Biology subjects

Neupane, S.

Publications and source records attributed to Neupane, S..

At least 19 recordsLinked to original sources

bioRxiv2026

PODXL regulates the neuronal entry of α-synuclein aggregates

Cell-to-cell transmission of -synuclein (-Syn) aggregates is a key event in Parkinson's disease (PD) pathogenesis, yet the neuronal surface factors that govern uptake of pathogenic -Syn fibrils remain undefined. We developed a flow cytometry-based CRISPR activation screen for modifiers of -Syn preformed fibril (PFF) uptake by human iPSC-derived cortical neurons. By interrogating 68 genes encoding cell-surface proteins prioritised by PD genetic associations, we identified podocalyxin-like protein 1 (PODXL) as a strong suppressor of -Syn fibril uptake. High-content imaging and PODXL cDNA overexpression confirmed reduced PFF uptake. Stable PODXL overexpression also reduced PFF-seeded pSynSer129 accumulation and uptake of structurally distinct recombinant and disease-derived -Syn fibrils. Conversely, shRNA-mediated PODXL knockdown increased -Syn PFF uptake, and analysis of PODXL domain-deletion and N-glycosylation mutants suggested that the ectodomain and N-glycosylation contribute to the PODXL-mediated reduction in uptake. Transcriptomic profiling further identified membrane metalloendopeptidase (MME) as a PODXL-responsive candidate mediator. MME activation and treatment with conditioned medium from MME-activated neurons reduced PFF uptake. Thiorphan, an MME inhibitor, partially attenuated the PODXL-associated reduction in uptake. Together, our findings identify PODXL as a neuronal brake on -Syn uptake and implicate its glycan-dependent surface properties together with MME-associated extracellular activity.

neuroscience↗

bioRxiv2026

Plastome phylogenomics of the tribe Spermacoceae (Rubiaceae): taxonomic implications and a key to the genera

The tribe Spermacoceae (Rubiaceae) comprises a morphologically diverse assemblage of approximately 1,400 species distributed across the Neotropics, Africa, Asia, Australia, and Pacific region. It remains one of the most taxonomically intractable groups in the family, with generic limits repeatedly redefined for more than two centuries. Previous phylogenetic studies based on a limited number of plastid and nuclear markers left numerous relationships unresolved and provided sparse representation of Neotropical lineages. Here, we present the first phylogenomic study of the tribe based on plastome-scale data and expanded sampling of Neotropical taxa. We sampled 121 species representing 55 genera spanning all major clades and generated 123 new plastomes, including 25 species incorporated into a molecular phylogenetic framework for the first time. Maximum-likelihood and Bayesian analyses recovered a highly resolved and strongly supported phylogeny, with uncertainty restricted to a small number of deep backbone nodes. Pollen and seed micromorphology provided additional evidence for evaluating phylogenetic relationships. The resulting phylogenetic framework clarifies generic boundaries across several problematic lineages and supports multiple taxonomic changes. Pervasive homoplasy in seed and floral characters rendered several traditionally recognized genera non-monophyletic, warranting new combinations, including Edrastima oxycoccoides, Stenotis alexanderae, and S. prostrata, and a reassessment of taxa such as Terrellianthus serpyllaceus and Oldenlandia dusenii. We further identify genera requiring additional study and provide an updated key to the 82 recognized genera of Spermacoceae. Together, these results provide the most robust phylogenetic framework yet available for the tribe and establish a foundation for future systematic, biogeographic, and evolutionary research.

plant biology↗

bioRxiv2026

Intrinsic T-cell programming and immune spatial organization govern sex-biased tuberculosis immunity

