Background
Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease after Alzheimer’s disease (AD). An autosomal recessive variant of PD, PARK6, is caused by loss-of-function mutations in PINK1 (PTEN-induced kinase 1) [
1]. PINK1 activates ubiquitin by phosphorylation [
2‐
4] and exerts quality control over mitochondria, controlling their translational repair, fusion, and elimination by mitophagy [
5‐
9]. In this role, it cooperates with the downstream ubiquitin ligase PARKIN, which is responsible for another autosomal recessive variant of PD, named PARK2 [
10‐
12].
Independent from their role for mitochondria, PINK1 and PARKIN are transcriptionally induced by trophic and nutrient deprivation stress [
13,
14], and they influence the trophic cell state through modulation of the signaling from glial cell line-derived neurotrophic factor (GDNF) and its receptor tyrosine kinase RET [
15‐
17]. Unexpectedly, PARKIN was recently discovered to modulate also the cellular resistance against microbial invasion [
18].
Thus, in spite of the deep knowledge about the roles of PINK1 and PARKIN for selective mitophagy, there is an important need to conduct unbiased surveys to elucidate additional functions of PINK1 and PARKIN in stress responses. Our previous OMICS work observed only mild changes in mRNA, protein abundance and posttranslational modifications in response to PINK1 loss-of-function, failing to identify individual biomarkers that correlate with disease progression [
19‐
22].
Transcriptome dysregulations below 1.5-fold are usually regarded with skepticism and are difficult to validate with other experimental techniques. However, in age-associated neurodegenerative disorders, they cannot be disregarded. It is known that the 1.5-fold increase of beta-amyloid precursor protein (APP) dosage on chromosome 21 leads to typical AD symptoms and neuropathology already by the age of 40 years in most Down syndrome cases [
23], so the triggers of any AD manifestation at ages 60–90 must be equivalent to an APP gene dosage much smaller than 1.5-fold. Similarly, the manifestation of PD is triggered by alpha-synuclein around age 35 years via a twofold gene dosage increase [
24], around age 50 via a 1.5-fold gene dosage [
25], and around age 70 by a 1.3-fold gene dosage [
26,
27]. In practically all chromosomal trisomies, the 1.5-fold increase in dosage of some genes results in embryonal lethality, so any old-age pathology triggered from these genes would result from <1.5-fold expression dysregulation.
The relevance of subtle expression changes has been taken into account by modern analysis tools based on “gene set enrichment analyses” [
28]. Therefore, we now re-investigated our global transcriptome data with automated biomathematics tools, accepting that some false positive and false negative results will have to be dealt with, but hoping that the significant enrichment of pathways and subcellular compartments will identify PINK1-deficiency effects that are validated by the consistency over time as well as across tissues and species.
For this aim, we (1) analyzed the global transcriptome profile of Pink1
−/− mouse brain tissue at three ages, (2) surveyed Pink1-dependent regulations of the global transcriptome in neuron-rich primary cultures from postnatal mouse brain at 12 days after the acute brain dissection stress, (3) validated the results in aged Pink1
−/− brain where the transgenic overexpression of A53T-alpha-synuclein (gene symbol SNCA) exerted chronic neurotoxic stress, (4) tested the cellular response of microglia and astrocytes in Pink1
−/− brain by immunohistochemistry, (5) used lipidomics to study pro-inflammatory signals, (6) performed a systematic assessment of the expression of key factors of antiviral state in human neuroblastoma cells with lentiviral PINK1-Knock-Down (KD), studying the time course after acute starvation stress, (7) re-assessed the same key factors of antiviral state in human PINK1-(KD) neuroblastoma versus Pink1
−/− murine embryonal fibroblasts after mitophagy via FCCP drug treatment, and (8) tested the same factors after stress with the pathogenic poly(I:C) RNA regarding PINK1-dependent expression regulation. Primary skin fibroblasts from three patients at advanced age with manifest PD due to G309D-PINK1 mutations were employed to assess the relevance of these data for the human disease.
Methods
Mouse breeding and brain dissection
Pink1
−/− and wildtype (WT) control mice, which were derived from common ancestors and share the strain 129/SvEv genetic background, were bred and genotyped as previously reported [
29]. Brain tissue from
Pink1
−/−+A53T-SNCA double mutant mice was obtained as published [
20].
