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Halliday, G.

Publications and source records attributed to Halliday, G..

At least 19 recordsLinked to original sources

Alpha-synuclein and neuromelanin converge to promote Parkinsons disease pathology

Parkinsons disease (PD) is defined by the preferential degeneration of neuromelanin (NM)-containing dopamine-producing neurons in the substantia nigra (SN), accompanied by intraneuronal inclusions rich in alpha-synuclein (aSYN). However, the mechanistic relationship between NM accumulation and aSYN pathology remains unclear. Here, we reveal a bidirectional pathogenic relationship between aSYN and NM. In human post-mortem midbrain tissue, ventral nigral neurons with high NM content display increased aSYN mRNA expression and are preferentially lost in PD. In a rat model that recapitulates age-dependent, human-like NM accumulation via targeted tyrosinase (TYR) expression, co-expression of aSYN accelerates NM buildup, enhances aSYN oligomerization, and aggravates nigrostriatal degeneration. Mechanistically, aSYN oligomerization in NM-producing rats decreases vesicular dopamine storage and impairs vesicle fusion with the plasma membrane, increasing cytosolic dopamine availability for oxidation into NM. Together, these findings support a pathogenic feedback loop in which elevated aSYN accelerates NM synthesis through disrupted dopamine compartmentalization, while NM accumulation further promotes aSYN aggregation and neuronal loss. This aSYN-NM axis may underlie the preferential vulnerability of pigmented nigral neurons in PD and provide a mechanistic framework for the development of future targeted therapeutics.

neuroscience↗

Astrocyte-Specific dsRNA-ADAR1 Signalling Links Innate Immunity to Complement Activation in Parkinson Disease

Background: Dysregulated innate immune activation is a key feature of Parkinson disease (PD), but the upstream triggers and cell-type-specific mechanisms remain unclear. Double-stranded RNA (dsRNA) has emerged as a potential driver of innate immune responses. Adenosine deaminase acting on RNA 1 (ADAR1), particularly its interferon-inducible p150 isoform, edits dsRNA to limit aberrant immune activation. Whether this dsRNA-ADAR1 axis contributes to neuroinflammation in PD in a cell-type-specific manner is unknown. Methods: We performed immunofluorescence on post-mortem cingulate cortex tissue from PD cases and controls to localise dsRNA, ADAR1 p150 and pathological alpha-synuclein protein. We integrated these findings with single-nucleus RNA sequencing data from three independent human brain datasets. An eight-module gene scoring framework was applied to assess dsRNA processing, sensing, and downstream innate immune pathways in neurons and astrocytes. Results: In PD cortex, the proportion of dsRNA-positive astrocytes was higher than in controls, whereas neuronal dsRNA positivity did not differ between groups. ADAR1 p150 positivity increased in both astrocytes and neurons, and the proportion of ADAR1 p150 positive astrocytes correlated with astrocytic -synuclein burden. Transcriptomic analyses showed that neurons were enriched for dsRNA editing and processing machinery, whereas astrocytes exhibited higher expression of dsRNA sensing pathways, innate immune responses, and transposable element control. While overall pathway activity did not differ between PD and controls after covariate adjustment, network analyses revealed cell-type-specific coupling patterns. Notably, complement gene expression showed a strong and selective association with dsRNA-related pathways in astrocytes, whereas interferon and NF-{kappa}B signalling were shared across cell types. In both cell types, ADAR1-associated gene programmes were enriched for oxidative phosphorylation and PD-related pathways. Conclusions: These findings identify astrocytes as a central site of relative dsRNA accumulation and ADAR1 p150 induction in the PD cortex. The selective coupling of dsRNA sensing to complement activation in astrocytes highlights a cell-type-specific innate immune pathway that is constitutively present rather than induced by disease. Together, our protein-level and network-level findings converge on a coherent and testable model in which a constitutive astrocytic circuit is engaged by disease-associated dsRNA accumulation, with potential relevance for disease progression and therapeutic targeting.

