📋 Browse Articles

Although large-scale studies and potential pathways of genes on intramuscular fat (IMF) in livestock have been reported, research on circRNAs in yaks-a unique, low-IMF-content animal species that is native to the Qinghai-Tibetan Plateau-is still lacking. Based on previous high-throughput sequencing results on Show less

Convergent evolution offers a unique lens through which to explore the molecular underpinnings of significant phenotypic transformations. Similar selective pressures likely drove the evolution of analogous milk traits in sheep and goats. Consequently, the current study aimed to identify common selection signals for milk traits across dairy and non-dairy breeds of sheep and goats worldwide. In this study, a total of 308 whole-genome sequences from diverse sheep (n = 108) and goat (n = 200) breeds, including both dairy and non-dairy types, across the world were utilized. The population structure and genetic diversity of dairy and non-dairy sheep and goat breeds were characterized. Species-specific genes associated with milk traits, such as POU2F1, ABCD2, TRNAC-GCA in sheep and PRPF6, VPS13C, TPD52L2, NFX1 and B4GALT1 in goats, were identified. Further gene annotation and bioinformatics analyses indicated that different biological pathways are important for milk traits in each species: fatty acid oxidation and AMP metabolic process in sheep, the U2-type spliceosomal complex and propanoate metabolism in goats. Additionally, common signatures of selection such as CLASP1, PDS5B, ZNF831, CCDC73 were found in sheep and goats. Haplotype and transcriptional analyses further confirmed the role of these genes in milk production and provided evidence for their analogous evolution in sheep and goats. The CLASP1 gene was identified as a target of convergent selection, representing a promising candidate for genetic improvement programs in dairy species. These results provide insights into the genetic basis of convergent dairy traits, offering valuable targets for improving milk production and advancing dairy sheep and goat breeding programs. Show less

Mutations in the vacuolar protein sorting 13 homolog C (VPS13C) gene have been associated with Parkinson disease (PD). However, the mutation of VPS13C in Parkinsonism is uncommon and the clinical characteristics are highly heterogeneous. This study identifies 2 novel pathogenic variants in VPS13C, with particular emphasis on follow-up brain magnetic resonance imaging (MRI) images. The patient first exhibited resting tremor in the right limb at the age of 26. As the disease progressed, he developed bradykinesia, rigidity, gait instability, cognitive decline, dysarthria, myoclonus, depressed mood, irritability, and aggression. He was treated with levodopa/benserazide, pramipexole, and rasagiline, but the benefit was only temporary. By the age of 32, his gait instability was further aggravated, manifested as frequent falls, requiring bed rest or wheelchair use. Follow-up brain MRI showed progressive cortical atrophy. Whole-exome sequencing of the patient revealed compound heterozygous pathogenic variants (c.1699C > T, chr15: 62156504-62352664) in VPS13C. VPS13C-related early onset PD. The patient was treated with levodopa/benserazide 125 mg 4 times daily, rasagiline 1 mg once daily, donepezil 5 mg once nightly, and quetiapine 50 mg once nightly. After 6 months of follow-up, his symptoms were further aggravated. This study identifies 2 novel pathogenic variants in VPS13C, expanding the known mutational spectrum of the gene. Additionally, brain MRI may serve as a potential imaging marker for disease progression. A review of the literature indicates that VPS13C-related Parkinsonism appears as a heterogeneous disorder, including PD and dementia with Lewy bodies. VPS13C mutations are highly diverse, with point mutations being the most common, followed by splice-site variants. Genetic screening is essential for an accurate diagnosis and distinction between different forms of early onset PD. This increases clinicians' understanding of the clinical and genetic characteristics of VPS13C-related Parkinsonism. Show less

While VPS13C is a recessively inherited Parkinson's disease (PD) gene, its potential dominant effects in idiopathic Rapid-eye movement (REM) sleep behavior disorder (iRBD) remain unexplored. The relation between its monogenic form and the onset of PD suggested that subtype specificity may need to be considered. We examined the presence of likely pathogenic VPS13C variants in 150 iRBD and 180 α-synucleinopathy patients (iRBD-first and movement disorder-first). VPS13C variants were significantly enriched in iRBD patients, and ten iRBD risk variants have been identified. iRBD risk VPS13C variant carriers demonstrated more severe RBD symptoms and greater autonomic dysfunction, correlating with REM sleep EEG and autonomic network activity abnormalities. Notably, enrichment was specific to the iRBD-first α-synucleinopathy subtype, and iRBD risk VPS13C variant carriers showed accelerated progression to overt α-synucleinopathy. These results suggest that VPS13C not only contributes to iRBD susceptibility but also serves as a marker for the iRBD-first α-synucleinopathy and faster disease conversion. Show less