Global transcriptomics
Affymetrix oligonucleotide microarray profiling was performed with Genechip mouse genome 430 2.0 arrays as previously [
30,
31], using cRNA from the brain cerebellar tissue as reported before [
20] and from neuron-rich primary cultures from 3
Pink1
−/− versus 3 age and sex-matched WT control mice. Hybridization occurred on Affymetrix Genechip mouse genome 430 2.0 arrays, which represent 39,000 transcripts, of which more than half are anonymous or poorly understood, according to PubMed and GeneCards database searches. The biomathematical analysis was performed in the institute for medical genetics at Tuebingen University.
For protein-protein interaction (PPI) network analysis, the software tool String v.10 (
https://string-db.org/) with standard settings has been employed to visualize networks of significant dysregulations [
32]. As recommended, gene symbols of factors with significant dysregulation were entered into the Multiple Proteins window with the
Mus musculus option, the matching of the input with the correct factors was accepted, and the graphic interaction diagram was generated and archived. The Analysis button was used to generate automated network statistics; significant functional enrichments of GO (Gene Ontology) terms and KEGG pathways were exported into EXCEL files.
For an additional comprehensive transcriptome analysis, gene set enrichment analysis (GSEA, v2.2.3,
http://software.broadinstitute.org/gsea/index.jsp) [
28] was applied in order to see, if a priori defined sets of genes show statistically significant, concordant differences between mutant/WT in 18 months old cerebellum samples. For every gene, only the one entry with the lowest adjusted
p value and the according log
2 transformed ratio was taken. GSEA default settings and Reactome v5.2 and KEGG v5.2 gene set database were used. Pathways with
p value ≤0.05 and FDR
q ≤ 0.25 were regarded as significant. Heat maps were produced with the Perseus software.
Primary neuron culture
Neuron-rich primary cultures from the dissociated brain cerebral cortex of postnatal mice were prepared as previously described [
33]. In short, 500,000 cells per well were seeded on a 0.01% (
w/
v) poly-
d-lysine coated 6-well plate. In order to limit the growth of dividing cells, cytosine ß-D-Arabinoside was added on the second day of culture as before. The 3 plate pairs (mutant versus WT), where many singular neurons in homogeneous density with a dense network of processes contrasted with very few astrocytes and microglia present, were chosen out of a total of 12 plate pairs on culture day 12 for RNA extraction.
Brain homogenate from aged mice
Mouse aging and dissection of mice was carried out as before, employing cerebellum from single mutant
Pink1
−/− at three ages (10 mutants versus 10 WT) and midbrain from adult double mutant
Pink1
−/−+A53T-SNCA mice at age 18 months (5 mutants versus 5 WT) for the extraction of global RNA and cDNA synthesis [
20].
GFAP and Iba1 immunohistochemistry
Immunohistochemistry was performed using an automated staining system (Leica Bond-III, Nussloch, Germany). The following antibodies were used: anti-GFAP, rabbit polyclonal antibody, dilution 1:14,000 (DakoCytomation, Glostrup, Denmark); anti-Iba1, rabbit antibody, dilution 1:1000 (Wako Pure Chemical Industries, Osaka, Japan).
Representative areas of striatum, substantia nigra, neocortex, and brainstem of Pink1
−/− (n = 1) and wild-type (n = 1) animals were analyzed using ImageJ software (Version 1.51 h; National Institutes of Health, Bethesda, Maryland, USA). We quantified positive cells in relation to all cells.
Tissue preparation for lipid analysis
Matched pairs of male and female Pink1
−/− and Pink1
+/+ mice were used for analysis of bioactive lipids in brain tissue. Mice were 9–13 months (four each), 17 months (three each), and 21 months (four each) old at the time of tissue preparation (mean age 15.5 −/− and 17 +/+). Mice were sacrificed by carbon dioxide. Blood was drawn into K+ EDTA microvettes (Sarstedt) for plasma analysis by cardiac puncture. Subsequent intracardial perfusion with saline removed rests of blood. The lumbar spinal cord, olfactory bulb, and hippocampus were dissected, and tissue pieces of 3–5 mg were excised, rapidly frozen in liquid nitrogen, and stored at −80 °C until analysis. The precise tissue weight was determined on precision scales directly before tissue homogenization.