neuroscience↗

Netrin-1 drives cell-type-specific plasticity of human dopaminergic neurons during circuit integration in a Parkinsonian model

The survival of transplanted ventral midbrain (vm) dopaminergic neurons (DAn) and their innervation of host striatal tissue are crucial for ameliorating motor symptoms in Parkinsons disease (PD). However, human pluripotent stem cells (hPSC) show inferior axonal plasticity compared to fetal donor tissue. While modulation of the host environment with trophic cues, such as glial cell-derived neurotrophic factor (GDNF), can improve graft outcomes, these cues lack specificity for DAn, resulting in plasticity of other neurons within the graft. Using single nuclei RNA sequencing, we identified axonal guidance pathways (Semaphorin, Netrin and Wnt) that were preferentially activated in DAn within the graft. Overexpression of Semaphorin3A/SEMA3A, Netrin1/NTN1 or WNT5A in the striatum of Parkinsonian mice following vm DA progenitor transplantation promoted A9-DA specification and selectively increased DA innervation of the host striatum, without off-target extrastriatal DA innervation observed in response to GDNF. In Parkinsonian rats, NTN1 overexpression promoted graft-induced motor recovery, selective DA plasticity and activation of postsynaptic striatal neurons without evidence of non-DAn plasticity. Further, snRNA-sequencing of NTN1 or GDNF-treated grafts confirmed the upregulation of DA-specific plasticity by NTN1, while GDNF promoted plasticity in both DA and non-DAn. These findings highlight the capacity to improve on-target integration of hPSC-derived DAn in grafts by selectively targeting DA-specific plasticity. Taken together, these results demonstrate the utility of DA-specific cues to promote functional recovery, improve graft predictability, and limit off-target innervation.

neuroscience↗

Systematic screening identifies elevated neurovascular BCL-XL in Parkinson's disease.

BackgroundVascular cells are emerging as active players in Parkinsons disease (PD), yet their molecular contribution to -Synuclein (-Syn) pathology remains undefined. Here, we show that human brain pericytes respond in a distinct manner to unique -Syn strains, with systematic validation identifying BCL-XL as a potential regulator of the neurovascular unit in PD. MethodsPrimary human brain-derived pericytes were exposed to five recombinant -Syn strains (Fibrils, Fibrils-65, Fibrils-91, Fibrils-110, and Ribbons). Transcriptomic profiling identified differentially expressed genes (DEGs), which were validated at the protein level using multiplex immunocytochemistry and in situ labelling of post-mortem middle temporal gyrus (MTG) tissue microarrays from PD (n = 24) and neurologically normal (n = 24) cases. Results-Syn strain exposure produced 300 DEGs with limited overlap between strains. BCL-XL and CSNK1D were upregulated in -Syn-treated pericytes. In post-mortem PD tissue BCL-XL showed marked pericyte-specific elevation in the MTG and increased pericytic and microglial expression in the substantia nigra. ConclusionBCL-XL emerges as a potential regulator of pericyte and microglial resilience in PD, linking acute -Syn strain-specific responses in pericytes to broader neurovascular alterations. Its upregulation likely represents a generalised compensatory response to chronic -Syn-associated stress beyond individual strain effects, identifying BCL-XL as a possible therapeutic target within the neurovascular unit.

neuroscience↗

Seeding patient-derived tau induces tauopathy-specific aggregation and lysosomal disruption in human cells

