Biology subjects

Nguyen, M.

Publications and source records attributed to Nguyen, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Glycosphingolipids Regulate Phosphatidylserine Transport at ER-PM Contact Sites

Plasma membrane (PM) localization of KRAS requires specific glycosphingolipids in the outer leaflet and phosphatidylserine (PS) in the inner leaflet. PM PS content is controlled by lipid transport proteins ORP5 and ORP8, which operate at ER-PM membrane contact sites (MCSs). Using high-resolution imaging, we now show that GSLs including GM3 and SM4, are required to maintain ORP5 and ORP8 localization to MCSs. Genetic deletion or pharmacologic inhibition of enzymes required for the biosynthesis of GM3 or SM4, displace PI4-kinase Type III (PI4KIII) and its adaptor EFR3A from the PM, thereby reducing PM phosphatidylinositol 4-phosphate (PI4P) content. PM interactions of ORP5 and ORP8 are also disrupted. Since ORP5 and ORP8 transport PS to the PM by counter-transporting PI4P to the ER, PM PS content is substantially reduced. We further show that GM3 and GM2 regulate the assembly of ER-PM-MCSs, such that the function of other MCS-localized macromolecular machineries including calcium release-activated calcium channels is abrogated when glycosphingolipid biosynthesis is blocked. Together, this study establishes glycosphingolipids as organizers of PS transport and ER-PM MCSs, expanding the regulators of MCSs beyond protein tethers to include glycosylated lipids and revealing how glycosphingolipids control KRAS function.

molecular biology↗

bioRxiv2025

Zika virus induces persistent phenotypic changes in natural killer cells distinct from dengue virus infection

Zika virus (ZIKV) is a mosquito-borne orthoflavivirus of global concern due to its ability to cause congenital neurological defects in infants. Natural killer (NK) cells are innate lymphocytes that can directly kill virus-infected cells. It is thought that NK cells are protective against ZIKV, although the mechanisms by which NK cells detect and respond to ZIKV are not well understood. Here, we evaluated NK cell receptor expression on isolated NK cells from a Panamanian cohort of ZIKV-infected participants, and corresponding NK receptor ligand expression on participant PBMCs and ZIKV-infected cells in vitro using mass cytometry. We found that during acute ZIKV infection, NK cells express high levels of activation markers, proliferative markers, and cytotoxic effector proteins, indicating that NK cells are mounting a response to ZIKV. Interestingly, many markers elevated during acute infection remain elevated post-acute infection, suggesting ZIKV infection may have potential long-term effects on NK cell function. Analysis of NK receptor ligand expression on ZIKV-infected participant PBMCs and ZIKV-infected cells in vitro did not identify a cellular source of NK cell activation, suggesting that either soluble or tissue-specific factors are responsible for modulating NK cell activity during ZIKV infection. Comparison of the NK cell receptor expression with a previously characterized cohort of dengue-infected participants revealed both common and virus-specific changes in NK cell phenotype during acute infection. This work improves our understanding of the NK cell response to orthoflavivirus infection, which will aid in the development of vaccines and therapeutics.

immunology↗

bioRxiv2025

LRRK2G2019S acts as a dominant interfering mutant in the context of iron overload

Altered iron homeostasis has long been implicated in Parkinsons Disease (PD), although the mechanisms have not been clear. Given the critical role of PD-related activating mutations in LRRK2 (leucine-rich repeat protein kinase 2) within membrane trafficking pathways we examined the impact of a homozygous mutant LRRK2G2019S on iron homeostasis within the RAW macrophage cell line with high iron capacity. Proteomics analysis revealed a dysregulation of iron-related proteins in steady state with highly elevated levels of ferritin light chain and a reduction of ferritin heavy chain. LRRK2G2019S mutant cells showed efficient ferritinophagy upon iron chelation, but upon iron overload there was a near complete block in the degradation of the ferritinophagy adaptor NCOA4. These conditions lead to an accumulation of phosphorylated Rab8 at the plasma membrane, which is selectively inhibited by LRRK type II kinase inhibitors. Iron overload then leads to increased oxidative stress and ferroptotic cell death. These data implicate LRRK2 as a key regulator of iron homeostasis and point to the need for an increased focus on the mechanisms of iron dysregulation in PD.