Biological sex can profoundly influence the susceptibility to infectious diseases, yet the mechanisms behind the sex-dependent protective immunity against tuberculosis (TB) remain poorly understood. Here we show that sexually divergent immunity during chronic Mycobacterium tuberculosis (Mtb) infection is governed by both intrinsic T cell programming and pulmonary immune spatial organization. Using the Four Core Genotype (FCG) mouse model, adoptive cell transfer, pathway-specific blockade and B cell depletion, we demonstrate that CD4 T cells from gonadal females (XXF), but not XX males (XXM), confer enhanced protection to susceptible XY male recipients, independently of sex chromosome complement. Female-derived CD4 T cells reduce Mtb burdens while promoting pulmonary Bcl6 CD4 T cell responses and limiting neutrophilic inflammation. Mechanistically, blockade of CXCR3 or CD40L abrogates female-associated protection, with CD40L signaling additionally required to maintain organized pulmonary B cell structures. Although depletion of conventional B-2 B cells did not impair bacterial control, it disrupted tertiary lymphoid organization and revealed striking sex-specific functions of pulmonary B cells. Loss of B cell follicles (BCFs) primarily remodeled adaptive T cell responses in females, whereas in males it drove inflammatory myeloid activation, exaggerated neutrophil recruitment and widespread neutrophil extracellular trap (NET) formation. Together, these findings identify two complementary layers of sex-dependent immune regulation during TB: intrinsic programming of protective female CD4 T cells, and B cell-dependent spatial organization that coordinates adaptive immunity in females while restraining pathological inflammation in males. These findings establish immune tissue organization as a key determinant of the sexually dimorphic host defense during chronic TB.

immunology↗

bioRxiv2026

Single-cell RNA editing defines clinically relevant cellular states in chronic myelomonocytic leukemia

BackgroundChronic myelomonocytic leukemia (CMML) is a clinically heterogeneous myeloid malignancy with limited therapeutic options and suboptimal risk stratification. Although single-cell RNA sequencing has refined disease classification through gene expression profiling, post-transcriptional mechanisms--particularly adenosine-to-inosine (A-to-I) RNA editing--remain unexplored at single-cell resolution. We hypothesized that cell-specific RNA editing programs contribute to CMML heterogeneity and define distinct, clinically actionable cellular states in CMML. MethodsWe developed a single-cell-aware computational framework for high-confidence identification and quantification of RNA editing events. Candidate sites were detected at pseudo-bulk depth using stringent filters and subsequently quantified at single-cell resolution. The pipeline incorporated dual alignment, barcode correction, artifact removal, and exclusion of genomic variants to ensure specificity. We applied this framework to discovery and independent validation CMML cohorts. Editing-defined cellular states were identified by unsupervised clustering of single-cell editing profiles and evaluated for associations with clinical stage, TET2 status, survival, and response to hypomethylating agent (HMA) therapy. Regulatory mechanisms were assessed by analyzing ADAR1/ADAR2 expression and relationships between editing levels and target gene expression. ResultsWe identified 3,326 high-confidence A-to-I RNA editing sites and delineated reproducible editing-defined cellular states. A granulocyte-monocyte progenitor-like editing state (edClu1_sub0) aligned with an inflammatory, monocytic-biased transcriptional program and was significantly associated with adverse survival, advanced-stage disease and TET2-mutant CMML, supporting it as a high-risk biomarker-defined subpopulation. In contrast, states such as edClu3 and edClu6 were enriched in earlier-stage, TET2-wild-type CMML and correlated with improved outcomes. Editing-defined states demonstrated systematic remodeling following HMA therapy, indicating treatment-responsive post-transcriptional programs. The high-risk state exhibited elevated ADAR1 and reduced ADAR2 expression, suggesting enzyme-specific regulatory imbalance as a potential therapeutic vulnerability. Integrative analyses further nominated immune-related genes--including LAPTM5, CTSS, and CD83--as CMML-specific oncogenic RNA editing targets, with coordinated increases in editing and expression within the aggressive state. ConclusionsRNA editing represents a clinically informative and mechanistically relevant layer that refines CMML stratification at single-cell resolution, independent of gene expression. These findings provide a framework for integrating post-transcriptional regulation into precision oncology and highlight RNA editing signatures as biomarkers for risk assessment, treatment monitoring, and therapeutic targeting in hematologic malignancies.