BackgroundTau aggregation is the defining feature of tauopathies, however, the mechanisms by which distinct tau strains drive disease-specific responses remain unclear. Existing models largely rely on recombinant tau seeding or tau overexpression, which fail to capture the biochemical diversity of pathological tau. The aim of this study was to develop a robust and reproducible human cell-based model of disease-specific tau pathology and to use this model to determine how tau from unique diseases impact tau accumulation and lysosomal dysfunction. MethodsPatient-derived tau aggregates were enriched from post-mortem brain tissue obtained from sporadic Alzheimers disease (AD), Picks disease (PiD), progressive supranuclear palsy (PSP), and control cases using phosphotungstic acid precipitation. Patient-derived tau preparations were biochemically characterised by immunoblotting and mass spectrometry and normalised for tau content prior to seeding. Patient-derived tau aggregates were seeded into multiple human immortalised cell lines (SH-SY5Y, M03.13, U-87 MG, and U-118 MG cells) and iPSC-derived astrocytes. Tau seeding efficiency, aggregate morphology, and integrity of the autophagy-lysosomal pathway was assessed using quantitative imaging approaches. ResultsPatient-derived tau seeds retained disease-specific phosphorylation patterns and isoform composition and led to reproducible, dose-dependent insoluble tau accumulation in all cell lines tested. Despite equivalent tau input and similar background protein composition, PiD-derived tau had the most aggressive pathological signature, showing the highest number of tau aggregates per cell and inducing system wide disruptions in the autophagy lysosomal system including increased SQSTM1 puncta and lysosomal damage markers. Seeding with AD-derived tau led to a high number of tau aggregates per cell and more specifically depleted the lysosomal protease CTSD and uniquely co-seeded A{beta} pathology. Seeding with PSP-derived tau resulted in only a moderate number of tau aggregates per cell and uniquely caused increased lysosomal biogenesis. ConclusionsTogether, these results demonstrate that intrinsic properties of human tau strains drive disease-specific cellular responses and establish a scalable, physiologically relevant platform for dissecting tau-cell interactions and screening therapeutics across tauopathies.

cell biology↗

Location and mapping of the human rostromedial tegmental nucleus and associated midbrain inhibitory nuclei regulating dopamine neurons

Animal experiments reveal distinct GABAergic cell clusters within the dopaminergic midbrain regions in the rostromedial tegmental nucleus (RMTg) and retrorubral fields (RRF) that have yet to be clearly defined in humans. These neurons send prominent inhibitory projections to dopaminergic neurons in the substantia nigra and ventral tegmental area that impact motor, reward and threat processing. We have identified GABAergic RMTg and RRF cell clusters in 6{micro}m formalin-fixed paraffin-embedded transverse human midbrain sections from ten control cases obtained from the Sydney Brain Bank using immunohistochemistry for GABA and tyrosine hydroxylase. We determined the location and cell size of RMTg and RRF GABAergic neurons, further mapping these cell cluster in transverse 50{micro}m thick cresyl violet stained serial midbrain sections (every 750{micro}m) from previously published controls (Halliday et al. 1990a). GABAergic neurons were cytoarchitecturally distinct, with the largest GABAergic neurons in the RRF, followed by RMTg neurons which were larger than GABAergic neurons in the well-defined interpedunclular nucleus (Kruskal-Wallis test, p<0.0001). RMTg and RRF GABAergic neurons first appear in caudal transverse midbrain sections approximately 38mm above the obex. RMTg moves rostrally and medially from underneath the decussation of the superior cerebellar peduncle to just lateral to the interpeduncular nucleus. The RRF cluster also moves rostrally and medially to the parabrachial pigmented nucleus (PBP) just under the red nucleus. The GABAergic neurons in RMTg and RRF/PBP that modulate dopamine neuronal excitability have distinct morphologies in humans. Identifying these inhibitory neurons is key to evaluating their role in neurodegenerative diseases.

neuroscience↗

Overexpression of alpha synuclein in Midbrain Dopamine Neurons Reduces Dopamine Release Without Cell Loss and Drives Mild Motor Deficits in Mice

It has proven challenging to faithfully recapitulate the key pathological, physiological, and behavioral features of Parkinsons Disease (PD) in animals. Here we used adeno-associated virus (AAV) vectors to achieve cell type-specific overexpression of wild-type human -synuclein (syn) and a fluorophore (mCherry) in midbrain dopamine neurons to model PD in mice. We found that AAVs drove selective expression of both syn and mCherry in midbrain dopamine neurons. In conjunction with approximately 2-fold overexpression of syn, we found several histopathological markers of PD-like pathology, including progressive accumulation of phosphorylated and aggregated syn, ubiquitin, and a reduction in the expression of tyrosine hydroxylase, without overt cell loss. In parallel, syn overexpression drove a profound loss of evoked dopamine release, without a substantive change in the intrinsic properties of dopamine neurons, nor in striatal dopamine content. Finally, syn overexpression led to mild locomotor deficits. Together, these findings suggest that moderate syn overexpression can mimic some aspects of premotor and early symptomatic phases of PD, including markers of Lewy Body-like pathology and functional loss of evoked dopamine release. This model may be useful for investigating cellular and circuit mechanisms related to PD pathogenesis and progression.