cell biology↗

bioRxiv2025

SH2scan: Mapping SH2 domain-ligand binding selectivity for inhibitors and degraders

Drug discovery targeting SH2 domains (key protein-protein interaction modules) has been hampered by a lack of assay systems evaluating synthetic ligand binding selectivity toward SH2 domains, to reduce potential off-target effects. In addition, the molecular determinants for synthetic ligand engagement to SH2 domains across the target class have yet to be defined. Here, we developed SH2scan, a high-throughput competition binding assay platform to quantify ligand-SH2 domain interactions, covering >80% of the target class. We uncovered unique binding selectivity profiles and quantified a broad range of dissociation constants (KDs) for 9 synthetic ligands of SH2 domains from the scientific literature with a range of reported primary targets. These results demonstrate that SH2scan can be used to design more selective compounds targeting SH2 domains. The platform can be further leveraged for the discovery of new molecular probes for the dissection of cellular protein-protein interaction networks.

pharmacology and toxicology↗

bioRxiv2025

Effect of Chronic Stress on Whole Blood Transcriptome: A Meta-Analysis of Publicly Available Datasets from Rodent Models

BackgroundChronic stress increases risk for neuropsychiatric disorders in humans. By modeling stress-induced changes in animals, we may improve diagnosis or treatment of these disorders. Successful translation benefits from studies with sufficient statistical power and outcome measurements that can be directly compared across species. We performed a meta-analysis to examine the impact of chronic stress on the whole blood transcriptome. MethodsDatasets were systematically identified in Gemma, a database of reprocessed public transcriptional profiling studies; datasets GSE68076, GSE72262, and GSE84185 met inclusion/exclusion parameters. Each study exposed eight-week old mice to chronic stress (5-10 days social defeat stress or 6-8 weeks chronic mild stress). The final sample size was n=92 (n=45 Non-Stress/n=47 Stress). Stress-related differential expression in each dataset was quantified using the Limma pipeline followed by empirical Bayes moderation. For the 9,219 genes represented in all three datasets, we ran a meta-analysis of Log(2) Fold Changes using a random effects model and corrected for false discovery rate (FDR). Functional patterns were assessed with fast Gene Set Enrichment Analysis. Cell type specific enrichment for each of the differentially expressed genes was further explored using a public 10x genomics scRNA-Seq dataset from mouse peripheral blood mononuclear cells. ResultsFindings included 23 downregulated and 16 upregulated transcripts in stress-exposed mice (FDR<0.05). Results indicated a down-regulation in gene sets related to B cells, immune response, DNA and chromatin regulation, ribosomal activity, translation, and catabolic cellular processes. Upregulated gene sets related to erythrocytes and oxygen binding. ConclusionOur results provide molecular insight into stress-related immune dysregulation and add weight to the hypothesis that environmental stress escalates cellular aging, supporting the use of blood transcriptome as a bridge between human and rodent models. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/657043v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@161fc2eorg.highwire.dtl.DTLVardef@1f358b9org.highwire.dtl.DTLVardef@145ef33org.highwire.dtl.DTLVardef@5b1169_HPS_FORMAT_FIGEXP M_FIG C_FIG Key pointsSuccessful translational research benefits from studies with outcome measurements that can be directly compared across species and sufficient statistical power. The present report is a meta-analysis of three mouse experiments examining the impact of chronic stress on the whole blood transcriptome. Our results provide insight into stress-related immune dysregulation and add weight to the hypothesis that environmental stress escalates cellular aging. These findings illustrate the utility of the blood transcriptome as a bridge between human and rodent models.

genomics↗

bioRxiv2025

Selective Knockout of Murine Glutamic Acid-rich Protein 2 (GARP2) Significantly Alters Cellular Dark Noise in Rod Photoreceptors