To report a clinical series of four patients diagnosed with early-onset Parkinson's disease (EOPD) who exhibit heterozygous pathogenic variants in the VPS13C gene. VPS13C encodes vacuolar protein sorting 13C, a lipid transport protein that localizes between the endoplasmic reticulum and endosomes-lysosomes, functioning as a bridge to allow phospholipids to traverse the cytosol. Mutations in this gene have been associated with early-onset PARK23 and dementia with Lewy bodies (DLB), highlighting its importance in mitochondrial and lysosomal homeostasis. Cases were identified through the Mayo Clinic Data Explorer. We included all subjects with a clinical diagnosis of PD who tested positive for a heterozygous VPS13C variant defined as pathogenic by the ACMG guidelines. DaT-SCAN imaging was consistent with PD diagnosis in three patients. Non-motor symptoms and cognitive impairment were prominent phenotypical characteristics in all cases: all the patients presented with insomnia, anxiety, depression, severe fatigue, and short-memory loss. The response to oral levodopa treatment was suboptimal, with an initial benefit followed by rapid decreased responsiveness. Additionally, two patients developed wearing-off episodes and one of them also exhibited treatment-induced dyskinesias. We hypothesize that VPS13C may confer an increased risk of EOPD in carriers of pathogenic variants, and may function as a phenotype modifier gene, contributing to significant non-motor symptoms development and suboptimal levodopa response. Specifically, we propose that the suboptimal treatment response is associated with a decrease level of dopamine L-type amino acid transporter 1 (LAT1). Show less

The majority of available transcriptomics-related cancer prognosis studies strive to define one collection of biomarkers that can be used to predict high-risk patients. However, using a single biomarker profile could restrict its strength and applicability to diverse groups of patients. In order to fill this gap, we discuss the prospect of determining several, discrete sets of prognostic biomarkers in Skin Cutaneous Melanoma (SKCM). Our search identifies various genes including CREG1, PCGF5 and VPS13C whose expression pattern depicts significant correlations with overall survival (OS) in SKCM patients. We developed machine learning-based prognostic models using SKCM gene expression data to predict 1-, 3-, and 5-year overall survival. Advanced feature selection approaches were applied to identify prognostic biomarkers. The primary biomarker set consisted of 20 genes selected using state-of-the-art feature selection techniques. Machine learning classifiers were trained to distinguish high-risk from low-risk patients using these biomarkers. The process was systematically repeated to identify seven independent biomarker sets, each containing 20 unique genes without overlap. Model performance was evaluated using AUC and Cohen's Kappa metrics on an independent test dataset. Validation was further performed using the GEO dataset GSE65904, employing subsets of biomarkers from the primary and third sets. The primary biomarker-based prognostic model demonstrated strong predictive ability, achieving an AUC of 0.90 and a Kappa of 0.58 in identifying high-risk SKCM patients. A second independent 20-gene set, with no overlap with the first, produced an AUC of 0.89 and Kappa of 0.56. Across all seven biomarker sets, performance ranged from 0.84 to 0.91 (AUC) and 0.48 to 0.64 (Kappa). Notably, the fifth biomarker set yielded the highest performance with an AUC of 0.91 and Kappa of 0.64. External validation confirmed the predictive utility of selected biomarkers where genes from the primary set achieved an AUC of 0.83 on GSE65904. While genes from the third set achieved an AUC of 0.86 on the same dataset. Our results show that only one gene-expression signature is not sufficient to predict SKCM prognosis. Alternatively, high-risk patients can be accurately predicted using multiple independent biomarker sets providing flexibility in both clinical and computational practices. The high similarity in the results of all seven sets (AUC 0.84-0.91; Kappa 0.48-0.64) signifies the stability and strength of the method. The external validation of these biomarkers with GEO data also helps to confirm the reliability of these biomarkers and hints at their potential wider applicability. This work facilitates transparency by ensuring that all the data and code is publicly accessible (https://github.com/raghavagps/skcm_prognostic_biomarker), which also promotes future developments in creating multi-signature prognostic tools in melanoma. Show less