neuroscience↗

Region-specific variations in the cerebrovasculature underlie disease progression in Parkinson's disease

Parkinsons disease is a progressive neurodegenerative disorder characterised by motor dysfunction, dopaminergic neuronal loss in the substantia nigra and abnormal accumulation of -synuclein Lewy bodies. Research suggests that the cerebrovascular system plays a role in fluid dynamics, waste clearance, and removal of abnormal proteins. Imaging studies show that this waste clearance system, known as the glymphatic system, is disrupted in Parkinsons disease, highlighting its involvement in the disease. This immunohistochemical human brain tissue study quantified changes in the cerebrovascular system (perivascular space, string vessels, pericytes, aquaporin-4 and astrocytes) in Parkinsons disease (n=18) cases with variable disease durations (median=14, range= 19) compared to age and post-mortem matched (P >0.05) control cases (n=7). Analysis was carried out in brain regions variably affected by cell loss (substantia nigra) and protein deposition (substantia nigra and medial temporal cortex). The occipital cortex was included, as this region is not affected by cell loss or protein deposition. Group differences were analysed and the relationship with protein deposition (Lewy body stage, amyloid score, neurofibrillary tangle score) was assessed. Although total astrocyte density did not change (P >0.05), Parkinsons disease cases exhibited reduced aquaporin-4 in astrocytic endfeet and enlargement of the arteriolar and venular perivascular space. Significant changes in the capillary network were also observed with increased string vessel formation (P <0.001) and pericyte loss (P <0.001), changes likely to impact blood flow and its regulation. The formation of string vessels significantly correlated with disease duration (P <0.05), especially in the occipital cortex. The occipital cortex demonstrated the greatest decreases in pericytes (P <0.001) and aquaporin-4 mislocalisation (P <0.05), while changes in pericyte density were also significant in the substantia nigra. In contrast, these changes were not significant in the medial temporal cortex despite protein deposition in this region. Although no Lewy pathology was detected in the occipital cortex, there was a positive relationship between Lewy body stage and perivascular space size (Rho =0.6, P <0.05). These findings reveal progressive, region-specific alterations in the cellular components of the glymphatic system and vascular integrity in Parkinsons disease. Notably, the correlation between string vessel formation and disease duration, even in a region unaffected by protein deposition, suggests that vascular changes may play an important role in disease progression. These results emphasize the need for further investigation into the interplay between regional vascular changes and Parkinsons disease progression, which may offer novel insights for therapeutic strategies.

neuroscience↗

Standardised TruAI automated quantification of intracellular neuromelanin granules in human brain tissue sections

