Biology subjects

Krueger, R.

Publications and source records attributed to Krueger, R..

At least 19 recordsLinked to original sources

bioRxiv2026

Generation of an induced pluripotent stem cell line, LCSBi021-A, from a Parkinson's disease patient harboring the missense mutation c.213C>G (p.Ser71Arg) in the RAB32 gene

Dermal fibroblasts were obtained from a 40-year-old male patient with Parkinson's disease (PD), harboring the c.213C>G (p.Ser71Arg) variant in the RAB32 gene. Induced pluripotent stem cells (iPSCs) were generated using the CytoTune-iPS 2.0 Sendai Reprogramming Kit (Thermo Fisher Scientific). The presence of the c.213C>G base exchange in exon 1 of RAB32 was confirmed by Next Generation Sequencing. The iPSCs are free of genomically integrated reprogramming genes, express pluripotency markers, display in vitro differentiation potential into all three germ layers and exhibit karyotypic integrity. Our iPSC line is available for research purposes to dissect molecular mechanisms of neurodegeneration in PD.

cell biology↗

bioRxiv2026

EIDD-3525 is a broad-spectrum antiviral against alphavirus infection that targets the nsP4 RNA-dependent RNA polymerase

Mosquito-transmitted alphaviruses, including chikungunya (CHIKV), Mayaro, Eastern equine encephalitis, and Venezuelan equine encephalitis viruses, cause severe arthritic or neurologic disease in humans. There are currently no approved antiviral treatments against alphavirus infection. Here, we report that the purine ribonucleoside EIDD-3525 is a potent inhibitor of alphavirus replication in vitro with broad spectrum antiviral activity against the Alphavirus genus. Using a trans-replicase assay, we find that EIDD-3525 blocks alphavirus RNA replication. Mutational profiling suggests that EIDD-3525 targets the alphavirus nsP4 RNA-dependent RNA polymerase that is conserved across medically important alphaviruses. In a pre-clinical mouse model of CHIKV infection and disease, oral treatment with EIDD-3525 reduced viral tissue burdens and the severity of virus-induced disease. Collectively, our findings support the continued development of the purine ribonucleoside EIDD-3525 as an orally available antiviral therapeutic for use against a broad group of alphaviruses.

microbiology↗

bioRxiv2026

SNCA triplication shapes neuronal extracellular vesicle biology and promotes microglial activation in patient-derived iPSC-based models of Parkinson's disease

Extracellular vesicles (EVs) are emerging as key mediators of intercellular communication and potential biomarkers in Parkinson's disease (PD), yet how disease-causing genetic alterations shape neuronal EV biology remains incompletely understood. Here, we used PD-patient iPSC-derived midbrain dopaminergic neurons (mDANs) harboring SNCA triplication (SNCA-4x), gene-corrected controls (SNCA-GC), and SNCA knockout (SNCA-KO) to investigate the impact of -synuclein overexpression on neuronal-enriched EV (nEV) biology and neuron to microglia communication. SNCA-4x mDANs exhibited marked transcriptional alterations in pathways related to vesicle trafficking and extracellular matrix organization. Using an optimized isolation workflow, SNCA-4x neurons released significantly more and smaller nEVs enriched in -synuclein, mitochondrial DNA (mtDNA), and PARK7/DJ-1 mRNA, while displaying reduced acetylcholinesterase activity. Functionally, SNCA-4x-derived nEVs were taken up more efficiently by isogenic control iPSC-derived microglia than SNCA-GC nEVs and induced stronger pro-inflammatory activation than both SNCA-GC nEVs and untreated microglia, characterized by altered microglial morphology and increased TNF- and IL-1{beta}, consistent with damage-associated molecular pattern (DAMP)-mediated signaling. Together, these findings demonstrate that SNCA-4x reshapes the properties and molecular cargo of nEVs, enhancing their capacity to trigger microglial activation, and identify EV-associated -synuclein, mtDNA, and PARK7 mRNA as candidate mechanistic and biomarker features in PD.

neuroscience↗

bioRxiv2026

Benchmarking SNP-Calling Accuracy Against Known Citrus Pedigrees Reveals Pangenome Advantages Over Linear References