Analysis of lipid signaling molecules
Sphingolipids were analyzed by liquid chromatography tandem mass spectrometry (LC-MS/MS) in different regions of the nervous system (olfactory bulb, hippocampus, spinal cord) at three different ages (8.5–12.5 weeks, 17.5 weeks, and 21 weeks). LC-MS/MS analyses were done on an API4000 triple quadrupole mass spectrometer equipped with an APCI (atmospheric pressure chemical ionization) ion source for the analysis of ceramides and with an ESI (Electrospray Ionization) ion source for the analysis of sphingosines, Glu-Cer/Lac-Cer (Sciex, Darmstadt, Germany) [
34,
35]. All quadrupoles were working at unit resolution. Concentrations of the calibration standards, quality controls, and samples were evaluated by MultiQuant 3.0 (Sciex, Darmstadt, Germany) using the internal standard method (isotope-dilution mass spectrometry). Calibration curves were calculated by linear regression with 1/x weighting. The coefficient of correlation for all measured sequences was at least 0.99.
Tissue pieces of approximately 4 mg were homogenized in 200-μl extraction buffer (50 μl per mg). For analysis of sphingolipids, 20 μl plasma or homogenized tissue samples consisting in 0.4 mg tissue were extracted with methanol:chloroform:HCl (15:83:2) after spiking with the respective internal standards, which was Cer17:0 for ceramides and sphingosine-D7 and sphingosine-1-phosphate-D7 for sphingosines. A Luna C18 column (150 mm × 2 mm ID, 5 μm particle size, 100 Å pore size; Phenomenex, Aschaffenburg, Germany) was used for chromatographic separation. The HPLC mobile phases consisted of water-formic acid (100:0.1, v/v) (A) and acetonitrile-tetrahydrofuran-formic acid (50:50:0.1, v/v/v) (B). For separation, a gradient program was used at a flow rate of 0.3 ml/min. The initial buffer composition was 60% (A)/40% (B). It was maintained for 0.6 min, then linearly changed to 0% (A)/100% (B) over 3.9 min, and held for 6.5 min. Subsequently, the ratio was linearly changed back within 0.5 min to 60% (A)/40% (B) and then held for another 4.5 min. The running time for every sample was 16 min. The injection volumes were 15 μl for ceramides and 10 μl for sphingosines. The analyses were done in multiple reaction monitoring (MRM) mode. For every analyte, two transitions were recorded, one for quantification and the other for identification. The peak area of the analyte was normalized for the peak area of the internal standard. Precursor to product ion transitions for quantification were: m/z 539 → 264 for C16:0-Cer, m/z 567 → 264 for C18:0-Cer, m/z 595 → 264 for C20:0-Cer, m/z 651 → 264 for C24:0-Cer, m/z 649 → 264 for C24:1-Cer, m/z 700 → 264 for C16:0-GluCer, m/z 729 → 264 for C18:0-GluCer, m/z 862 → 264 for C16:0-LacCer, m/z 891 → 264 for C18:0-LacCer, m/z 973 → 264 for C24:1-LacCer, m/z 553 → 264 for C17:0-Cer, m/z 300 → 282 for Sph and m/z 380 → 264 for S1P. The dwell times were 15 or 50 ms.
To assess genotype-dependent differences on individual ceramides in specific regions, mice of different ages were summarized. To assess progression over age, ceramides across regions were pooled, log2-transformed to linearize the data, and subsequently summed to get a global readout for all ceramides. Total ceramides were then plotted over time and genotype-dependent differences at different ages were analyzed using two-way ANOVA for “genotype x age”.
Neuroblastoma starvation
The human SH-SY5Y neuroblastoma cell line with dopaminergic properties was stably transduced by lentivirus either with a control (NT for Non-Target knock-down) shRNA or a shRNA directed against
PINK1 and maintained under puromycin (1 μg/ml) selection in RPMI medium containing 10% Fetal Calf Serum (FCS), as published already [
6]. These
PINK1-KD and NT control cell lines had the stability of their KD controlled repeatedly over many months. They were switched to HBSS medium without FCS, to subject them to a starvation time course as previously described [
13].