AimsTo standardise and automate the quantitation of human-unique neuromelanin granules in catecholamine neurons in post-mortem tissue sections from healthy individuals at different ages to understand any changes in these granules with age. Methods5-6 {micro}m-thick fixed and paraffin-embedded transverse midbrain tissue sections were supplied from 47 cases from three brain banks following ethical approvals. Sections were prepared and automated digital images acquired. Standardisation and automation of the quantification of neuromelanin granules was performed using the TruAI feature of the Olympus VS200 desktop platform. Comparisons between stained and unstained sections as well as correlations with age were performed. ResultsThe automated platform reliably identified both stained and unstained intracellular neuromelanin granules and extracellular pigments, showing high reproducibility in measurements across laboratories using different tissue processing methods. Extraneuronal pigments were significantly smaller than intracellular neuromelanin granules. Sections processed for haematoxylin and eosin staining impacted the size and colour of both neuromelanin and the neurons containing neuromelanin. Haematoxylin made neuromelanin bluer, and the increased tissue processing made the intracellular area occupied by neuromelanin smaller in younger people. There was an increase in neuromelanin optical density and colour change (browner) with age. ConclusionsThe TruAI automated platform reliably quantifies individual neuromelanin granules in catecholamine neurons. Extraneuronal pigments are considerably smaller in size than intracellular neuromelanin, and intracellular neuromelanin changes its properties with age. The darkening and colour change of intracellular neuromelanin suggests an increase in eumelanin over time in healthy individuals. These changes can be reliably identified using the automated platform. Key pointsO_LIStandardised, reliable TruAI automated quantitation of intracellular neuromelanin granules in human brain sections gives novel insights into their structure and function C_LIO_LIExtraneuronal pigments, including neuromelanin granules released from dying pigmented neurons, are significantly smaller than intracellular neuromelanin granules C_LIO_LIIntracellular neuromelanin granules change their properties with healthy ageing becoming darker, consistent with more antioxidant eumelanin C_LI

neuroscience↗

Transgenic A53T mice have astrocytic α-synuclein aggregates in dopamine and striatal regions

AimsParkinsons disease is considered biologically a neuronal -synuclein disease, largely ignoring the more widespread -synuclein deposition that occurs in astrocytes, with the aim of this study to identify whether astrocytes accumulate small -synuclein aggregates before or after neurons. MethodsFixed serial midbrain and striatal sections from M83 A53T transgenic mouse model of Parkinsons disease and wild-type controls were histologically processed for multiplex labelling of -synuclein and astrocytic markers and astrocyte quantitation performed on digital images using QuPath software. ResultsThe density of astrocytes within the substantia nigra pars compacta was approximately 30% greater compared with other sampled regions (P<0.005). Small aggregates of -synuclein were observed in astrocytic processes, including in wild-type mice where a quarter of all astrocytes had an obvious -synuclein aggregate. Compared to wild-type, A53T transgenic astrocytes had significantly enlarged somas (P<0.001) with more processes (P<0.001) consistent with a reactive phenotype. The A53T transgenic mice had more than double the numbers of astrocytes (P<0.001) and 2.5 times more astrocytes with -synuclein aggregates compared to wild-type mice (P<0.001). ConclusionsThese data suggest that small -synuclein aggregates are normally cleared by astrocytes and that the substantia nigra pars compacta requires more astrocytic support for this function than other midbrain dopaminergic regions or the striatum. This adds another vulnerability factor to those already known for the substantia nigra with early deficits in clearance of small -synuclein aggregates by astrocytes associated with an increased astrocytic reactivity in the A53T transgenic mouse model. Key PointsO_LIThe substantia nigra pars compacta contains a higher density of astrocytes than the ventral tegmental area or striatum, indicating a greater reliance on astrocytic function and a greater vulnerability to astrocyte dysfunction C_LIO_LISmall aggregates of -synuclein were observed in wild-type midbrain and striatal astrocytes, indicating normal clearance of -synuclein by these astrocytes C_LIO_LIMidbrain and striatal astrocytes from A53T transgenic astrocytes have more than double the number of astrocytes and more astrocytes containing -synuclein aggregates which have a reactive morphological phenotype. C_LI

neuroscience↗

Dopamine and cortical iPSC-derived neurons with different Parkinsonian mutations show variation in lysosomal and mitochondrial dysfunction: implications for protein deposition versus selective cell loss