BackgroundPangenomes are a promising new approach to genomics that can reduce reference bias in genotyping, but the reliability of such a data model remains unclear in tracking variation across species. To test the utility of graph-based pangenomes for interspecific breeding, we developed a Minigraph-Cactus super-pangenome representing four Citrus species derived from the founder lines of a citrus breeding program. To benchmark SNP calling accuracy using graph and linear-based approaches, we performed whole genome short read sequencing for two sets of pedigreed progeny: 30 F1 hybrids and 244 advanced hybrids from an F1 crossed with a parent not included in the pangenome. ResultsThe linear approach yielded more SNP calls than the graph-based approach, however, both methods exhibited similar Mendelian Inheritance Error Rates (MIER) in a tool-dependent manner. Reconstruction of parental haplotype blocks in the advanced hybrids revealed a striking improvement in performance in the pangenome graph-based calls, suggesting MIER is vulnerable to error when reference bias influences both parental and progeny genotype calls. Masking of regions diverged from the reference path improved MIER accuracy metrics and haplotype block reconstruction in both the linear and graph-based SNP calls. ConclusionsIn non-model systems, inheritance patterns observed from pedigreed hybrids provide a framework for benchmarking variant-calling accuracy using pangenomes. SNP miscalls originating from diverged regions can falsely satisfy MIER filters, thus we recommend haplotype blocks. The inherent structure of the pangenome graph has promising applications for removing regions of unreliable mapping quality, which cannot otherwise be reliably removed using traditional filtering metrics.

genomics↗

bioRxiv2026

Mechanotranscriptomic Profiling of Breast Cancer Cells Intravasated from Engineered Microtumors

Intravasation is the process by which cancer cells breach the physical boundaries of a primary tumor and enter blood or lymphatic vessels. In this work, MCF-7 breast cancer cells were cultured within polymer-based microcapsules (here referred to as artificial microtumors) to investigate the transcriptomic and morpho-mechanical changes occurring in cancer cells during their release from these matrices, mimicking in vitro the process of intravasation. Our results show that even confined and released cancer cells share approximately 95% of their global transcriptomic profiles, intravasation-like cells exhibited marked differences in the expression of pathogenic hallmarks, including pathways associated with cell proliferation, immunosurveillance, and dormancy. Notably, a clear upregulation of YAP/TAZ signaling was observed in released cells, a result further supported by single-cell traction force microscopy assays, demonstrating that those cells exhibit higher biomechanical activity compared to cells located within artificial microtumors or those cultured on conventional 2D flasks, as shown for intravasated cells in vivo. To further enrich our investigation, the mechanotranscriptomic activity of MCF-7 cells was compared with suspended spheroids cultured on non-adherent surfaces (i.e., agarose hydrogels). Our results show that released cells displayed increased biomechanical activity and elevated expression of malignant markers, indicating that mechanical stress, beyond cell-cell contact alone, is required to trigger malignant responses. These observations were further supported by co-culture studies of MCF-7 cells with human fibroblasts and endothelial cells, which showed reduced proliferative and invasive capacities under confinement. Overall, our findings demonstrate that shifts in mechanical and metabolic stress, as experienced during intravasation, act as critical stimuli driving mechanotranscriptomic programs associated with cancer progression.

cancer biology↗

bioRxiv2025

Developmental candidate GHP-88310/EIDD-3608 with high tolerability and oral efficacy in measles and respiratory paramyxovirus models

Orthoparamyxoviruses such as human parainfluenza virus type-3 (HPIV3) and measles virus (MeV), are a major health threat. We discovered an orally efficacious broad-spectrum inhibitor of orthoparamyxovirus polymerases. However, here we found that tolerability in higher mammals was limited. We report development of clinical candidate analog GHP-88310 (EIDD-3608), which combines improved oral efficacy with favorable tolerability in non-rodents (ferrets and dogs). GHP-88310 was active against HPIV3, Sendai virus (SeV), MeV, and related canine distemper virus (CDV). In 7-day tolerability studies, daily doses of 2,000 mg/kg were well tolerated. Pharmacokinetic analysis revealed altered plasma exposure of GHP-88310 compared to the original hit. In HPIV3-infected cotton rats, GHP-88310 lowered respiratory tract viral load. Dosing of ferrets infected with CDV, causing lethal measles-like disease, resulted in complete survival, reduction of viremia and shed viral load, and alleviated lymphocytopenia. Once-daily GHP-88310 was efficacious in the CDV-ferret and HPIV3-cotton rat models. The compound was sterilizing against HPIV3 at physiological concentrations in human airway epithelium organoids.

microbiology↗

bioRxiv2025

Deep Learning for RNA Secondary Structure Determination: Gauging Generalizability and Broadening the Scope of Traditional Methods