GARP2, a glutamic-acid-rich protein found exclusively in rod photoreceptors, has been suggested to function as a structural protein, a modulator of the cGMP phosphodiesterase enzyme (PDE6), and a gating inhibitor of the rod cGMP-gated cation channel. GARP2 is a splice variant of the Cngb1 gene, which in the rods encodes the {beta}-subunit of the cyclic nucleotide-gated cation channel. Mutations in Cngb1 cause retinitis pigmentosa (RP45), and {beta}-subunit knockout mice are being studied as models of this disease. In this study, using ZFN-mediated gene editing, we have selectively eliminated GARP2 expression, while not affecting expression of the cyclic nucleotide gated cation channel {beta} -subunit, to determine its essential functions in mouse rods. The absence of GARP2 caused no consistent perturbations of retinal structure. Transiently, rod outer segment length was regionally greater than WT and infrequently misaligned, appearing parallel to the retinal pigment epithelium. Electroretinography of the knockout mice did reveal consistent functional alterations over time, seen as a reduction in the ERG response amplitudes in older mice, albeit with no significant alterations in sensitivity to light. Interestingly, single-cell patch-clamp recordings showed a significant reduction in rod photoreceptor dark noise consistent with a previously proposed role for GARP2 in binding to PDE6 and affecting its basal activity. Our results suggest a role for the GARP2-PDE6 interaction in stabilizing the PDE6 enzyme and controlling the turnover rate of cGMP in darkness, adjusting the level of dark noise and implicating an influence on the signal and noise properties of rod photoreceptors. Key PointsO_LIGlutamic acid-rich protein 2 (GARP2), an alternatively spliced variant of the Cngb1 gene, is exclusively expressed in rod photoreceptors, but the in vivo role of GARP2 remains unestablished. C_LIO_LIWe used precision gene editing technology to selectively knockout soluble GARP2 expression in rods, to determine its essential functions in structure and function of the retina. C_LIO_LIWe show that GARP2 has a minor role in maintaining the structural integrity of the rod outer segments as a function of age. C_LIO_LIOur study indicates that GARP2 has an important role in regulating rod photoreceptor dark noise, likely through stabilization of PDE6 basal activity to maintain the appropriate cGMP turnover rate. C_LIO_LIThis regulation is critical to facilitate the single-photon sensitivity and function of the rod photoreceptors. C_LI

neuroscience↗

bioRxiv2025

Structural Plasticity of RRE Stem-Loop II Modulates Nuclear Export of HIV-1 RNA

The Rev Response Element (RRE) forms an oligomeric complex with the viral protein Rev to facilitate the nuclear export of intron-retaining viral RNAs during the late phase of HIV-1 infection. However, our structural understanding of this crucial virological process remains limited. In this study, we determined several crystal structures of an intact RRE stem-loop II in two distinct conformations, performed negative-staining electron microscopy and molecular dynamics simulations, and revealed that this three-way junction RNA exhibits remarkable structural plasticity. Through in vitro Rev-binding and in vivo Rev-activity assays using various stem-loop II mutants designed to favor one of the conformers, we demonstrated that the structural plasticity of stem-loop II modulates Rev binding and oligomerization. Our findings illuminate emerging perspectives on RRE dynamics-based regulation of HIV-1 RNA nuclear export and provide a framework for developing anti-HIV drugs that target specific RRE conformations.

biophysics↗

bioRxiv2025

Beyond Blacklists: A Critical Assessment of Exclusion Set Generation Strategies and Alternative Approaches

Short-read sequencing data can be affected by alignment artifacts in certain genomic regions. Removing reads overlapping these exclusion regions, previously known as Blacklists, help to potentially improve biological signal. Tools like the widely used Blacklist software facilitate this process, but their algorithmic details and parameter choices are not always clearly documented, affecting reproducibility and biological relevance. We examined the Blacklist software and found that pre-generated exclusion sets were difficult to reproduce due to variability in input data, aligner choice, and read length. We also identified and addressed a coding issue that led to over-annotation of high-signal regions. We further explored the use of "sponge" sequences--unassembled genomic regions such as satellite DNA, ribosomal DNA, and mitochondrial DNA--as an alternative approach. Aligning reads to a genome that includes sponge sequences reduced signal correlation in ChIP-seq data comparably to Blacklist-derived exclusion sets while preserving biological signal. Sponge-based alignment also had minimal impact on RNA-seq gene counts, suggesting broader applicability beyond chromatin profiling. These results highlight the limitations of fixed exclusion sets and suggest that sponge sequences offer a flexible, alignment-guided strategy for reducing artifacts and improving functional genomics analyses.

bioinformatics↗

bioRxiv2024

FAK activity exacerbates disturbed flow-mediated atherosclerosis via VEGFR2-Cbl-NF-κB signaling.