Quantitative reverse transcriptase real-time polymerase chain reaction (qPCR)
RNA was isolated with the RNeasy mini kit (Qiagen) and then treated with DNase I. cDNA was synthesized with SuperScript III reverse transcriptase using oligo(dT)
20 and random primers (Invitrogen). cDNA from 20 to 25 ng RNA were utilized in a 20 μl reaction volume using the StepOnePlus Real-Time PCR System and the appropriate murine (lowercase) or human (uppercase) TaqMan gene expression assays (Applied Biosystems): for mouse
Pink1 (Mm00550827_m1),
Creb3 (Mm00501607_m1),
Ddx58 (Mm01216853_m1),
Hebp1 (Mm00469161_m1),
Ifit1 (Mm00515153_m1),
Ifit3 (Mm01704846_s1),
Irf3 (Mm00516784_m1),
Mapk8 (Mm01218957_m1, Mm01218946_m1, Mm00489514_m1),
Mapk9 (Mm00444239_m1),
Mapk14 (Mm01301009_m1),
Mavs (Mm00523170_m1),
Mfn1 (Mm00612599_m1),
Nfkbia (Mm00477798_m1),
Rsad2 (Mm00491265_m1),
Srsf10 (Mm01193320_m1),
Tbk1 (Mm00451150_m1),
Tnf (Mm00443258_m1), for human
PINK1 (Hs00260868_m1),
DDX58 (Hs01061436_m1),
HEBP1 (Hs00211123_m1),
IFIT1 (Hs03027069_s1),
IFIT3 (Hs00155468_m1),
IRF3 (Hs01547283_m1),
LRRK2 (Hs00411197_m1),
MAVS (Hs00920075_m1),
MFN1 (Hs00966851_m1),
RSAD2 (Hs00369813_m1),
SQSTM1 (Hs00177654_m1),
TBK1 (Hs00179410_m1). mRNA expression was normalized to the TATA binding protein gene expression or the Hypoxanthine Phosphoribosyltransferase 1 gene expression (
Tbp: Mm00446973_m1,
TBP: Hs99999910_m1,
HPRT1: Hs99999909_m1). Relative expression changes were calculated with the 2
−ΔΔCt method [
36].
Triggering mitophagy via treatment with FCCP
The drug FCCP, which is known to uncouple the mitochondrial membrane gradient and trigger mitophagy [
37], was administered over 24 h at 10 μM concentration to human SH-H5Y neuroblastoma cells or murine embryonal fibroblasts, which had been cultured in DMEM plus 10% FCS and grown to confluency (approximately 4 × 10
6 cells) in T25 flasks as previously described [
38]; then, the cells were collected, and the RNA was extracted with TRIzol methodology.
Stressing cells with a pathogenic RNA-analogue
The synthetic dsRNA polymer poly(I:C), which induces the RNA sensors that activate innate immunity [
39,
40], was purchased from InvivoGen in the low molecular weight variant with the transfection agent LyoVec and used at a concentration of 1 μg/ml (for SH-SY5Y cells) or 2 μg/ml (for MEFs) as recommended by the manufacturer during 16 h before harvesting the cells and extracting RNA/protein.
Human primary skin fibroblast cultures
Previously established primary skin fibroblast cultures from 3 homozygous PARK6 patients (passages 12–14) were employed as published [
12,
19,
41‐
43], in addition to one sex-/age-matched control (the principal investigator G.A., passage 14) and four matched control fibroblast lines from Coriell depository (catalog number AG02261/passage 6/age 61, AG06103/passage 16/age 29, AG06858/passage 5, age 47, AG12207/passage 14/age 68).