The diverse regulatory functions, protein production capacity, and stability of natural and synthetic RNAs are closely tied to their ability to fold into intricate structures. Determining RNA structure is thus fundamental to RNA biology and bioengineering. Among existing approaches to structure determination, computational secondary structure prediction offers a rapid and low-cost strategy and is thus widely used, especially when seeking to identify functional RNA elements in large transcriptomes or screen massive libraries of novel designs. While traditional approaches rely on detailed measurements of folding energetics and/or probabilistic modeling of structural data, recent years have witnessed a surge in deep learning methods, inspired by their tremendous success in protein structure prediction. However, the limited diversity and volume of known RNA structures can impede their ability to accurately predict structures markedly different from the ones they have seen. This is known as the generalization gap and currently poses a major barrier to progress in the field. In this Perspective article, we gauge method generalizability using a new benchmark dataset of structured RNAs we curated from the Protein Data Bank. We also discuss the emergence of deep learning methods for predicting structure probing data and use a new dataset to underscore generalization challenges unique to this domain along with directions for future improvement. Expanding beyond improving predictive accuracy, we review how advances in deep learning have recently enabled scalable and accessible optimization of traditional structure prediction methods and their seamless integration with modern neural networks.

bioinformatics↗

bioRxiv2025

Loss of the Parkinson's disease-associated protein DJ-1 impacts dopamine metabolism in astrocytes

The selective loss of dopaminergic neurons in the substantia nigra is a hallmark of Parkinsons disease (PD), yet the contribution of glial cells to this vulnerability is not fully understood. Studies in rodent models suggest that astrocytes can take up and metabolize dopamine (DA), potentially protecting neurons by detoxifying reactive DA metabolites via glutathione S-transferase mu 2 (GSTM2) release. However, these mechanisms remain underexplored in human systems, particularly in the context of PD. Here, we used CRISPR-engineered iPSC-derived human astrocytes with a PD-linked DJ-1 mutation and isogenic controls to investigate astrocytic DA metabolism. Upon DA exposure, control astrocytes upregulated quinone-reducing enzymes NAD(P)H quinone dehydrogenase 1 (NQO1) and GSTM2, whereas DJ-1 mutant astrocytes failed to adaptively respond. In addition, only control astrocytes presented with increased DA quinone products upon DA exposure, not DJ-1 mutants. These results demonstrate astrocytic DA handling being disrupted in DJ-1-linked PD, implicating astroglial dysfunction as an important contributor to PD pathogenesis and potential target for therapeutic intervention.

neuroscience↗

bioRxiv2025

Sex-specific microRNA regulators of Parkinson disease: insights from cohort-stratified simulations of compensatory pathway dynamics

Parkinsons disease (PD) exhibits sex differences in prevalence, symptom severity, and progression, suggesting distinct underlying molecular mechanisms. However, the pathophysiological mechanisms remain largely obscure, particularly in the context of the post-transcriptional regulations, where microRNAs (miRNAs) suppress the expression of multiple genes. Bulk transcriptomic data often blur these effects, especially when regulatory patterns vary by sex or cell type. miRNAs have emerged as key regulators of PD-related processes, but their complexity demands computational methods that enable capturing the functional impact at the pathway level. In this study, we investigated how sex may affect miRNA-regulated PD pathways using Boolean modeling across two large PD cohorts, the Parkinsons Progression Markers Initiative (PPMI) and the Luxembourg Parkinsons Study (LuxPark). First, differential expression analysis identified significant variations in miRNA expression between the sexes across both cohorts. These miRNAs were analysed to identify molecular pathways that are over-represented among the predicted targets of the dysregulated microRNAs (i.e. enrichment analysis). The enriched pathways were used to build Boolean models to simulate the effects of sex-specific miRNA dysregulation. These simulations showed consistent male-specific impairment in mitochondrial biogenesis, and respiratory chain activity. Mitophagy and oxidative stress response pathways were also disrupted, alongside dysregulation of autophagy-related protein-folding mechanisms. Our findings suggest that sex-specific miRNA dysregulation contributes to differences in molecular patterns in PD by influencing compensatory related pathways and responses. These results highlight the need for sex-stratified approaches in modeling, translational research, and precision medicine strategies for disease-modifying treatments.

systems biology↗

bioRxiv2024

An estrogen receptor signaling transcriptional program linked to immune evasion in human hormone receptor-positive breast cancer