Atherosclerosis develops at predictable sites in the vasculature where branch points and curvatures create non-laminar disturbed flow. This disturbed flow causes vascular inflammation by increased endothelial cell (EC) barrier permeability and the expression of inflammatory genes such as vascular cell adhesion molecule-1 (VCAM-1). Vascular endothelial growth factor receptor 2 (VEGFR2) is important for flow-induced EC inflammation; however, there are still some gaps in the signaling pathway. Focal adhesion kinase (FAK) is a protein tyrosine kinase whose expression has been implicated in flow-mediated signaling in ECs. However, the link between FAK and VEGFR2 in flow-mediated inflammation signaling has remained unelucidated. Here we found that priming of VEGFR2 with VEGF was critical for flow-mediated activation of FAK and NF-kB. Mechanistically, FAK activation triggers tyrosine phosphorylation of Casitas B-lineage lymphoma (CBL; an E3 ubiquitin ligase) that interacts with VEGFR2 under flow conditions. Further, Apoe-/- mice fed a western diet (WD) exhibited increased FAK activity within the atheroprone disturbed flow region of the inner aortic arch compared to the outer arch. Disturbed flow-induced FAK activation is associated with elevated VEGFR2 on the surface of ECs of the inner aortic arch, but not in the outer arch. Taken together, these data suggest that suppression of augmented FAK activity under disturbed flow may prove beneficial in reducing pro-inflammatory signaling of the endothelial layer.

cell biology↗

bioRxiv2024

scHiCcompare: an R package for differential analysis of single-cell Hi-C data

Changes in the three-dimensional (3D) structure of the human genome are key indicators of cancer and developmental disorders. Techniques like chromatin conformation capture (Hi-C) have been developed to study these global 3D structures, typically requiring millions of cells and an extremely high sequencing depth (around 1 billion reads per sample) for bulk Hi-C. In contrast, single-cell Hi-C (scHi-C) captures 3D structures at the individual cell level but faces significant data sparsity, marked by a high proportion of zeros. While differential analysis methods exist for bulk Hi-C data, they are limited for scHi-C data. To address this, we developed a method for differential scHi-C analysis, building on existing techniques in the HiCcompare R package. Our approach imputes sparse scHi-C data by considering genomic distances and creates pseudo-bulk Hi-C matrices by summing condition-specific data. The data are normalized using LOESS regression, and differential chromatin interactions are detected via Gaussian Mixture Model (GMM) clustering. Our workflow outperforms existing methods in identifying differential chromatin interactions across various genomic distances, fold changes, resolutions, and sample sizes in both simulated and experimental contexts. This allows for effective detection of cell type-specific differences in chromatin structure, which has meaningful associations with biological and epigenetic features. Our method is implemented in the scHiCcompare R package, available at https://github.com/dozmorovlab/scHiCcompare. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=74 SRC="FIGDIR/small/622369v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@b94f54org.highwire.dtl.DTLVardef@72fddorg.highwire.dtl.DTLVardef@1d77702org.highwire.dtl.DTLVardef@c63088_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2024

Inactivity-mediated molecular adaptations: insights from a novel pre-clinical model of physical activity reduction

Insufficient physical activity is associated with increased relative risk of cardiometabolic disease and is an independent risk factor for mortality. Experimentally reducing physical activity rapidly induces insulin resistance, impairs glucose handling, and drives metabolic inflexibility. These adaptations manifest during the early stages of physical inactivity, even when energy balance is maintained, suggesting that inactivity-mediated metabolic reprogramming is an early event that precedes changes in body composition. To identify mechanisms that promote metabolic adaptations associated with physical inactivity, we developed a mouse model of physical activity reduction that permits the study of inactivity in animals prior to the onset of overt changes in body composition. Adult mice were randomized into three groups: an inactive control group (standard rodent housing), an active control group (treadmill running 5 d/week for 6-weeks), and an activity reduction group (treadmill running for 4-weeks, followed by 2-weeks of inactivity). Transcriptional profiling of gastrocnemius muscle identified seven transcripts uniquely altered by physical activity reduction compared to the inactive and active control groups. Most identified transcripts had reported functions linked to bioenergetic adaptation. Future studies will provide deeper characterization of the function(s) of each the identified transcripts while also determining how inactivity affects transcriptional regulation in other tissues.

