Biology subjects

Plun-Favreau, H.

Publications and source records attributed to Plun-Favreau, H..

10 recordsLinked to original sources

bioRxiv2026

The Structured RNA-binding Domains and Condensation Capacity of FUS Shape its RNA-binding Landscape and Function.

RNA-binding proteins (RBPs) are key regulators of gene expression and often contain intrinsically disordered regions that drive biomolecular condensation. Yet, how condensation affects RBP specificity and function remains poorly defined. Here, we use strategically designed point mutations to selectively impair canonical RNA-binding and condensation of the amyotrophic lateral sclerosis (ALS)-linked RBP Fused in Sarcoma (FUS). Using automated high-content imaging, we show that both properties shape nuclear ribonucleoprotein condensates and govern distinct aspects of FUS function in the DNA damage response. Transcriptome-wide mapping of FUS-RNA interactions reveals that the canonical RNA-binding domains recognise G-rich and C-rich motifs, whereas condensation selectively enhances binding to G-rich and structured sequences, often acting in concert with canonical RNA-binding to control transcriptional programs and splicing decisions. These findings provide a mechanistic framework for how FUS integrates condensation with sequence-specific RNA recognition to orchestrate nuclear organisation, genome stability and RNA metabolism. Furthermore, our rigorously validated mutants offer a platform for future mechanistic dissection of ALS pathogenesis and the development of targeted therapeutic strategies. HighlightsO_LIFUS condensation and RNA-binding can be functionally uncoupled with targeted point mutations C_LIO_LICondensation drives FUS recruitment and assembly of nuclear RNP condensates C_LIO_LIFUS condensation and RNA-binding play distinct roles in the DNA damage response C_LIO_LIThe structured RNA-binding domains confer specificity to G-rich and C-rich motifs C_LIO_LICondensation enhances FUS binding to G-rich, structured RNA elements C_LIO_LIFUS condensation and canonical RNA-binding synergistically regulate gene expression C_LI

molecular biology↗

bioRxiv2025

The SNCA A53T mutation sensitizes human neurons and microglia to ferroptosis

The major pathological hallmarks of sporadic and familial forms of Parkinsons disease (PD) are the targeted and progressive loss of midbrain dopaminergic neurons (mDA), associated with systemic iron accumulation, -synuclein (syn) accumulation and aggregation, and lipid peroxidation amongst other reactive oxygen species (ROS) generation. Therapeutic strategies aimed towards dopamine restoration, syn removal and iron chelation have provided symptomatic relief but failed to prevent or slow disease progression. This is in part due to the lack of understanding of the exact pathways leading to neuronal death in PD. In this study, we investigate ferroptosis, a unique cell death mechanism sharing multiple features with PD pathology, as a relevant pathway with implications in disease pathogenesis. We identified an enrichment of ferroptosis genes dysregulated throughout PD postmortem brain samples and several neuronal and glial PD models. Using CRISPR/Cas9 technology, we generated a rapid iPSC-derived synucleinopathy neuronal model harbouring the SNCA A53T mutation and report increased ROS generation, reduced levels of antioxidant glutathione (GSH), impaired mitophagy and a heightened vulnerability to ferroptosis-induced lipid peroxidation and cell death. Critically, inhibition of the key lipid peroxidation enzyme and driver of ferroptosis, 15-lipoxygenase (15-LO), rescued synucleinopathy associated pathologies and prevented pathological syn oligomerisation in SNCA A53T neurons. Furthermore, we report enhanced microglial ferroptosis susceptibility in models of synucleinopathy. In summary, we highlight a new mechanism by which the familial PD-associated SNCA A53T mutation causes cell death and propose 15-LO inhibition as a tractable therapeutic opportunity in PD.