T cells are generally sparse in hormone receptor-positive (HR+) breast cancer, potentially due to limited antigen presentation, but the driving mechanisms of low T cell abundance remains unclear. Therefore, we defined and investigated programs ( gene modules), related to estrogen receptor signaling (ERS) and immune signaling using bulk and single-cell transcriptome and multiplexed immunofluorescence of breast cancer tissues from multiple clinical sources and human cell lines. The ERS gene module, dominantly expressed in cancer cells, was negatively associated with immune-related gene modules TNF/NF-{kappa}B signaling and type-I interferon (IFN-I) response, which were expressed in distinct stromal and immune cell types, but also, in part, expressed and preserved as a cancer cell-intrinsic mechanisms. Spatial analysis revealed that ERS strongly correlated with reduced T cell infiltration, potentially due to its association with suppression of TNF/NF-{kappa}B-induced angiogenesis and IFN-I-induced HLA expression in macrophages. Preoperative endocrine therapy in ER+/HER2-breast cancer patients produced better responses in ERS-high patients, with TNF/NF-{kappa}B expression associated with reduced ERS. Targeting these pathways may enhance T cell infiltration in HR+ breast cancer patients. Statement of SignificanceThis study elucidates the immunosuppressive role of ER signaling in breast cancer, highlighting a complex interplay between cancer, stromal, and immune cells and reveals potential approaches to enhance immunogenicity in HR+ breast cancer. These findings offer crucial insights into immune evasion in breast cancer and identify strategies to enhance T cell abundance.

cancer biology↗

bioRxiv2024

DJ-1 mediates regulation of metabolism and immune response in Parkinsons disease astrocytes and Glioblastoma cells

An inverse correlation for the expression of Parkinsons disease (PD)- and cancer-associated genes has been previously reported. Genes that are upregulated in cancer are frequently downregulated in PD and vice versa. PARK7, encoding DJ-1, was initially identified as an oncogene, but loss of DJ-1 causes early-onset PD. However, it remains elusive how differential DJ-1 levels contribute to opposite cell fates in cancer and PD. Here, we demonstrate specific effects of differential DJ-1 protein levels on the energy metabolism and cell growth in patient-derived cellular models of PD and glioblastoma (GBM) cell lines. Impaired energy metabolism was associated with an increased immune response upon IL-1{beta} stimulation and increased apoptosis and decreased cell growth in models of PD, whereas in GBM cells increased metabolic activity translated into a reduced immune response and increased cell growth. Furthermore, we found decreased glutathione (GSH) synthesis and therefore increased levels of reactive oxygen species (ROS) and oxidized glutathione (GSSG) in models of DJ-1 deficiency and decreased ROS levels in GBM cell lines. Thus, the mechanism by which DJ-1 modulates these phenotypes is the same in both diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/621212v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@4eccb4org.highwire.dtl.DTLVardef@161669corg.highwire.dtl.DTLVardef@197bfc3org.highwire.dtl.DTLVardef@1aecb36_HPS_FORMAT_FIGEXP M_FIG C_FIG DJ-1 levels modulate GSSG/GSH ratio and ROS levels, which results in divergent effects on cell growth and immune response in DJ-1-dependent glial pathologies in glioblastoma and PD. In models of PD, DJ-1 level dependent phenotypes can be rescued by antioxidant treatment that reduces the GSSG/GSH ratio and ROS levels.

neuroscience↗

bioRxiv2024

Generalized design of sequence-ensemble-function relationships for intrinsically disordered proteins

The design of folded proteins has advanced significantly in recent years. However, many proteins and protein regions are intrinsically disordered (IDPs) and lack a stable fold i.e., the sequence of an IDP encodes a vast ensemble of spatial conformations that specify its biological function. This conformational plasticity and heterogeneity makes IDP design challenging. Here, we introduce a computational framework for de novo design of IDPs through rational and efficient inversion of molecular simulations that approximate the underlying sequence to ensemble relationship. We highlight the versatility of this approach by designing IDPs with diverse properties and arbitrary sequence constraints. These include IDPs with target ensemble dimensions, loops and linkers, highly sensitive sensors of physicochemical stimuli, and binders to target disordered substrates with distinct conformational biases. Overall, our method provides a general framework for designing sequence-ensemble-function relationships of biological macromolecules.

biophysics↗

bioRxiv2024

Morphological profiling in human dopaminergic neurons identifies mitochondrial uncoupling as a neuroprotective effect