physiology↗

bioRxiv2024

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↗

bioRxiv2024

FAST-STEM: A human pluripotent stem cell engineering toolkit for rapid design-build-test-learn development of human cell-based therapeutic devices

Very recent clinical advances in stem cell derived tissue replacement and gene therapy, in addition to the rise of artificial intelligence-aided scientific discovery, have placed the possibility of sophisticated human cell-based therapies firmly within reach. However, development of such cells and testing of their engineered gene circuit components, has proven highly challenging, due to the need for generating stable cell lines for each design-build-test-learn engineering cycle. Current approaches to generating stable human induced pluripotent stem cell (hiPSC) lines are highly time-consuming and suffer from lack of control, poor integration efficiency, and limited functionality. Validation in clinically relevant stem cell derived tissues is also broadly lacking. Such drawbacks are prohibitive to repeatably conducting cutting-edge stem cell engineering with broad application within a realistic timeframe and will not scale with the future of regenerative medicine. We have developed FAST-STEM (Facile Accelerated Stem-cell Transgene integration with SynBio Tunable Engineering Modes), a hPSC engineering platform that drastically reduces the time to generate differentiation ready stem cell lines from several weeks to 5 days, exhibiting a ~612-fold improvement in transgene integration rate over previous methodologies. Additional FAST-STEM innovations include: (i) rapid and highly efficient transgene integration; (ii) copy number control; (iii) simultaneous or consecutive integration of multiple gene cassettes; (iv) library screen capability. In addition to this unique functional versatility, platform transportability and broad use case for stem cell-engineering was confirmed by differentiation into eight different cell types across nine different laboratories. This platform dramatically lowers the bar for integration of synthetic biology with regenerative medicine, enabling experiments which were previously deemed logistically impossible, thus paving the way for sophisticated human cell device development.

bioengineering↗

bioRxiv2024

Genome-Wide CRISPR-Cas9 Screening Identifies a Synergy between Hypomethylating Agents and SUMOylation Blockade in MDS/AML

Hypomethylating agents (HMAs) are frontline therapies effective at altering the natural course of Myelodysplastic Neoplasms (MDS) and Acute Myeloid Leukemia (AML). However, acquired resistance and treatment failure are hallmarks of HMA therapy. To address this clinical need, we performed a genome-wide CRISPR-Cas9 screen in a human MDS-derived cell line, MDS-L, and identified TOPORS as a highly ranked loss-of-function target that synergizes with HMAs, reducing leukemic burden and improving survival in xenograft models. We demonstrate that the depletion of TOPORS mediates sensitivity to HMAs by predisposing leukemic blasts to an impaired DNA damage response (DDR) accompanied by an accumulation of SUMOylated DNMT1 in HMA-treated TOPORS-depleted cells. Importantly, the combination of HMAs with targeting of TOPORS did not functionally impair healthy hematopoiesis. While inhibitors of TOPORS are currently unavailable, we show that inhibition of protein SUMOylation (upstream of TOPORS functions) with TAK-981 partially phenocopies HMA-sensitivity and DDR impairment. Overall, our data suggest that the combination of HMAs with the inhibition of SUMOylation or TOPORS demonstrates a favourable therapeutic index and is a rational treatment framework for High-Risk MDS (HR-MDS) or AML.