neuroscience↗

bioRxiv2025

TDP-43 loss of function drives aberrant splicing in Parkinson's disease

Introductory paragraphWhile mRNA splicing dysregulation is a well-established contributor to neurodegeneration in disorders such as amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), its role in Parkinsons disease (PD) remains underexplored. Here, we analyse transcriptomic data from >500 post-mortem human brain samples from individuals with and without PD to show that splicing alterations are frequently detected. Differentially spliced genes were significantly more enriched for those causally-implicated in both PD and ALS than genes that were differentially expressed. Furthermore, we observed a strong association between these splicing alterations and dysfunction of the RNA-binding protein (RBP), TAR DNA-binding protein 43 (TDP-43). Strikingly, genes and exon junctions affected by TDP-43 knockdown overlapped significantly with those dysregulated across brain regions in PD. In brains from individuals with the LRRK2 c.6055G>A (p.G2019S) mutation, the most common genetic cause of PD, we also observed significant enrichment of TDP-43-dependent splicing changes. This finding was corroborated in human pluripotent stem cell-derived midbrain dopaminergic neurons and a LRRK2 p.G2019S knock-in mouse model, where reduced nuclear TDP-43 levels evidenced the well-recognised loss-of-function mechanism contributing to splicing dysregulation. By leveraging our RNA-based analyses we predicted TDP-43-dependent novel peptide sequences and validated their existence within human LRRK2 mutation mDNs, while also demonstrating an overall loss of protein and mRNA expression in mis-spliced genes. Collectively, our findings reveal that PD is marked by extensive splicing dysregulation dependent on TDP-43, making TDP-43 a promising new therapeutic target in PD.

neuroscience↗

bioRxiv2025

A CRISPR-CAS9 high throughput machine-learning platform for modulation of genes involved in Parkinson's disease-associated PINK1-mitophagy in iPSC-derived dopaminergic neurons

Parkinsons disease (PD) is a progressive neurodegenerative disorder characterised by the loss of dopaminergic neurons, driven by complex molecular mechanisms that are not fully understood. To address this issue, we have developed a novel high-content phenotypic screening platform using human induced pluripotent stem cell-derived dopaminergic neurons to investigate the PINK1-PARKIN mitophagy pathway, a critical process in PD pathogenesis. Utilising high throughput, 384 well arrayed CRISPR-CAS9 genetic manipulation and high-content immunofluorescence imaging complemented with machine learning analysis, we examined ubiquitin (Ub) pSer65 levels. Ub pSer65, a potential PD clinical biomarker, is a key marker of mitophagy initiation in dopaminergic neurons upon mitophagy initiation using exogenous stimuli to mimic the disease relevant environment. The CRISPR-CAS9 knockout (KO) screen revealed two distinct phenotypic classes: essential genes causing cell death upon deletion, and genes modulating Ub pSer65 levels. Notably, KO of PINK1, PARKIN, and TOM7 genes decreased Ub pSer65 upregulation during mitophagy activation, confirming their established roles in the pathway and validating the suitability of the platform for target identification. This innovative platform provides a precise tool to further interrogate PD-associated genes, offering insights into mitophagy-related pathogenic mechanisms and identification of potential therapeutic targets. By bridging functional genomics with disease-specific neuronal models, this approach presents a promising strategy for advancing PD research and developing targeted interventions. To our knowledge, this is the first reported use of a human, translationally relevant cell model to study genetic perturbation within a disease relevant phenotype.

neuroscience↗

bioRxiv2025

iNeurons are sweet, maybe too sweet? Exploring the impact of media composition on PINK1-dependent mitophagy

Parkinsons disease associated proteins PINK1 and Parkin collaboratively regulate stress-induced mitophagy. While in vitro human neuronal cultures are valuable for studying the roles of PINK1 and Parkin in a disease-relevant context, the impact of culture conditions on these processes remains largely underexplored. Here, it is shown that human induced neurons (iNeurons) cultured in N2B27 and BrainPhys medium exhibit distinct PINK1-Parkin dependent mitophagy phenotypes. Specifically, BrainPhys-cultured iNeurons show greater resistance to PINK1-dependent mitophagy initiation, linked to a reduction in glucose availability and reduced PINK1 protein availabilities, leading to decreases in stress-induced and basal mitophagy fluxes. These findings highlight the critical impact of culture conditions on mitophagy dynamics and emphasise the need to account for media-specific differences when using in vitro models to investigate mitophagy mechanisms in human neurons.