Emerging evidence suggests that the genetic architecture of Alzheimer's (AD) and Parkinson's diseases (PD) risk varies across ancestries. This study seeks to explore distinct and universal genetic targets across individuals of Latino, African/African Admixed, East Asian, and European populations by implementing Population Attributable Risk (PAR) comparisons on summary statistics from genome-wide association studies (GWAS). PAR was calculated for the most significant disease variants using summary statistics derived from select multi-ancestry GWAS meta-analyses, followed by fine-mapping analysis to validate genetic contribution of disease variants to European, African/African Admixed, East Asian, and Latino individuals. For both AD, Show less

Salmonella enterica serovar Typhimurium (S. Typhimurium) is a facultative intracellular bacterial pathogen that grows within a specialized membrane-bound compartment known as the Salmonella-containing vacuole (SCV). The molecular composition and regulatory mechanisms governing SCV dynamics remain incompletely understood. In this study, we employed proximity-dependent biotin identification (BioID) to analyze the SCV proteome during infection. For this, we targeted the UltraID biotin ligase to the SCV by fusing it to a type 3 secreted effector. We demonstrate that the bacteria express and translocate the effector-UltraID fusion protein directly into host cells for labeling of the cytosolic face of the SCV surface. Proteomic analysis of biotinylated proteins revealed previously undescribed proteins associated with the SCV, including regulators of vesicular trafficking, cellular metabolism and lipid transport. Among these, VPS13C, a lipid transporter and membrane contact site protein, was identified as a critical regulator of SCV morphology and fission. Functional studies revealed that VPS13C also promotes ER-SCV contact formation, controls SCV positioning in host cells, and facilitates cell-to-cell spread by the bacteria. Together, our findings highlight the utility of BioID as a tool to study host-pathogen interactions in the context of infection and characterize VPS13C as a novel modulator of the intracellular life cycle of S. Typhimurium. Show less

Periodontitis (PD) is a chronic inflammatory disease in which oxidative stress plays a crucial role in its progression. Mitophagy eliminates damaged mitochondria and alleviates oxidative stress; however, its specific regulatory mechanisms in PD remain unclear. This study utilized single-cell and bulk RNA sequencing data to identify core genes and investigate their potential roles. We utilized single-cell RNA sequencing data and applied 4 algorithms - area under the curve cell level enrichment, U-statistics-based single-cell signature scoring, single-sample gene set scoring, and AddModuleScore - to assess mitophagy activity and identify candidate genes. Subsequently, based on bulk RNA-seq data, 5 machine learning algorithms, including Least Absolute Shrinkage and Selection Operator Regression, random forest, Boruta, gradient boosting machine, and eXtreme Gradient Boosting, were employed to further screen core genes from the candidate gene set. Finally, immune infiltration analysis, cell communication analysis, and gene interaction network construction were integrated to systematically elucidate the regulatory mechanisms of core genes in the progression of PD. Single-cell RNA sequencing combined with multiple algorithms revealed significantly elevated mitophagy activity in PD tissues, particularly in monocytes/macrophages and endothelial cells. Additionally, we identified 4 core genes: BNIP3L, VPS13C, CTTN, and MAP1LC3B. BNIP3L and CTTN were downregulated in periodontitis, correlating negatively with disease prevalence, immune infiltration, and inflammatory pathways, whereas VPS13C and MAP1LC3B were upregulated, showing positive correlations. CellChat analysis highlighted monocytes/macrophages and endothelial cells with high core gene expression as key mediators of intercellular communication. This study identified BNIP3L, VPS13C, CTTN, and MAP1LC3B as core mitophagy-related genes associated with PD, and highlighted the pivotal roles of monocytes/macrophages and endothelial cells in disease progression. These findings provide new insights into the pathogenesis of PD and offer a theoretical foundation for mitophagy-targeted diagnosis, biomarker identification, and precision therapy. Show less