cancer biology↗

bioRxiv2026

Galectin-1 Modulates Cell Adhesions, Caveolae, and Vascular Permeability in Kidney Endothelial Cells -- Insights from Proteomics, Phosphoproteomics, and Functional Studies

Microvascular inflammation and endothelial injury, triggered by interferon-gamma (IFN{gamma}), are hallmarks of antibody-mediated rejection (ABMR), the leading cause of premature kidney allograft loss. Glomerular extracellular matrix (ECM) remodeling and endothelial caveolae formation are important aspects of chronic ABMR. We found galectin-1, an immunomodulatory protein that interacts with the ECM, to be increased in the glomeruli of patients with ABMR, while its gene (LGALS1) expression was decreased by IFN{gamma} stimulation in glomerular endothelial cells. Mechanisms underlying endothelial dysfunction in ABMR, its links to ECM remodeling, and the role of immunomodulatory proteins such as galectin-1 remain incompletely understood. Here we studied the effects of galectin-1 modulation in glomerular microvascular endothelial cells (GMECs) in vitro. We demonstrated that galectin-1 was mainly expressed by glomerular endothelial cells in ABMR kidneys. To model key aspects of endothelial injury in ABMR, we knocked down LGALS1 in GMECs, followed by stimulation with IFN{gamma} and performed label-free quantitative proteomic and phosphoproteomic profiling of GMECs. Proteomic analysis identified 5446 proteins (FDR<0.01), of which 236, 827, and 267 were differentially expressed in response to LGALS1 knockdown, IFN{gamma} treatment, and their interaction, respectively (FDR<0.05). Both LGALS1 knockdown and the interaction between treatments significantly altered expression of adhesion proteins (FDR<0.01), particularly integrin subunit {beta}5, which was validated. Phosphoproteomic profiling identified 2727 phosphopeptides (FDR<0.01), with 28 that were differentially expressed across LGALS1 knockdown, IFN{gamma} treatment, and their interaction (P<0.01). Phosphorylation of CAVN1 and co-localization with its partner CAV1, critical for caveolar formation, were decreased in GMECs upon LGALS1 knockdown, IFN{gamma} stimulation, or both. In a microfluidic model of the glomerular microvasculature, addition of recombinant galectin-1 increased both endothelial permeability and secretion of proinflammatory cytokines, in LGALS1-silenced GMECs. Thus, endothelial signaling pathways regulated by inflammatory cues and galectin-1 contribute to endothelial injury and caveolae formation, highlighting galectin-1 as a potential therapeutic target in ABMR. SynopsisGalectin-1 is expressed by kidney glomerular endothelium. This study reveals that modifying galectin-1 in endothelial cells, in the presence of IFN{gamma} perturbs cytoskeletal, adhesion and caveolar proteins resulting in altered endothelial permeability. O_LILGALS1 knockdown increased ECM proteins and decreased interferon-induced proteins. C_LIO_LILGALS1 knockdown and IFN{gamma} treatment perturbed cell adhesion proteins such as ITGB5. C_LIO_LICAVN1 phosphorylation and colocalization with CAV1 decreased upon LGALS1 knockdown. C_LIO_LIExtracellular galectin-1 increased microvascular permeability in response to IFN{gamma}. C_LI