Quantitative immunoblotting
The isolation of total proteins from the primary skin fibroblasts was carried out as described [
42]. Samples of 20 μg were heated at 90 °C for 5 min and then separated in 10% tris–glycine polyacrylamide gels, using Precision Plus Protein™ All Blue Standards as size marker. Transfer to nitrocellulose membranes (Protran, GE Healthcare) was done at 50 V for 90 min, with blocking in 5% BSA solution in 1X TBS-T for 1 h at room temperature (RT). Primary antibodies against LRRK2 (1:1000, NBP1–49954, Novus), IFIT3 (1:500, 15,201–1-AP, Proteintech), IFIT1 (1:500, 23,247–1-AP, Proteintech), DDX58 (1:700, 3743, Cell Signaling Tech), RSAD2 (1:500, 11,833–1-AP, Proteintech), and β-Actin (1:5000, A5441, Sigma-Aldrich) occurred in 1X TBS-T solutions overnight at 4 °C. Fluorescent-labeled α-mouse (1:15,000, IRDye 800CW, Li-Cor) and α-rabbit (1:15,000, IRDye 680RD, Li-Cor) were the secondary antibodies. Fluorescence detection occurred on the Li-Cor Odyssey Classic Instrument.
Statistical analyses
Statistical significance was assessed using ANOVA or unpaired t test with Welch’s correction in the GraphPad Prism 5 software.
Discussion
The progression of pathology in PD tissues and its animal and cell models is being documented intensively at the clinical, histology, imaging, neurophysiology, and molecular levels, especially in cases with monogenic pathogenesis [
140‐
143]. There is an urgent need of risk biomarkers for the presymptomatic detection and preventive therapy, as well as of progression biomarkers for the objective quantification of disease severity and of therapeutic benefits. However, the brain tissue from patients is available only at final stages of disease, and most available autopsies are from genetically undefined and therefore heterogeneous variants of PD. Conversely, the peripheral cells and tissues from patients reflect only some initial abnormalities of pathogenesis [
19,
41,
43] and do not progress to a selective cell death. Thus, the analysis of brain tissue from postnatal age until the multimorbid old age, e.g., in PINK1-mutant or alpha-synuclein-mutant mice [
30,
133,
144,
145], holds great promise. Several studies in the past have employed unbiased global OMICS approaches to screen the activity of practically all known genes [
20‐
22,
29,
30]. Nonetheless, in spite of the enormous recent progress in PD genetics and in the characterization of corresponding disease models, it has remained difficult to identify and establish individual molecular progression biomarkers. It was expected that the levels of any such molecular marker would correlate with the severity of disease, similar to hemoglobin levels in anemia or to creatinine levels in kidney dysfunction.
Our novel progression analysis of global transcriptome profiles in PINK1-deficient brain tissue across lifespan now indicates that subsequent stages of pathology are characterized by the involvement of increasing numbers of subtly dysregulated pathways rather than stronger expression anomalies of individual candidates. This in vivo approach identified several pathways to be prominently PINK1-dependent, in good agreement with previous in vitro findings in most cases. Importantly, for the first time, we establish a temporal order and provide a quantitative value for the significance of each pathway.
In the scenario documented, a first disease stage is defined by a mild adaptation of the nuclear splicing machinery, which persists without increase throughout all ages. This is completely novel evidence; the notion of a splicing adaptation to PINK1-deficiency is currently supported only by an OMICS study into posttranslational modifications of the brain in a genetic mouse model of PD, where a strongly altered arginine-methylation of the splicing factor PSF was observed, caused either by PINK1 deficiency or by alpha-synuclein gain of function [
22]. The transcriptional dysregulation of
Srsf10 as a spliceosome component was reproduced by qPCR. Given that spliceosomal alteration is a constant feature in
Pink1
−/− brain and that
Ube3a and
Mapk8 are regulated by alternative splicing, we investigated the dysregulation of their splice isoforms and demonstrated a selective effect on the shorter splice isoform of UBE3A, a ubiquitination enzyme responsible for alpha-synuclein degradation [
59].