neuroscience↗

bioRxiv2025

17q21.31 locus regulates Parkinson's disease relevant pathways through KANSL1 activity

An inversion polymorphism at the 17q21.31 locus defines the H1 and H2 haplotypes, with the former linked to multiple neurodegenerative disorders, including an increased risk of Parkinsons disease (PD). Although the high linkage disequilibrium at this locus has made it difficult to decipher which gene(s) drive the PD association, there is increasing evidence to support the role of KANSL1 as a risk gene. KANSL1 has been shown to regulate the expression of some PD-associated genes and pathways, likely as part of the histone acetylating non-specific lethal (NSL) complex. Here for the first time, we studied the global effects of 17q21.31 haplotype variation using bulk and single-nuclear RNA-sequencing data from control and PD patient brain. We first analysed differential gene expression across haplotype groups, and then assessed the contribution of KANSL1 by comparing with the results of an siRNA knockdown in neuronal and glial human cell lines. We demonstrated that the PD risk-associated H1 haplotype downregulates autophagy, lysosomal and mitochondrial processes, all of which have already been implicated in PD aetiology. Furthermore, these effects were apparent in both neuronal and glial cell types, and in the case of the latter, appear to be associated with the modulation of innate and adaptive immune responses. Thus, we identify important links between NSL complex activity and PD pathophysiology that can be leveraged for novel therapeutic interventions.

neuroscience↗

bioRxiv2023

KAT8 compound inhibition inhibits PINK1/Parkin-dependent mitophagy and initiates mitochondrial delivery to lysosomes

It has recently been shown that KAT8, a genome-wide association study (GWAS) candidate risk gene for Parkinsons Disease, is involved in PINK1/Parkin-dependant mitophagy. The KAT8 gene encodes a lysine acetyltransferase and represents the catalytically active subunit of the non-specific lethal (NSL) epigenetic remodelling complex. In the current study, we show that contrary to KAT5 inhibition, dual inhibition of KAT5 and KAT8 via the MG149 compound inhibits the initial steps of the PINK1-dependant mitophagy process. More specifically, our study shows that following mitochondrial depolarisation induced by mitochondrial toxins, MG149 treatment inhibits PINK1-dependant mitophagy initiation by impairing PINK1 activation, and subsequent phosphorylation of Parkin and ubiquitin. While this inhibitory effect of MG149 on PINK1-activation is potent, MG149 treatment in the absence of mitochondrial toxins is sufficient to depolarise the mitochondrial membrane, recruit PINK1 and promote partial downstream recruitment of the autophagy receptor p62, leading to an increase in mitochondrial delivery to the lysosomes. Altogether, our study provides additional support for KAT8 as a regulator of mitophagy and autophagy processes.

neuroscience↗

bioRxiv2023

Protein network analysis links the NSL complex to Parkinson's disease and mitochondrial biology

Whilst the majority of PD cases are sporadic, much of our understanding of the pathophysiological basis of disease can be traced back to the study of rare, monogenic forms of disease. In the past decade, the availability of Genome-Wide Association Studies (GWAS) has facilitated a shift in focus, toward identifying common risk variants conferring increased risk of developing PD across the population. A recent mitophagy screening assay of GWAS candidates has functionally implicated the non-specific lethal (NSL) complex in the regulation of PINK1-mitophagy. Here, a bioinformatics approach has been taken to investigate the proteome of the NSL complex, to unpick its relevance to PD progression. The mitochondrial NSL interactome has been built, mining 3 separate repositories: PINOT, HIPPIE and MIST, for curated, literature-derived protein-protein interaction (PPI) data. We built; i) the mitochondrial interactome, applying gene-set enrichment analysis (GSEA) to explore the relevance of the NSL mitochondrial interactome to PD and, ii) the PD-oriented interactome to uncover biological pathways underpinning the NSL /PD association. In this study, we find the mitochondrial NSL interactome to be significantly enriched for the protein products of PD associated genes, including the Mendelian PD genes LRRK2 and VPS35. Additionally, the PD associated interactome is enriched for mitochondrial processes; "mitochondrial cell death", "mitochondrial protein localisation", "membrane protein localisation" and "mitochondrial transport". Our data points to NSL complex members OGT and WDR5 as key drivers of this increased PD association. These findings strengthen a role for mitochondrial quality control in both familial and sporadic disease.