cell biology↗

bioRxiv2026

Reward-driven emergence of auditory pattern encoding in the primate motor system

The ability to anticipate rhythmic patterns is fundamental to human experience, enabling music appreciation, speech comprehension, and dancing in sync to music. How the brain learns to use acoustic information to guide motor behavior remains a key question, with its neural underpinnings and evolutionary origins debated, especially in non-human primates. Reward contingencies improve monkeys ability to synchronize with musical beats with near-human accuracy. However, humans and certain birds spontaneously synchronize with musical beats. Behavioural work in monkeys suggests that the brains reward system can encode rhythmic patterns if sufficiently reinforced, known as the intrinsic reward hypothesis. To investigate the neural mechanism of how the reward gates rhythmic pattern learning, we recorded neural activity from the globus pallidus interna (GPi) of a rhesus macaque during passive listening to auditory patterns. We found that GPis ability to encode auditory patterns in a monkey is shaped by reward association. Specifically, during passive listening (Experiment 1), with reward only at the end of each trial, GPi showed at most a weak response to the auditory tone patterns that was not evident in single neurons or population responses, ruling out spontaneous entrainment of motor activity to auditory patterns. When each tone was simultaneously accompanied by a liquid reward (Experiment 2), GPi showed clear responses to the tone patterns. To test if the tone responses persisted, the reward contingency was subsequently removed (Experiment 3). Strikingly, although the reward was delivered only at the trials end as in Experiment 1, GPi neurons continued to track the occurrence of the tones. Besides GPi, we also recorded single-neuron activity across the primary somatosensory (S1), primary motor (M1), dorsal premotor (PMd), supplementary motor (SMA), pre-supplementary motor (preSMA) cortices, and the medial geniculate body (MGB) of the same animal in experiments 1 and 2. We found that during passive listening (Experiment 1) with a reward only at the end of each trial, primarily the MGB, not motor areas, responded to the auditory tone patterns, ruling out spontaneous entrainment of motor activity to auditory patterns across the primate motor system. When each tone was simultaneously accompanied by a liquid reward (Experiment 2), all areas except S1 showed clear responses to the tone patterns. These findings suggest that while basic sensory processing of tone patterns occurs in the MGB, the GPi exhibits reward-driven encoding of auditory patterns that persists after reward withdrawal. This reorganization of neural responsiveness shows that the capacity for auditory association can be elicited in the motor system through appropriate motivational contexts.

neuroscience↗

bioRxiv2026

CRISPR-Cas9-induced genetic mosaicism in three species of the microcrustacean Daphnia

Genetic mosaicism can arise from in vivo CRISPR-Cas9 gene editing, especially in the embryos. This study evaluates the extent of genetic mosaicism resulted from CRISPR-Cas9-mediated knockout for 11 genes in the freshwater microcrustacean Daphnia magna, D. pulex, and D. sinensis. Based on extensive genotyping data of the asexually produced progenies of successfully edited females, we find strong evidence of mosaicism in 9 of these genes. The genotyping data also suggest the gene editing activity can take place as early as the one-cell embryo stage and extends into the 32-cell and later stages. This study establishes genetic mosaicism as an important feature of Cas9-mediated gene editing in Daphnia.

genomics↗

bioRxiv2025

The Goldilocks effect drives plant diversification on middle-aged Hawaiian islands

Islands are natural laboratories for studying dispersal, speciation, and extinction, yet the historical dynamics of many insular radiations remain poorly understood because of the difficulty aligning the tempo and mode of diversification with paleogeography during phylogenetic inference. We introduce a phylogenetic modeling framework, named TimeFIG, that combines data about species ranges and genetic variation with paleogeographic information to simultaneously infer divergence times, ancestral ranges, and historical diversification rates, without relying on fossils to time-calibrate the phylogeny. Applying TimeFIG to the spectacular radiation of Hawaiian Kadua (Rubiaceae) points to colonization of either modern Kaua'i or ancient now-eroded islands, with island isolation as the strongest correlate of dispersal, and with a tendency for net diversification to be highest on "middle-aged" islands. Modeling diversification within an explicit spatiotemporal context, while accounting for historical uncertainty regarding the timing and placement of phylogenetic and biogeographic events, enables the rigorous testing of foundational hypotheses in island biology and evolutionary theory for clades beyond Kadua.

evolutionary biology↗

bioRxiv2025

Detection of CRISPR-Cas-induced mutations in Daphnia

CRISPR-Cas9 has established itself as a robust tool for conducting loss of function gene research in emerging model species including the freshwater zooplankton Daphnia. However, sensitive detection of mutations, especially in genetic mosaic and pooled samples, remains a challenge. In this study we evaluate two of the most widely used mutation screening techniques, the T7 Endonuclease I (T7EI) assay and Fragment Analysis (FA) for their sensitivity, accuracy, and practical use in detecting CRISPR-induced indels in four targeted genes, DNMT3A, DNMT3B, PERIOD2, and DMRT1 in Daphnia magna. Here, we show that T7EI, although it offers a quick and cost-effective screening method, often produces false positives, especially when examining pooled samples. Conversely, FA facilitates detecting allele size differences at a fine resolution, reproducibility in detecting indels, and distinguishing zygosity and is more reliable as a method to detect mutation. Our comparative analyses convey the importance of carefully selecting the appropriate screening methods depending on research questions.