Insulin sensitivity (IS) is a key determinant of metabolic health and may share genetic factors with obesity-related traits. Previous large-scale genetic studies have identified variants associated with IS as well as obesity related traits like body mass index (BMI) and waist-to-hip ratio (WHR). Notably, many of these associations are shared across traits, indicating a potential genetic overlap. However, the genetic intersection between IS and obesity-related traits remains underexplored. To explore this gap, we investigated associations between six IS indices, including fasting and post-glucose load measures, and genetic variants linked to BMI and WHR to determine their influence on IS and related cardiometabolic traits. To achieve this, we calculated six IS indices using fasting and oral glucose tolerance test (OGTT) data from 5,007 non-diabetic individuals, grouping them into fasting, OGTT Show less

Many drug targets in ongoing Parkinson's disease (PD) clinical trials have strong genetic links. While genome-wide association studies (GWAS) nominate regions associated with disease, pinpointing causal genes is challenging. Our aim was to prioritize additional druggable genes underlying PD GWAS signals. The polygenic priority score (PoPS) integrates genome-wide information from MAGMA gene-level associations and over 57,000 gene-level features. We applied PoPS to East Asian and European PD GWAS data and prioritized genes based on PoPS, distance to the GWAS signal, and non-synonymous credible set variants. We prioritized 46 genes, including well-established PD genes (SNCA, LRRK2, GBA1, TMEM175, VPS13C), genes with strong literature evidence supporting a mechanistic link to PD (RIT2, BAG3, SCARB2, FYN, DYRK1A, NOD2, CTSB, SV2C, ITPKB), and genes relatively unexplored in PD. Many hold potential for drug repurposing or development. We prioritized high-confidence genes with strong links to PD pathogenesis that may represent our next-best candidates for developing disease-modifying therapeutics. Show less

VPS13 is the founding member of a family of proteins that mediate lipid transfer at intracellular membrane contact sites by a bridge-like mechanism. Mammalian genomes comprise 4 VPS13 genes encoding proteins with distinct localizations and function. The gene duplication resulting in VPS13A and VPS13C is the most recent in evolution and, accordingly, these two proteins are the most similar to each other. However, they have distinct subcellular localizations and their loss of function mutations in humans are compatible with life but result in two different age-dependent neurodegenerative diseases, chorea-acanthocytosis and Parkinson's disease, respectively. Thus, it remains unclear whether these two proteins have overlapping functions. Here, we show that while Vps13a KO and Vps13c KO mice are viable, embryonic development of Vps13a/Vps13c double knockout (DKO) mice is arrested at midgestation. Prior to death, DKO embryos were smaller than controls, were anemic and had a smaller liver, most likely reflecting defective embryonic erythropoiesis which at this developmental stage occurs primarily in this organ. Further analyses of erythroid precursor cells showed that their differentiation was impaired and that this defect was accompanied by activation of innate immunity as revealed by upregulation of interferon stimulated genes (ISGs). Additionally, the RIG-I and MDA5 components of dsRNA triggered innate immunity were found upregulated in the DKO fetal liver. Activation of innate immunity may result from loss of integrity of the membranes of intracellular organelles, such as mitochondria and autophagic lysosomes, or to impaired autophagy, due to the absence of these lipid transport proteins. The surprising and striking synthetic effect resulting for the combined loss of VPS13A and VPS13C suggests that despite of the different localization of these two proteins, the lipid fluxes that they mediate are partially redundant. Show less

The SNP rs2414739 of Vacuolar protein sorting 13 homolog C(VPS13C) gene was identified to be linked with Parkinson's Disease (PD). Explore the clinical progression feature of PD patients with rs2414739 variant. Longitudinal data were obtained from the Parkinson's Progression Marker Initiative (PPMI) cohorts. Linear mixed models were used to test the effects of VPS13C with the progression of PD assessed by different scales. A total of 333 patients with PD were included and divided into rs2414739 carriers (n = 138) and noncarriers (n = 195). Patients with PD carrying VPS13C mutation had slower progression, assessed by total scores of MDS-UPDRS (II+III) (β = -1.834, p = 0.000, 95%CI: -2.767, -0.901) than noncarriers. The effect of VPS13C was significant both in the rate of change of UPDRS-II scores (β = -0.284, p = 0.028, 95%CI: -0.537, -0.031) and UPDRS-III scores (β = -0.894, p = 0.009, 95%CI: -1.558, -0.228). We further divided VPS13C carriers into heterozygous and homozygous carriers, and found that the rate of change of UPDRS(II+III) (β = -1.165, p = 0.039, 95%CI: -2.265,-0.062) scores and UPDRS-III scores (β = -9.521, p = 0.041, 95%CI: -18.524,-0.532) were significantly slow in heterozygous VPS13C carriers. There was only 20 homozygous VPS13C carriers, which was too small a sample to perform the analysis. VPS13C was associated with slow motor progression in PD patients. Show less