A second disease stage shows manifest anomalies in the ubiquitin-dependent degradation of proteins and in the protein processing at the endoplasmic reticulum (ER). These data are in excellent agreement with the established role of PINK1 as a ubiquitin kinase [
146]. Scarce evidence exists until now on the role of PINK1 as a modifier of ER stress [
147‐
151], but our microarray biomathematics support the notion that alterations at the ER appear earlier than mitophagy and have stronger significance. Indeed, the transcriptional dysregulation of
Creb3 and
Nfkbia as ER stress and inflammation factors was similarly reproduced by qPCR as the dysregulation of
Ube3a as a component of ubiquitination pathways. Thus, both the ubiquitin kinase effects and the early alteration of widespread protein processing support a novel concept, where PINK1 has a general role for subcellular degradation rather than a function restricted to the selective elimination of dysfunctional mitochondria. Vesicular and lysosomal pathway dysregulations are more prominent at early ages upon GSEA bioinformatics than mitochondrial pathways.
A third stage, at old age in the
Pink1
−/− mouse, cerebellar tissue shows no change of the effect size in expression dysregulation in parallel with the progression of pathology, e.g., for the components of the splicing machinery. Instead, the number of dysregulated factors and pathways, the significance of the intracellular membrane-bounded organelle enrichment, and the appearance of altered neurotransmission, mitophagy, anti-microbial, and neuroinflammatory profiles were clearly age-associated. Our experimental validation of increased
Mapk8 and Nfkbia transcript levels is in agreement with a previous report about
Pink1
−/− astrocyte JNK1 signaling [
51] and with evidence for an interaction between PINK1 and the NF-kappaB pathway [
152‐
156].
Indeed, neuroinflammation is well documented in late stages of PD [
157‐
161]. Initially, it was thought to be triggered by the debris resulting from neuronal loss [
162]. Further detailed study of genetic mouse and cell models demonstrated the neuroinflammation to precede neuronal loss [
163], and current concepts propose alpha-synuclein aggregates and their extracellular extrusion to act as triggers of toll-like-receptor upregulation, cytokine release, and microglia activation [
164‐
175]. In contrast, our observations demonstrate the enrichment of neuroinflammatory dysregulations quite early in the disease course, in brain tissues where alpha-synuclein aggregation was not detectable [
29]. The concept that mitochondrial dysfunction alone is sufficient to modulate the innate immunity factors was also supported by our FCCP and poly(I:C) experiments in human neuroblastoma cells and murine embryonal fibroblasts. These data showed the mitochondrial antiviral signaling factor MAVS to be selectively responsive to proton gradient and PINK1 changes, and the induction of DDX58, IFIT3 and IFIT1 as sensors of pathogenic dsRNA and of RSAD2 as viral replication suppressor to be modified by PINK1.
Thus, we suggest that innate immunity is triggered within neurons via PINK1-associated mitochondrial dysfunction. Indeed, evidence has accumulated over the past 5 years that dysfunctional mitochondria are releasing damage-associated molecular patterns (DAMPs), e.g., the hypomethylated DNA/RNA and formylated peptides which are characteristic for bacteria and the mitochondrial endosymbiont [
176,
177]. This release triggers the innate immune system and in particular a mitochondria-associated pathway of defense against abnormal DNA/RNA [
178‐
180]. In good compatibility with this concept, recent findings confirm that neuroinflammation in PD can be modulated by the formyl-peptide receptors [
181]. We have lately shown in another human hereditary disorder, Perrault syndrome, that mitochondrial dysfunction can be a strong trigger of the innate immune system via mtDNA accumulation, with subsequent early-onset infertility, growth deficits, and age-associated neurodegeneration [
38]. In the pathways involved, the IFIT protein family together with DDX58 (RIG-I) is responsible of the recognition of pathogenic DNA/RNA in the cytosol, while RSAD2 (viperin) inhibits viral budding from membranes via lipid raft alteration. The mitochondria-associated MAVS/MFN1/IFIT3 complex then triggers phosphorylation and ubiquitination events that ultimately lead to NFkappaB-mediated nuclear regulations and to TBK1/IRF3-mediated interferon signals for neighboring cells [
111,
182] (Fig.
3a). Of course, the resulting stress metabolism and impairment of cell growth together with alterations of mitochondrial calcium buffering would influence synaptic plasticity and excitability, contributing to the known alterations of calcium homeostasis and neural transmission in PARK6 mouse models [
44,
143,
183].