BackgroundMutations causing Parkinsons disease (PD) give diverse pathological phenotypes whose cellular correlates remain to be determined. For example, those with PRKN loss of function mutations have significantly earlier selective vulnerability of dopamine neurons, those with SNCA mutations have increased alpha-synuclein deposition, while those with LRRK2 mutations have additional deposition of tau. Yet all three mutation types are implicated in mitochondrial and/or lysosomal dysfunction. Direct comparison of cell models with these mutations would clarify the relative cellular dysfunctions associated with these different pathological phenotypes. MethodsAn unbiased high-content imaging platform using orthogonal probes to assess both lysosomal and mitochondrial dysfunction, along with alpha-synuclein and tau protein deposition was established using induced pluripotent stem cell (iPSC) derived cortical and ventral midbrain neurons. Three mutation types, SNCA A53T, LRRK2 R1441G and PRKN loss of function (lof), were selected as exemplars of divergent PD pathological phenotypes and compared to each other, and to control iPSC from subjects without PD. ResultsDifferent PD mutations caused cell type specific dysfunctions, likely to impact on both selective neuronal vulnerability and the pathologies observed in PD. Comparison of dopamine neurons identified that both lysosomal and mitochondrial dysfunction were predominant with PRKN lof mutations, whereas immunofluorescent staining revealed that SNCA A53T and LRRK2 R1441G mutations had increased tau deposition. In contrast, cortical neurons with SNCA and LRRK2 mutations both had mitochondrial and autophagy impairments without protein deposition, with LRRK2 cells additionally showing decreased glucocerebrosidase activity and increased alpha-synuclein phosphorylation. ConclusionsLysosomal and mitochondrial dysfunction are predominant in dopamine neurons with PRKN lof mutations, and may drive the early selective loss of dopamine neurons in PRKN mutation carriers. More subtle cellular abnormalities in the SNCA A53T cell lines are likely to predispose to alpha-synuclein aggregation and tau protein deposition over time. The LRRK2 R1441G may also predispose to tau deposition, but despite substantial lysosomal dysfunction with increased alpha-synuclein phosphorylation, pathological alpha-synuclein accumulations were not observed. Understanding the mechanistic differences in how lysosomal and mitochondrial dysfunction impact on PD pathogenesis in different disease subtypes may be important for therapeutic development.

neuroscience↗

CHCHD2 mutant mice display mitochondrial protein accumulation and disrupted energy metabolism

Mutations in the mitochondrial cristae protein CHCHD2 lead to a late-onset autosomal dominant form of Parkinsons disease (PD) which closely resembles idiopathic PD, providing the opportunity to gain new insights into the mechanisms of mitochondrial dysfunction contributing to PD. To begin to address this, we used CRISPR genome-editing to generate CHCHD2 T61I point mutant mice. CHCHD2 T61I mice had normal viability, and had only subtle motor deficits with no signs of premature dopaminergic (DA) neuron degeneration. Nonetheless, CHCHD2 T61I mice exhibited robust molecular changes in the brain including increased CHCHD2 insolubility, accumulation of CHCHD2 protein preferentially in the substantia nigra (SN), and elevated levels of -synuclein. Metabolic analyses revealed an increase in glucose metabolism through glycolysis relative to the TCA cycle with increased respiratory exchange ratio, and immune-electron microscopy revelated disrupted mitochondria in DA neurons. Moreover, spatial genomics revealed decreased expression of mitochondrial complex I and III respiratory chain proteins, while proteomics revealed increased respiratory chain and other mitochondrial protein-protein interactions. As such, the CHCHD2 T61I point-mutation mice exhibit robust mitochondrial disruption and a consequent metabolic shift towards glycolysis. These findings thus establish CHCHD2 T61I mice as a new model for mitochondrial-based PD, and implicate disrupted respiratory chain function as a likely causative driver.

neuroscience↗

Chronic hyperactivation of midbrain dopamine neurons causes preferential dopamine neuron degeneration