genetics↗

bioRxiv2025

Comparative Single-Cell Transcriptomics Uncovers Shared and Distinct Molecular Signatures in Cystic Fibrosis and Primary Ciliary Dyskinesia

RationalCystic Fibrosis (CF) and Primary Ciliary Dyskinesia (PCD) are both inherited respiratory disorders that result in impaired mucociliary clearance, and chronic sinopulmonary disease. Although the current approach to PCD management is extrapolated from CF care, both conditions arise from distinct genetic and molecular mechanisms. MethodsHere we performed a comparative transcriptomic analysis between CF and PCD to compare the cellular heterogeneity, molecular pathways and gene networks differences using publicly available sequencing data as well as those performed by our group. To explore gene regulatory networks, a pre-trained transformer model (scGPT) was fine-tuned using an integrated dataset, and differential attention analysis was conducted to identify genes and pathways with altered attention scores between the two conditions. ResultsThe comparative transcriptomic analysis revealed distinct molecular signatures between PCD and CF, which differed from normal cells. In ciliated cells, differential gene expression and pathway investigation highlighted the NRF2 pathways considerable overrepresentation in PCD compared to CF and healthy conditions. This observation was further supported by scGPT analysis, which revealed increased incoming attention to the NRF2 pathway markers. In secretory cells, PCD and CF exhibited increased immune and inflammatory signaling compared to controls. While similar inflammatory processes were active, results suggested a stronger inflammatory pattern in CF secretory cells compared to PCD and confirmed the activation of the unfolded protein response (UPR) pathway. ConclusionThese findings highlight the different molecular signatures between both conditions and the need for unique approaches to management in PCD compared to CF.

cell biology↗

bioRxiv2025

Machine Learning Analysis of Cilia-Driven Particle Transport Distinguishes Primary Ciliary Dyskinesia Cilia from Normal Cilia

RationalPrimary ciliary dyskinesia (PCD) is a genetic condition that results in dysmotile cilia and abnormal mucociliary clearance. Despite advances in understanding the pathogenesis of PCD, diagnosis continues to be challenging. Here we used feature-based machine learning and image-based deep learning to objectively quantify the directed particle transport of motile cilia and detect PCD-related cilia dysfunction. MethodsFluorescent microspheres were captured on cultured multiciliated cells using high-speed video microscopy as a proxy for motile cilia function. An interactive Jython script was designed to automatically detect, track and extract raw track metrics from videos. Data was subsequently analyzed to approximate a quantifiable and visual signature of ciliary transport through a custom-built Python Package, CiliaTracks. ResultsAirway epithelial cells were obtained from 14 individuals with genetically confirmed PCD, 10 healthy donors, and 2 patients with cystic fibrosis. A total of 602 videos (301 PCD and 301 non-PCD) were captured. Quantitative and visual analyses of fluorescent microsphere trajectories, including kinematic metrics and trajectory plots, revealed distinct motility profiles between PCD and non-PCD samples. Classical machine learning models and a convolutional neural network were employed to classify PCD using both modalities, demonstrating excellent accuracy of 95-97%, and the capacity to differentiate PCD from normal cells or cystic fibrosis. ConclusionCilia-propelled microsphere transport exhibits unique trajectory patterns in PCD, enabling differentiation from non-PCD samples. Machine learning provides an objective and accurate framework for characterizing ciliary dysfunction, offering potential as a diagnostic tool for PCD.

bioinformatics↗

bioRxiv2025

Structure-function relationship of alpha-synuclein fibrillar polymorphs derived from distinct synucleinopathies