Idiopathic Parkinson's Disease (iPD) involves genetic and environmental factors, including ionizing radiation. While high-dose radiation induces neurodegeneration, the effects of low-dose radiation (LDR) remain unclear. This study examined the impact of a single acute total-body LDR exposure (1.79 Gy) on the substantia nigra (SN) of swine, a large mammal model closely resembling humans. Fourteen male Göttingen minipigs were assigned to radiation (RAD; n = 6) or sham (SH; n = 8) groups. We analyzed iPD-related markers (α-synuclein, phosphorylated α-syn, tyrosine hydroxylase), genetic PD markers (LRRK2, GBA, VPS13C, Cathepsin D), neuroinflammation (GFAP), and mitochondrial proteins (ATP5A, SDHB, NDUF8). No significant molecular, histological, or immunohistochemical differences were observed between RAD and SH animals. LRRK2 was undetectable, and no structural damage or neuroglial changes were found. These findings suggest that single acute LDR exposure does not elicit short-term PD-related alterations in the SN of swine, although long-term or cumulative effects warrant further investigation. Show less

Parkinson's Disease (PD), a prevalent neurodegenerative condition, is distinguished by its motor dysfunction. Induced pluripotent stem cells (iPSCs), derived from PD patients, constitute an exquisite investigative tool for elucidating the pathophysiology of the disease, assessing candidate therapeutics, and probing the potential for regenerative medicine approaches. The present study was designed to establish an iPSC line, designated TUSMi013-A, from the dermal fibroblasts of a 66-year-old female afflicted with PD, harboring mutations in VPS13C and TBP. This iPSC line offers a significant resource for the dissection of PD etiology and the innovation of novel therapeutic strategies. Show less

The German Black Pied cattle (DSN) is an endangered dual-purpose breed valued for its genetic diversity and high milk fat and protein content. However, due to competition with higher-yielding dairy breeds, the DSN population has declined, leading to its designation as an endangered breed. While previous research has focused on the milk production traits of DSN, this study aims to address meat traits to further understand the genetic determination of the dual-purpose characteristics of the breed. We conducted genome-wide association studies on 669 DSN bulls to identify genetic loci associated with birth weight, BW, and BW gain at different growth stages. Using imputed whole-genome sequencing data, we identified 14 quantitative trait loci across ten chromosomes. Significant associations were found for birth weight on chromosomes 5 and 18, for body weight at 3 weeks (BW Show less

Early-onset Parkinson's disease (EOPD) is usually defined as Parkinson's disease (PD) occurring before the age of 40-50 years. Unlike late-onset PD, EOPD is often due to pathogenic mutations in autosomal recessive genes. Two phenotypes can be distinguished: typical EOPD, which progresses slowly (PRKN, PINK1 and DJ-1), and atypical PD, often associated with additional symptoms (ATP13A2, FBXO7, DNAJC6, VPS13C, SYNJ1, PLA2G6). In this review, we will highlight recent advances and remaining challenges. The frequency of causal genetic mutations and the genotype-phenotype landscape of PRKN-associated PD has been refined. Long-read sequencing has solved several undiagnosed cases with a single PRKN mutation. Five new genes have been reported to contribute to EOPD associated with various neurological signs (PTPA, DAGLB, PSMF1, EPG5, SGIP1). Small molecules targeting PRKN dysfunctions are expected to enter clinical trials in the coming years, paving the way for targeted therapies in EOPD. Show less

Bridge-like lipid transfer proteins (BLTPs) play central roles in redistributing lipids from their primary site of synthesis in the endoplasmic reticulum to other organelles. They comprise bridge-domains spanning between organelles at contact sites that allow lipids to transit the cytosol between adjacent membranes. The assembly of BLTPs into complexes with adaptor proteins enables their lipid transfer ability. To address the mechanisms underlying assembly and regulation of BLTP complexes, we used cryo-EM to resolve the structure of one such BLTP, the Parkinson's protein VPS13C, at near-atomic resolution. The structure identifies a lipid-transfer-nonpermissive conformation, where the built-in C-terminal VAB adaptor module blocks the end of the lipid transfer bridge, interfering with lipid delivery. We also identify calmodulin, central to calcium signaling, as a VPS13 partner, suggesting calcium regulation of VPS13 function. Altogether, this structure of intact VPS13C serves as starting point to understand its regulation and, more broadly, that of other BLTPs. Show less