Parkinsons disease (PD) is characterized by the death of substantia nigra (SNc) dopamine (DA) neurons, but the pathophysiological mechanisms that precede and drive their death remain unknown. The activity of DA neurons is likely altered in PD, but we understand little about if or how chronic changes in activity may contribute to degeneration. To address this question, we developed a chemogenetic (DREADD) mouse model to chronically increase DA neuron activity, and confirmed this increase using ex vivo electrophysiology. Chronic hyperactivation of DA neurons resulted in prolonged increases in locomotor activity during the light cycle and decreases during the dark cycle, consistent with chronic changes in DA release and circadian disturbances. We also observed early, preferential degeneration of SNc projections, recapitulating the PD hallmarks of selective vulnerability of SNc axons and the comparative resilience of ventral tegmental area axons. This was followed by eventual loss of midbrain DA neurons. Continuous DREADD activation resulted in a sustained increase in baseline calcium levels, supporting a role for increased calcium in the neurodegeneration process. Finally, spatial transcriptomics from DREADD mice examining midbrain DA neurons and striatal targets, and cross-validation with human patient samples, provided insights into potential mechanisms of hyperactivity-induced toxicity and PD. Our results thus reveal the preferential vulnerability of SNc DA neurons to increased neural activity, and support a potential role for increased neural activity in driving degeneration in PD.

neuroscience↗

A potential patient stratification biomarker for Parkinson's disease based on LRRK2 kinase-mediated centrosomal alterations in peripheral blood-derived cells

Parkinsos disease (PD) is a common neurodegenerative movement disorder and leucine-rich repeat kinase 2 (LRRK2) is a promising therapeutic target for disease intervention. However, the ability to stratify patients who will benefit from such treatment modalities based on shared etiology is critical for the success of disease-modifying therapies. Ciliary and centrosomal alterations are commonly associated with pathogenic LRRK2 kinase activity and can be detected in many cell types. We previously found centrosomal deficits in immortalized lymphocytes from G2019S-LRRK2 PD patients. Here, to investigate whether such deficits may serve as a potential blood biomarker for PD which is susceptible to LRKK2 inhibitor treatment, we characterized patient-derived cells from distinct PD cohorts. We report centrosomal alterations in peripheral cells from a subset of early-stage idiopathic PD patients which is mitigated by LRRK2 kinase inhibition, supporting a role for aberrant LRRK2 activity in idiopathic PD. Centrosomal defects are detected in R1441G-LRRK2 and G2019S-LRRK2 PD patients and in non-manifesting LRRK2 mutation carriers, indicating that they acumulate prior to a clinical PD diagnosis. They are present in immortalized cells as well as in primary lymphocytes from peripheral blood. These findings indicate that analysis of centrosomal defects as a blood-based patient stratification biomarker may help nominate PD patients who will benefit from LRRK2-related therapeutics. One-sentence summaryPeripheral blood-derived cells can be employed to stratify Parkinsos disease patients most likely to respond to LRRK2-related therapeutics.

neuroscience↗

Single-cell DNA methylation sequencing by combinatorial indexing and enzymatic DNA methylation conversion.

DNA methylation is a critical molecular mark involved in cellular differentiation and cell-specific processes. Single-cell whole genome DNA methylation profiling methods hold great potential to resolve the DNA methylation profiles of individual cell-types. Here we present a method that couples single-cell combinatorial indexing (sci) with enzymatic conversion (sciEM) of unmethylated cytosines. The method facilitates single-base resolution DNA methylation profiling of single-cells that is highly correlated with single-cell bisulfite-based workflows (r2 >0.99) whilst improving sequencing alignment rates, reducing adapter contamination and over-estimation of DNA methylation levels (CpG and non-CpG). As proof-of-concept we perform sciEM analysis of the temporal lobe, motor cortex, hippocampus and cerebellum of the human brain to resolve single-cell DNA methylation of all major cell-types.

genomics↗

Transcriptional profiling of Multiple System Atrophy cerebellar tissue highlights differences between the parkinsonian and cerebellar sub-types of the disease