The aggregation of the protein alpha-synuclein (Syn) is a common feature of multiple neurodegenerative diseases collectively called synucleinopathies, for which the pathobiology is not well understood. The different phenotypic characteristics of the synucleinopathies Parkinsons disease (PD), Dementia with Lewy Bodies (DLB) and Multiple System Atrophy (MSA) have been proposed to originate from the distinct structures adopted by Syn in its amyloid forms. Here, using covalent labeling and limited proteolysis coupled to mass spectrometry (LiP-MS) in vitro and in situ within neuronal cells and directly in native patient brain homogenates, we show that pathogenic Syn from distinct synucleinopathies (PD, DLB and MSA) are structurally different. Further, we found that fibrillar structural differences are associated with different fibril interactomes and neuronal responses. We discovered disease-specific ubiquitination patterns and turnover profiles for pathogenic Syn species, detected molecular pathways responding specifically to the uptake of different Syn fibrillar polymorphs, and identified a subset of the involved proteins as candidate direct interactors of Syn. In particular, components of the Ubiquitin-proteasomal System (UPS), including E3 ubiquitin ligases, chaperones, and Deubiquitinating proteins, showed disease/polymorph-specific interaction patterns, possibly accounting for different resistance of patient-derived Syn fibrils to degradation. Genetic modulation with CRISPR-based tools showed that members of the UPS degradation pathway (three E3 ligases: UBE3A, TRIM25, HUWE1 and the AAA+ ATPase VCP) reduced Syn inclusions, in a strain-specific manner. LiP-MS also identified sets of proteins with altered protease susceptibility in postmortem brain homogenates of PD, DLB, and MSA patients. These sets were largely disease-specific and included proteins altered in cells treated with fibrils derived from patients with the matching disease. Our findings provide insight into cellular processes involved in the accumulation and turnover of Syn pathogenic aggregates in PD, DLB and MSA in a disease specific manner and constitutes a resource of potential novel drug targets in these synucleinopathies.

systems biology↗

bioRxiv2025

Emergence of Genetic Sex Determination in an Environmentally Sex-Determined Animal

The evolution of genetic sex determination (GSD) from environmental sex determination (ESD) remains a fundamental issue in evolutionary biology. However, the mechanisms driving such a transition, particularly in its earliest stages, are largely unknown. Here, we report on a genetic variant in the ESD species, Daphnia pulex, in which structural variations and selection on chromosome have suppressed recombination. This suppression has facilitated the accumulation of antagonistic features of the two chromosome- haplotypes, resulting in heterozygosity and differentiation of the sex-determining gene Dfh on two haplotypes. Consequently, this process has driven the emergence of a mixed-mating system, in which sex determination is jointly regulated by genetic and environmental factors. Additionally, we detected ongoing divergence in chromosomal structure between the two haplotypes at the population level. These findings suggest that processes analogous to early sex-chromosome evolution are occurring in this ESD species, offering novel insights into the molecular mechanisms underlying the emergence of GSD.

evolutionary biology↗

bioRxiv2025

Development of a Nested Association Mapping (NAM) population for untangling complex traits in lentil (Lens culinaris Medik.)

Understanding the genetic basis of complex traits remains a key challenge in crop improvement. This study aimed to develop a structured, multi-parental mapping population to enhance the resolution of quantitative trait dissection, based on the hypothesis that a Nested Association Mapping (NAM) design would enable the detection of minor-effect loci often overlooked by traditional biparental or diversity panel-based approaches. A lentil (Lens culinaris Medik.) NAM population was developed by crossing the Canadian cultivar CDC Redberry with 32 diverse genotypes sourced globally from three major lentil-growing macro-environments: Northern temperate, Mediterranean, and South Asia. The resulting recombinant inbred lines were phenotyped for key phenological traits, days to emergence (DTE), flowering (DTF), and maturity (DTM), under field conditions, and genotyped using exome capture sequencing. Genome-wide association studies for DTF identified 14 significant loci across six chromosomes, including the known FTb locus and novel associations near AP3a, HUB2a, and PIF6 genes. These results demonstrate the utility of the NAM design in detecting both major and minor-effect loci that underlie complex trait variation. To our knowledge, this is the first publicly available NAM population in lentil. It provides a high-resolution, globally representative platform for trait discovery, pre-breeding, and collaborative genetic improvement of this nutritionally and agronomically important legume.