molecular biology↗

bioRxiv2024

LDL-Binding IL-10 Reduces Vascular Inflammation in Atherosclerotic Mice

Atherosclerosis is a chronic inflammatory disease associated with the accumulation of low-density lipoprotein (LDL) in arterial walls. Higher levels of the anti-inflammatory cytokine IL-10 in serum are correlated with reduced plaque burden. However, cytokine therapies have not translated well to the clinic, partially due to their rapid clearance and pleiotropic nature. Here, we engineered IL-10 to overcome these challenges by hitchhiking on LDL to atherosclerotic plaques. Specifically, we constructed fusion proteins in which one domain is IL-10 and the other is an antibody fragment (Fab) that binds to protein epitopes of LDL. In murine models of atherosclerosis, we show that systemically administered Fab-IL-10 constructs bind circulating LDL and traffic to atherosclerotic plaques. One such construct, 2D03-IL-10, significantly reduces aortic immune cell infiltration to levels comparable to healthy mice, whereas non-targeted IL-10 has no therapeutic effect. Mechanistically, we demonstrate that 2D03-IL-10 preferentially associates with foamy macrophages and reduces pro-inflammatory activation markers. This platform technology can be applied to a variety of therapeutics and shows promise as a potential targeted anti-inflammatory therapy in atherosclerosis.

bioengineering↗

bioRxiv2024

A missense variant effect map for the human tumour suppressor protein CHK2

The tumour suppressor CHEK2 encodes the serine/threonine protein kinase CHK2 which, upon DNA damage, is important for pausing the cell cycle, initiating DNA repair and inducing apoptosis. CHK2 phosphorylation of the tumour suppressor BRCA1 is also important for mitotic spindle assembly and chromosomal stability. Consistent with its cell cycle checkpoint role, both germline and somatic variants in CHEK2 have been linked to breast and multiple other cancer types. Over 90% of clinical germline CHEK2 missense variants are classified as variants of uncertain significance, complicating diagnosis of CHK2-dependent cancer. We therefore sought to test the functional impact of all possible missense variants in CHK2. Using a scalable multiplexed assay based on the ability of human CHK2 to complement DNA sensitivity of a S. cerevisiae lacking its ortholog RAD53, we generated a systematic missense variant effect map for CHEK2 missense variation. Map scores reflect known biochemical features of CHK2 and exhibit good performance in separating pathogenic from benign clinical missense variants. Thus, the missense variant effect map for CHK2 offers value in understanding both known and yet-to-be-observed CHK2 variants.

genetics↗

bioRxiv2024

Dissecting quantitative trait nucleotides by saturation genome editing

Genome editing technologies have the potential to transform our understanding of how genetic variation gives rise to complex traits through the systematic engineering and phenotypic characterization of genetic variants. However, there has yet to be a system with sufficient efficiency, fidelity, and throughput to comprehensively identify causal variants at the genome scale. Here we explored the ability of templated CRISPR editing systems to install natural variants genome-wide in budding yeast. We optimized several approaches to enhance homology-directed repair (HDR) with donor DNA templates, including donor recruitment to target sites, single-stranded donor production by bacterial retrons, and in vivo plasmid assembly. We uncovered unique advantages of each system that we integrated into a single superior system named MAGESTIC 3.0. We used MAGESTIC 3.0 to dissect causal variants residing in 112 quantitative trait loci across 32 environmental conditions, revealing an enrichment for missense variants and loci with multiple causal variants. MAGESTIC 3.0 will facilitate the functional analysis of the genome at single-nucleotide resolution and provides a roadmap for improving template-based genome editing systems in other organisms.

genetics↗

bioRxiv2023

Parkinson's genes orchestrate pyroptosis through selective trafficking of mtDNA to leaky lysosomes

Inflammation is an age-related factor that underlies numerous human disorders. A key driver of inflammation is the release of mitochondrial DNA (mtDNA), which binds and activates cytosolic sensors. This induces transcriptional responses and, ultimately, pyroptotic cell death. The main challenge has been to understand how mtDNA can cross the two mitochondrial membranes to access the cytosol. Through a genome-wide CRISPR knockout screen we identified a new pyroptotic pathway defined by mtDNA exit within mitochondrial-derived vesicles that are delivered to lysosomes. Critically, breach of lysosomes allows mtDNA to access cytosol, requiring multiple Parkinsons Disease-related proteins and Gasdermin pores, identified in the screen. These data place mitochondria-to-lysosome transport as a driver of pyroptosis and link multiple PD proteins along a common pathway. One sentence summaryParkinsons disease-related proteins regulate pyroptosis

cell biology↗