Multiple system atrophy (MSA) is a rare adult-onset neurodegenerative disease of unknown cause, with no effective therapeutic options, and no cure. Limited work to date has attempted to characterize the transcriptional changes associated with the disease, which presents as either predominating parkinsonian (MSA-P) or cerebellar (MSC-C) symptoms. We report here the results of RNA expression profiling of cerebellar white matter (CWM) tissue from two independent cohorts of MSA patients (n=66) and healthy controls (HC; n=66). RNA samples from bulk brain tissue and from oligodendrocytes obtained by laser capture microdissection (LCM) were sequenced. Differentially expressed genes (DEGs) were obtained and were examined before and after stratifying by MSA clinical sub-type. We detected the highest number of DEGs in the MSA-C group (n = 747) while only one gene was noted in MSA-P, highlighting the larger dysregulation of the transcriptome in the MSA-C CWM. Results from both bulk tissue and LCM analysis of MSA-C showed a downregulation of oligodendrocyte genes and an enrichment for myelination processes with a key role noted for the QKI gene. Additionally, we observed a significant upregulation of neuron-specific gene expression in MSA-C and an enrichment for synaptic processes. A third cluster of genes was associated with the upregulation of astrocyte and endothelial genes, two cell types with a key role in inflammation processes. Finally, network analysis in MSA-C showed enrichment for {beta}-amyloid related functional classes, including the known Alzheimers disease (AD) genes, APP and PSEN1. This is the largest RNA profiling study ever conducted on post-mortem brain tissue from MSA patients. We were able to define specific gene expression signatures for MSA-C highlighting the different stages of the complex neurodegenerative cascade of the disease that included alterations in several cell-specific transcriptional programs. Finally, several results suggest a common transcriptional dysregulation between MSA and AD-related genes despite the clinical and neuropathological distinctions between the two diseases.

genomics↗

Targeted, High-Resolution RNA Sequencing Of Non-Coding Genomic Regions Associated With Neuropsychiatric Functions

The human brain is one of the last frontiers of biomedical research. Genome-wide association studies (GWAS) have succeeded in identifying thousands of haplotype blocks associated with a range of neuropsychiatric traits, including disorders such as schizophrenia, Alzheimers and Parkinsons disease. However, the majority of single nucleotide polymorphisms (SNPs) that mark these haplotype blocks fall within non-coding regions of the genome, hindering their functional validation. While some of these GWAS loci may contain cis-acting regulatory DNA elements such as enhancers, we hypothesized that many are also transcribed into non-coding RNAs that are missing from publicly available transcriptome annotations. Here, we use targeted RNA capture ( RNA CaptureSeq) in combination with nanopore long-read cDNA sequencing to transcriptionally profile 1,023 haplotype blocks across the genome containing non-coding GWAS SNPs associated with neuropsychiatric traits, using post-mortem human brain tissue from three neurologically healthy donors. We find that the majority (62%) of targeted haplotype blocks, including 13% of intergenic blocks, are transcribed into novel, multi-exonic RNAs, most of which are not yet recorded in GENCODE annotations. We validated our findings with short-read RNA-seq, providing orthogonal confirmation of novel splice junctions and enabling a quantitative assessment of the long-read assemblies. Many novel transcripts are supported by independent evidence of transcription including cap analysis of gene expression (CAGE) data and epigenetic marks, and some show signs of potential functional roles. We present these transcriptomes as a preliminary atlas of non-coding transcription in human brain that can be used to connect neurological phenotypes with gene expression.

genomics↗

Accelerated loss of hypoxia response and biased allele expression in zebrafish with Alzheimer’s disease-like mutations

Ageing is the major risk factor for Alzheimers disease (AD), a condition involving brain hypoxia. The majority of early onset familial AD (EOfAD) cases involve dominant mutations in the gene PSEN1. PSEN1 null mutations do not cause EOfAD. We exploited putative hypomorphic and EOfAD-like mutations in the zebrafish psen1 gene to explore the effects of age and genotype on brain responses to acute hypoxia. Both mutations accelerate age-dependent changes in hypoxia-sensitive gene expression supporting that ageing is necessary, but insufficient, for AD occurrence. Curiously, the responses to acute hypoxia become inverted in extremely aged fish. This is associated with an apparent inability to upregulate glycolysis. Wild type PSEN1 allele expression is reduced in post-mortem brains of human EOfAD mutation carriers (and extremely aged fish), possibly contributing to EOfAD pathogenesis. We also observed that age-dependent loss of HIF1 stabilisation under hypoxia is a phenomenon conserved across vertebrate classes.

genomics↗