Parkinson's disease (PD) arises from genetic and environmental factors. Human genetics has identified mutations in ~20 inherited familial genes linked to monogenic forms of PD. To investigate the effects of individual familial PD mutations, human pluripotent embryonic stem cells (hPSCs) carrying 12 distinct familial PD mutations were differentiated into midbrain lineage cells, including dopaminergic (mDA) neurons. Global gene expression and pre-mRNA splicing patterns were analyzed in midbrain cultures carrying pathogenic PD mutations in the Show less

Background: Parkinson's disease (PD), although widely heterogeneous and manifesting with numerous motor and non-motor symptoms, presents clinically as a single entity worldwide. Its genetic causes are also heterogeneous and include highly penetrant variants in a single gene representing rare monogenic forms, and rare or common variants conferring a relative disease risk representing more frequent multigenic forms. Most of these variants have been discovered in patients of European ancestry. Since the genetic basis of PD can vary significantly between populations due to differences in allele frequencies, little is known about the genetics of PD in other populations, particularly from Africa. Morocco, located in a region of North Africa, constitutes a subcontinent known for a weak external genetic influence and for a local genetic continuity for millennia, which makes it a region of interest to study the genetic causes of PD. Summary: This review aimed to summarize published research data on the genetic profile of PD patients from the Moroccan population to describe its genetic architecture. Unlike in Western countries, PD in Morocco is predominantly a Mendelian disease reaching up to 50%, due to the high prevalence of the LRRK2 G2019S dominant variant and to relatively less frequent PRKN and PINK1 recessive variants due to the high rate of consanguinity. Additionally, rare high-risk variants in LRRK2, VPS13C, MAPT, and POLG, in oligo- or polygenic ways, may contribute to increasing the genetic risk of the disease. Key Messages: We, therefore, show that the genetic architecture of PD in Morocco, a country in the subcontinent of North Africa, was different from that of sub-Saharan Africa and the rest of the world. This will help improve diagnostic accuracy, subdivide the clinical variability of the disease into groups of common genetic and biological causes for a better therapeutic management strategy, and test molecules from ongoing clinical trials.

. Show less

Based on genetic studies, lysosome dysfunction is thought to play a pathogenetic role in Parkinson's disease (PD). Here we show that VPS13C, a bridge-like lipid transport protein and a PD gene, is a sensor of lysosome stress/damage. Upon lysosome membrane perturbation, VPS13C rapidly relocates from the cytosol to the surface of lysosomes where it tethers their membranes to the ER. This recruitment depends on Rab7 and requires a signal at the damaged lysosome surface that releases an inhibited state of VPS13C which hinders access of its VAB domain to lysosome-bound Rab7. While another PD protein, LRRK2, is also recruited to stressed/damaged lysosomes, its recruitment occurs at much later stages and by different mechanisms. Given the role of VPS13 proteins in bulk lipid transport, these findings suggest that lipid delivery to lysosomes by VPS13C is part of an early protective response to lysosome damage. Show less

Parkinson's disease (PD) is a genetically complex neurodegenerative disorder. Up to 15% of cases are considered monogenic. However, research on monogenic PD has largely focused on populations of European ancestry, leaving gaps in our understanding of genetic variability in other populations. This study addresses this gap by analysing the allele frequencies of pathogenic and likely pathogenic variants in known monogenic PD genes across eight global populations, using data from the gnomAD database. We compiled a list of 27 genes associated with Mendelian PD from the Online Mendelian Inheritance in Man (OMIM) database, and identified pathogenic and likely pathogenic variants using ClinVar. We then performed pairwise comparisons of allele frequencies across populations included in the gnomAD database. Variants with significant frequency differences were further assessed using in silico pathogenicity predictions. We identified 81 variants across 17 genes with statistically significant allele frequency differences between at least two populations. Variants in Our findings reveal substantial population-specific differences in the allele frequencies of pathogenic variants linked to monogenic PD, emphasising the need for broader genetic studies beyond European populations. These insights have important implications for PD research, genetic screening, and understanding the pathogenesis of PD in diverse populations. Show less