Parkinsons disease (PD) involves multiple pathological processes in midbrain dopaminergic (mDA) neurons, including protein degradation defects, vesicular trafficking disruption, endolysosomal dysfunction, mitochondrial issues, and oxidative stress. Current PD models often lack complexity and focus on single phenotypes. We used patient-derived SNCA triplication (SNCA-4x) and isogenic control (SNCA-corr) mDA neurons, applying high-content imaging-based morphological profiling to identify and rescue multiple phenotypes. Screening 1,020 compounds, we identified top-scoring compounds that restored healthy profiles in SNCA-4x neurons, increasing Tyrosine hydroxylase (TH) and decreasing -synuclein (Syn) levels. Several hits were linked to mitochondrial biology. Tyrphostin A9, a mitochondrial uncoupler, and several of its structural analogues decreased ROS levels, normalized mitochondrial membrane potential, and increased respiration. Western blotting confirmed that Tyrphostin A9 reduces Syn levels. Our study highlights the neuroprotective potential of mild mitochondrial uncoupling in mDA neurons.

neuroscience↗

bioRxiv2024

The Role of Alpha Synuclein in Synucleinopathy: Impact on Lipid Regulation at Mitochondria ER Membranes

The protein alpha-synuclein (Syn) plays a critical role in the pathogenesis of synucleinopathy, which includes Parkinsons disease and multiple system atrophy, and mounting evidence suggests that lipid dyshomeostasis is a critical phenotype in these neurodegenerative conditions. Previously, we identified that Syn localizes to mitochondria-associated endoplasmic reticulum membranes (MAMs), temporary functional domains containing proteins that regulate lipid metabolism, including the de novo synthesis of phosphatidylserine. In the present study, we have analyzed the lipid composition of postmortem human samples, focusing on the substantia nigra pars compacta of Parkinsons disease and controls, as well as three less affected brain regions of Parkinsons donors. To further assess synucleinopathy-related lipidome alterations, similar analyses were performed on the striatum of multiple system atrophy cases. Our data show region-and disease-specific changes in the levels of lipid species. Specifically, our data revealed alterations in the levels of specific phosphatidylserine species in brain areas most affected in Parkinsons disease. Some of these alterations, albeit to a lesser degree, are also observed multiples system atrophy. Using induced pluripotent stem cell-derived neurons, we show that Syn contributes to regulating phosphatidylserine metabolism at MAM domains, and that Syn dosage parallels the perturbation in phosphatidylserine levels. Our results support the notion that Syn pathophysiology is linked to the dysregulation of lipid homeostasis, which may contribute to the vulnerability of specific brain regions in synucleinopathy. These findings have significant therapeutic implications. Significance StatementSynucleinopathy is a complex group of neurodegenerative disorders whose causes and underlying mechanisms remain unknown. In this work, we examined synucleinopathy postmortem brain samples and patient-derived neuron models and identified the functional impairment of the mitochondrial-associated endoplasmic reticulum membrane (MAM) domain, which facilitates lipid regulation. The protein alpha-synuclein is associated with synucleinopathy and increasing levels result in the mislocalization of this protein and the disruption of MAM domains, which, in turn, results in lipid and membrane composition alterations. Specifically, we report that increased alpha-synuclein expression impairs the regulation of phosphatidylserine synthase 2 and the levels of phosphatidylserine in cellular membranes from affected cells. Our study offers mechanistic insight tying alpha-synuclein pathology and lipid dysregulation as seminal factors in synucleinopathy, which may have pathogenic and therapeutic implications.

neuroscience↗

bioRxiv2024

Scalable Differentiable for mRNA Design

mRNA is an emerging therapeutic platform with applications ranging from vaccines to genome editing. However, there are an exponential number of mRNA sequences to deliver a given payload and the choice in nucleotide sequence largely determines stability and translation efficiency. There exist several computational approaches for optimizing mRNA sequences but these algorithms are limited in performance or the choice of optimization metric. In this work we describe a new mRNA design algorithm that overcomes both of these limitations and is based on differentiable folding, a recently developed paradigm for RNA design in which a probabilistic sequence representation is optimized via gradient-based methods. First, we present major improvements to the original differentiable folding algorithm that drastically reduce the memory overhead of the gradient calculation. Second, we formulate the mRNA design problem in the context of continuous sequences, requiring the generalization of existing metrics and careful treatment of constraints. Given this scaled algorithm and our mRNA design formalism, we then developed a generative deep learning approach that treats our differentiable folding algorithm as a module in a larger optimization pipeline to learn a network that samples optimized sequences. As a demonstration of our method, we optimize mRNA sequences via complex, therapeutically relevant objective functions.