neuroscience↗

bioRxiv2023

The chromatin modulating NSL complex regulates genes and pathways genetically linked to Parkinsons disease

Genetic variants conferring risk for Parkinsons disease have been highlighted through genome-wide association studies, yet exploration of their specific disease mechanisms is lacking. Two Parkinsons disease candidate genes, KAT8 and KANSL1, identified through genome-wide studies and a PINK1-mitophagy screen, encode part of the histone acetylating non-specific lethal complex. This complex localises to the nucleus, where it has a role in transcriptional activation, and to mitochondria, where it has been suggested to have a role in mitochondrial transcription. In this study, we sought to identify whether the non-specific lethal complex has potential regulatory relationships with other genes associated with Parkinsons disease in human brain. Correlation in the expression of non-specific lethal genes and Parkinsons disease-associated genes was investigated in primary gene co-expression networks utilising publicly available transcriptomic data from multiple brain regions (provided by the Genotype-Tissue Expression Consortium and UK Brain Expression Consortium), whilst secondary networks were used to examine cell-type specificity. Reverse engineering of gene regulatory networks generated regulons of the complex, which were tested for heritability using stratified linkage disequilibrium score regression and then validated in vitro using the QuantiGene multiplex assay. Significant clustering of non-specific lethal genes was revealed alongside Parkinsons disease-associated genes in frontal cortex primary co-expression modules. Both primary and secondary co-expression modules containing these genes were enriched for mainly neuronal cell types. Regulons of the complex contained Parkinsons disease-associated genes and were enriched for biological pathways genetically linked to disease. When examined in a neuroblastoma cell line, 41% of prioritised gene targets showed significant changes in mRNA expression following KANSL1 or KAT8 perturbation. In conclusion, genes encoding the non-specific lethal complex are highly correlated with and regulate genes associated with Parkinsons disease. Overall, these findings reveal a potentially wider role for this protein complex in regulating genes and pathways implicated in Parkinsons disease.

neuroscience↗

bioRxiv2020

Regulation of mitophagy by the NSL complex underlies genetic risk for Parkinson's disease at Chr16q11.2 and on the MAPT H1 allele.

Parkinsons disease (PD) is a common incurable neurodegenerative disease. The identification of genetic variants via genome-wide association studies (GWAS) has considerably advanced our understanding of the PD genetic risk. Understanding the functional significance of the risk loci is now a critical step towards translating these genetic advances into an enhanced biological understanding of the disease. Impaired mitophagy is a key causative pathway in familial PD, but its relevance to idiopathic PD is unclear. We used a mitophagy screening assay to evaluate the functional significance of risk genes identified through GWAS. We identified two new regulators of PINK1-mitophagy, KAT8 and KANSL1, previously shown to modulate lysine acetylation. We show that KAT8 and KANSL1 modulate PINK1 gene expression and subsequent PINK1-mitophagy. These findings suggest PINK1-mitophagy is a contributing factor to idiopathic PD. KANSL1 is located on chromosome 17q21 where the risk associated gene has long been considered to be MAPT. While our data does not exclude a possible association between the MAPT gene and PD, it provides strong evidence that KANSL1 plays a crucial role in the disease. Finally, these results enrich our understanding of physiological events regulating mitophagy and establish a novel pathway for drug targeting in neurodegeneration.

neuroscience↗