A similar mechanism could operate in PINK1 and PARKIN deficient cells, which are being used as models of PD and are known to have an impairment of selective mitophagy, as was suggested by a recent report of high visibility that PARKIN also mediates resistance to microbial invasion [
18]. The PINK1-dependent subtle molecular mismanagement of variably reoccurring life events such as infections (in our data mimicked by polyI:C) or hunger (mimicked by HBSS medium) may determine, if the clinical manifestation of Parkinson’s disease occurs early or late in life. It was recently demonstrated that the downregulation of Ataxin-2, a lipid-storage factor and mTOR-repressor upstream from PINK1, may postpone death in a mouse model of motor neuron disease from 20 to over 300 days [
135,
184‐
186].
The innate immunity problems of PINK1-deficient cells become detectable even at the postnatal age upon the presence of a stressor. Stress exposure of
Pink1
−/− primary neuron-rich cultures leads to the significant expression dysregulation of the abnormal DNA/RNA sensor
Ifit3 and the iron-sulfur-cluster detector
Rsad2, confirmed in Pink1-KO+A53T-SNCA double mutant brain, in human neuroblastoma cells, in
Pink1
−/− MEFs, and in PARK6 patient skin fibroblasts. The starvation dataset links PINK1 deficiency to a transcriptional downregulation of mitochondria-associated innate immunity factors such as
MAVS,
MFN1, and
IFIT3, and the FCCP dataset shows altered expression of
MAVS and
MFN in MEFs and a PINK1-dependent blunting of
MAVS induction in SH-SY5Y cells. MFN1 and MAVS are localized to the mitochondrial outer membrane, respond to an alteration in the mitochondrial proton gradient, and mediate the elimination of dysfunctional mitochondria via autophagy [
187‐
190]. In addition, MAVS expression also modulates antiviral signaling via IFIT3 [
112]. The starvation dataset also indicates a parallel PINK1-dependent transcriptional induction of downstream innate immunity factors such as
TBK1,
IRF3, and
RSAD2. As shown in the poly(I:C) dataset at transcript and protein level, the regulation of IFIT3 and RSAD2 is altered by PINK1 deficiency. RSAD2 upregulation and mitochondrial relocalization triggers the lipogenesis for viral envelope formation [
191,
192]. Beyond the established role of PINK1 for selective mitophagy, our novel data therefore indicate that PINK1 also modulates the mitochondria-associated anti-microbial defense pathway.
The changes in very young
Pink1
−/− brain and
Pink1
−/− cells are perfectly compatible with previous in vitro observations [
84,
153,
154,
193‐
198]. Importantly, a highly visible publication was made during the final stage of our project, which reported PINK1 and Parkin in murine macrophages and fibroblasts to repress an immune-response eliciting pathway via the trafficking of mitochondrial-derived-vesicles, but not via mitophagy [
199]. The present data from
Pink1
−/− mouse brain, human neuroblastoma cells, and patient fibroblasts serve as additional corroboration in vivo, providing a spatio-temporal framework and identifying crucial molecular mediators.
Still, as an important caveat, we have to mention several limitations of our findings: (I) Various technical approaches were focused on different brain regions. The previously published global transcriptome profiles had focused on midbrain/brainstem, which were selected because they are responsible for the characteristic mid-stage motor deficit of Parkinson’s disease. The re-assessment of these data showed these regions to be less informative within the 2-year lifespan of mice than the cerebellum. Consequently, for a deeper understanding of the subtle early consequences of Pink1-ablation, we focused the studies of histology and ceramides on the brainstem and olfactory bulb, where Parkinson’s disease starts. Furthermore, demonstration of the expected glial pathology uncovered a preferential affection of myelinated tracts. Thus, at present, it is cumbersome to extrapolate the expression data and other findings into a coherent picture of phenomenology and pathology progression in time and space, integrating observations from mouse and man, so further analyses in-depth are needed. (II) The impaired response of Pink1
−/−-deficient cells against polyI:C suggests a vulnerability towards viral infections. Although we present suggestive data at the transcript, protein, and cellular level, with several artificial stressors, this issue can only unequivocally be proven once Pink1
−/− organisms are exposed to virus in future experiments, with quantification of viability and propagation rates.