bioinformatics↗

bioRxiv2024

Insulin resistance compromises midbrain organoid neural activity and metabolic efficiency predisposing to Parkinsons disease pathology

Growing evidence indicates that Type 2 Diabetes (T2D) is associated with an increased risk of developing Parkinsons disease through shared disease mechanisms. Studies show that insulin resistance, which is the driving pathophysiological mechanism of T2D plays a major role in neurodegeneration by impairing neuronal functionality, metabolism, and survival. To investigate insulin resistance caused pathological changes in the human midbrain, which could predispose a healthy midbrain to PD development, we exposed iPSC-derived human midbrain organoids from healthy individuals to either high insulin concentrations, promoting insulin resistance, or to more physiological insulin concentrations restoring insulin signalling function. We combined experimental methods with metabolic modelling to identify the most insulin resistance-dependent pathogenic processes. We demonstrate that insulin resistance compromises organoid metabolic efficiency, leading to increased levels of oxidative stress. Additionally, insulin-resistant midbrain organoids showed decreased neural activity and reduced amount of dopaminergic neurons, highlighting insulin resistance as a significant target in PD prevention.

neuroscience↗

bioRxiv2024

psudo: Exploring Multi-Channel Biomedical Image Data with Spatially and Perceptually Optimized Pseudocoloring

Over the past century, multichannel fluorescence imaging has been pivotal in myriad scientific breakthroughs by enabling the spatial visualization of proteins within a biological sample. With the shift to digital methods and visualization software, experts can now flexibly pseudocolor and combine image channels, each corresponding to a different protein, to explore their spatial relationships. We thus propose psudo, an interactive system that allows users to create optimal color palettes for multichannel spatial data. In psudo, a novel optimization method generates palettes that maximize the perceptual differences between channels while mitigating confusing color blending in overlapping channels. We integrate this method into a system that allows users to explore multi-channel image data and compare and evaluate color palettes for their data. An interactive lensing approach provides on-demand feedback on channel overlap and a color confusion metric while giving context to the underlying channel values. Color palettes can be applied globally or, using the lens, to local regions of interest. We evaluate our palette optimization approach using three graphical perception tasks in a crowdsourced user study with 150 participants, showing that users are more accurate at discerning and comparing the underlying data using our approach. Additionally, we showcase psudo in a case study exploring the complex immune responses in cancer tissue data with a biologist. CCS ConceptsO_LIHuman-centered computing [->] Visualization systems and tools; C_LI

cell biology↗

bioRxiv2024

Park7 deletion leads to age- and sex-specific transcriptome changes involving NRF2-CYP1B1 axis in mouse midbrain astrocytes

AbstractdispeLoss-of-function mutations in PARK7, encoding for DJ-1, can lead to early onset Parkinsons disease (PD). In mice, Park7 deletion leads to dopaminergic deficits during aging, and increased sensitivity to oxidative stress. However, the severity of the reported phenotypes varies. To understand the early molecular changes upon loss of DJ-1, we performed transcriptomic profiling of midbrain sections from young mice. Interestingly, while at 3 months the transcriptomes of both male and female mice were unchanged compared to their wildtype littermates, an extensive deregulation was observed specifically in 8-month-old males. The affected genes are involved in processes such as focal adhesion, extracellular matrix interaction, and epithelial-to-mesenchymal transition (EMT), and enriched for primary target genes of Nuclear factor erythroid 2-related factor 2 (NRF2). Consistently, the antioxidant response was altered specifically in the midbrain of male DJ-1 deficient mice. Many of the misregulated genes are known target genes of estrogen and retinoic acid signaling and show sex-specific expression in wildtype mice. Depletion of DJ-1 or NRF2 in male, but not female primary astrocytes recapitulated many of the in vivo changes, including downregulation of cytochrome P450 family 1 subfamily B member 1 (CYP1B1), an enzyme involved in estrogen and retinoic acid metabolism. Interestingly, knock-down of CYP1B1 led to gene expression changes in focal adhesion and EMT in primary male astrocytes. Finally, male iPSC-derived astrocytes with loss of function mutation in the PARK7 gene also showed changes in the EMT pathway and NRF2 target genes. Taken together, our data indicate that loss of Park7 leads to sex-specific gene expression changes specifically in males through astrocytic alterations in the NRF2-CYP1B1 axis. These findings suggest higher sensitivity of males to loss of DJ-1 and might help to better understand variation in the reported Park7-/-phenotypes.

molecular biology↗