Parkinson's disease (PD) is a neurodegenerative disorder caused by complex genetic and environmental factors. Genome-edited human pluripotent stem cells (hPSCs) offer a unique experimental platform to advance our understanding of PD etiology by enabling the generation of disease-relevant cell types carrying patient mutations along with isogenic control cells. To facilitate this approach, we generated a collection of 65 human stem cell lines genetically engineered to harbor high risk or causal variants in genes associated with PD ( Show less

Based on genetic studies, lysosome dysfunction is thought to play a pathogenetic role in Parkinson's disease. Here we show that VPS13C, a bridge-like lipid-transport protein and a Parkinson's disease gene, is a sensor of lysosome stress or damage. Following lysosome membrane perturbation, VPS13C rapidly relocates from the cytosol to the surface of lysosomes where it tethers their membranes to the ER. This recruitment depends on Rab7 and requires a signal at the damaged lysosome surface that releases an inhibited state of VPS13C, which hinders access of its VAB domain to lysosome-bound Rab7. Although another Parkinson's disease protein, LRRK2, is also recruited to stressed or damaged lysosomes, its recruitment occurs at much later stages and by different mechanisms. Given the role of VPS13 proteins in bulk lipid transport, these findings suggest that lipid delivery to lysosomes by VPS13C is part of an early protective response to lysosome damage. Show less

The microbiome-gut-brain axis, by modulating bidirectional immune, metabolic, and neural signaling pathways in the host, has emerged as a target for the prevention and treatment of psychiatric and neurological disorders. Oral administration of the probiotic bacterium Lactobacillus rhamnosus GG (LGG; ATCC 53103) exhibits anti-inflammatory effects, although the precise mechanisms by which LGG benefits host physiology and behavior are not known. The goal of this study was to explore the general effects of LGG on the cerebrospinal fluid (CSF) proteome and a biological signature of anti-inflammatory signaling in the central nervous system (CNS) of undisturbed, adult male rats. Liquid chromatography-tandem mass spectrometry-based proteomics were conducted using CSF samples collected after 21 days of oral treatment with live LGG (3.34 × 107 colony-forming units (CFU)/mL in the drinking water (resulting in an estimated delivery of ∼1.17 × 109 CFU/day/rat) or water vehicle. Gene enrichment analysis (using DAVID, v. 6.8) and protein-protein interactions (using STRING, v. 11) were used to explore physiological network changes in CSF. Real-time reverse transcription polymerase chain reaction (real-time RT-PCR) was performed to assess gene expression changes of anti-inflammatory cytokines in the hippocampus. Genes associated with anti-inflammatory signaling that were analyzed included Il10, Tgfb1, Il4, and IL-4-responsive genes, Cd200, Cd200r1, and Mrc1 (Cd206). Oral LGG administration altered the abundance of CSF proteins, increasing the abundance of five proteins (cochlin, NPTXR, reelin, Sez6l, and VPS13C) and decreasing the abundance of two proteins (CPQ, IGFBP-7) in the CSF. Simultaneously, LGG increased the expression of Il10 mRNA, encoding the anti-inflammatory cytokine interleukin 10, in the hippocampus. Oral LGG altered the abundance of CSF proteins associated with extracellular scaffolding, synaptic plasticity, and glutamatergic signaling. These data are consistent with the hypothesis that oral administration of LGG improves memory and cognition, and promotes a physiological resilience to neurodegenerative disease, by increasing glutamatergic signaling and promoting an anti-inflammatory environment in the brain. Show less

ATG9A, a transmembrane protein of the core autophagy pathway, cycles between the Golgi, endosomes and a vesicular compartment. ATG9A was recently shown to act as a lipid scramblase, and this function is thought to require its interaction with another core autophagy protein, ATG2A, which acts as a lipid transfer protein. Together, ATG9A and ATG2A are proposed to function to expand the growing autophagosome. However, ATG9A is implicated in other pathways including membrane repair and lipid droplet homeostasis. To elucidate other ATG9A interactors within the autophagy pathway, or interactors beyond autophagy, we performed an interactome analysis through mass spectrometry. This analysis revealed a host of proteins involved in lipid synthesis and trafficking, including ACSL3, VPS13A and VPS13C. Furthermore, we show that ATG9A directly interacts with VPS13A and forms a complex that is distinct from the ATG9A-ATG2A complex. Show less