genes could represent the crosstalk that is apparent between PD and AD. MAPT is one of four genes not differentially expressed in the same direction between the two diseases, being downregulated in AD and upregulated in PD. MAPT encodes the tau protein, and tau pathologies are important in both diseases [4, 42]. It has been shown that in three brain regions of AD patients there is a reduction in MAPT expression [43], however for PD it has been proposed that brain regions expressing greater levels of MAPT are more susceptible to tau mediated neurodegeneration [44]. This difference in MAPT and the role of tau pathology in both diseases warrants further investigation as these processes are not greatly understood.

Repressor element 1-silencing transcription factor (REST) has been implicated as an important regulator of neurons in the normal aging brain, closely correlating with cognitive longevity [45]. In AD and other dementias, REST is lost from the nucleus and is found with misfolded proteins in autophagosomes. REST was identified as an upstream regulator of down-regulated PD DEGs, as it has been in AD previously [7]. In cell models of PD, abnormal levels of the REST neuronal splice form REST4 have been implicated in pathology of PD [46]. It has been suggested that overexpression of α-synuclein affects the histone maker distribution on REST complex associated genes and results in repression of the SNAP25 and L1CAM genes in both Drosophila and cell line models [47]. Reduction in these genes has been implicated in contributing to synaptic dysfunction in PD [47]. Here both genes have shown to be downregulated DEGs in PD supporting this mechanism underlying human PD pathogenesis.

The Sirtuin Signalling pathway was revealed to be perturbed in AD and PD and modulating their activities can alter the course of both diseases in both cell and animal models [48]. In PD SIRT1 and SIRT3 have protective effects against degeneration of SN neurons by neurotoxins, whereas activity of SIRT2 worsens the degeneration [48]. It is likely that SIRT1 and SIRT3 modulate homeostasis of mitochondria and anti-oxidative mechanisms, whereas activity of SIRT2 could result in adverse microtubule dynamics that disrupt clearance of toxic waste including Lewy bodies. In AD, the pan-sirtuin activator resveratrol has been shown to be safe, well-tolerated, and alter the trajectory of some biomarkers in a clinical trial [49]. Further research is needed to understand the therapeutic potential of sirtuins [48].

The SN was chosen as the brain region of interest in this study as neuron degeneration in this region is a hallmark of PD and it is the region with the most data for the meta-analysis [8]. We have excluded the SN microarray study GSE54282 from this meta-analysis due to low sample size and E-MEXP-1416 due to high variance in the data. There are also many studies using SN dopaminergic neurons, however including a number of these could lead the gene expression data to reflect these neuron types instead of the whole SN.

Although RNA-seq has demonstrated itself as a superior approach [50], there is not much data available for PD, although there is likely going to be further applications in the future. Microarrays are still very useful tools for measuring the gene expression and their power is further increased by using meta-analysis. Our microarray data has correlated gene expression values to the healthy SN RNA-seq data in the GTEx database [27], demonstrating that the microarray expression data used in this study has the similar quality to that of previous RNA-seq data (Additional file 1: Figure S2).

For PD there has been a limited application of RNA-seq to identify DEGs, in fact for the analysis of the SN only one RNA-seq study has been completed [51]. There are minimal similarities between the results of this RNA-seq analysis and our meta-analysis results. Only 70 of their 2961 identified DEGs are identified in our results, and only three of our top 30 DEGs (SLC18A2, FGF13, AASDHPPT) are identified in their results. However, pathways associated with oxidative phosphorylation, cardiac hypertrophy and the cytoskeleton were shared. A possible explanation for this is the very low power of the RNA-seq study, which only used three control and three PD samples and the fact that these samples were not age and gender matched. This is particularly important as age and gender are some of the largest risk factors for PD. The control samples had an average age of 87.3 (+/− 5.5) and were all females, and the PD samples had an average age of 79.0 (+/− 5.6) and only one sample was female.

A limitation of this study is that the SN is affected early in PD development, and by the time symptoms manifest much of the SN can be lost. This means our results reflect the perturbed genes and pathways present once the disease has been established, and not the changes that take place that lead to PD. To investigate early changes in disease more accessible tissues, such as blood and cerebrospinal fluid, would have to be investigated. Currently, there is no reliable way of diagnosing PD before it has had a substantial effect. As a result, investigating the perturbed pathways at this point in the disease would be difficult without development of effective early diagnosis biomarkers. Nonetheless identifying genes and pathways perturbed in the later stages of the disease can still help identify therapeutically important information and compare to similarly late stages of AD. A large limitation in this meta-analysis is the limited number of PD samples. As only 69 PD and 57 control samples are included in this study, the statistical power would be lower than that of our previous meta-analysis for AD which included 450 AD and 212 control samples [7]. This relatively low sample size could also introduce false positive and false negative DEGs and pathways, nevertheless, meta-analysis will outperform individual microarray studies. Moreover, our PPI networks would be best enriched by proteomics data of PD if such datasets are publicly available.

In conclusion, our meta-analysis strategy is the largest study of its type in PD SN tissue to date. We highlight REST as an important upstream regulator in PD and AD through the perturbation of Wnt signalling [45]. Our results reveal the importance of YWHAZ and 14–3-3 proteins in PD, through their down regulation, involvement in perturbed pathways and as hubs in PPIN. We demonstrate that PD and AD share significant number of DEGs that are differentially expressed in the same direction and perturbed pathways that indicate some novel shared pathogenesis between the two diseases. These insights suggest several new areas for mechanistic research into PD and cross-talk between AD and PD.