plant biology↗

bioRxiv2025

Large-scale bidirectional arrayed genetic screens identify OXR1 and EMC4 as modifiers of α-synuclein aggregation

In Parkinsons disease and other synucleinopathies, -synuclein (-Syn) misfolds and forms Ser129-phosphorylated aggregates (pSyn129). The factors controlling this process are largely unknown. Here, we used arrayed CRISPR-mediated gene activation and ablation to discover new pSyn129 modulators. Using quadruple-guide RNAs (qgRNAs) and Cas9, or an inactive Cas9 version fused to a synthetic transactivator, we ablated 2304 and activated 2428 human genes related to mitochondrial, trafficking and motility function in HEK293 cells. After exposure of cells to -Syn fibrils, pSyn129 signals were recorded by high-throughput fluorescence microscopy and aggregates were identified by image analysis. We found that pSyn129 was increased by activating the mitochondrial protein OXR1, which decreased ATP levels and altered the mitochondrial membrane potential. Instead, pSyn129 was reduced by ablation of the endoplasmic reticulum (ER)-associated protein EMC4, which enhanced ER-driven autophagic flux and lysosomal clearance. OXR1 activation preferentially modulated cellular reactions to fibrils derived from multiple system atrophy (MSA) patients, whereas EMC4 ablation broadly reduced pSyn129 across diverse -Syn polymorphs. These findings were confirmed in human iPSC-derived cortical and dopaminergic neurons, where OXR1 preferentially promoted somatic aggregation and EMC4 reduced both somatic and neuritic aggregates. These results uncover previously unrecognized roles for OXR1 and EMC4 in -Syn aggregation, thereby broadening our mechanistic understanding of synucleinopathies.

neuroscience↗

bioRxiv2024

TFAP2C and HNRNPK control mTOR cell metabolism and prion propagation

Heterogeneous Nuclear Ribonucleoprotein K (hnRNP K) is a limiting factor for prion propagation. However, little is known about the function of hnRNP K except that it is essential to cell survival. Here, we performed a synthetic-viability CRISPR ablation screen to identify epistatic interactors of HNRNPK. We found that deletion of Transcription Factor AP-2{gamma} (TFAP2C) suppressed the death of hnRNP K-depleted LN-229 and U-251 MG cells, whereas its overexpression hypersensitized cells to hnRNP K loss. HNRNPK ablation decreased cellular ATP, downregulated genes related to lipid and glucose metabolism, and enhanced autophagy. Co-occurrent deletion of TFAP2C reversed these effects, restoring transcriptional balance and alleviating energy deficiency. We linked HNRNPK and TFAP2C interaction to mTOR signaling, observing that HNRNPK ablation inhibited mTORC1 activity through downregulation of mTOR and Rptor, while TFAP2C overexpression enhanced mTORC1 downstream functions. In prion-infected cells, TFAP2C activation reduced prion levels and countered the increased prion propagation caused by HNRNPK suppression. Short-term pharmacological inhibition of mTOR also elevated prion levels and partially mimicked the effects of HNRNPK silencing. Our study identifies TFAP2C as a genetic interactor of HNRNPK, implicates their roles in mTOR metabolic regulation, and establishes a causative link between these activities and prion propagation.

cell biology↗

bioRxiv2024

Deep learning-driven imaging of cell division and cell growth across an entire eukaryotic life cycle

The life cycle of biomedical and agriculturally relevant eukaryotic microorganisms involves complex transitions between proliferative and non-proliferative states such as dormancy, mating, meiosis, and cell division. New drugs, pesticides, and vaccines can be created by targeting specific life cycle stages of parasites and pathogens. However, defining the structure of a microbial life cycle often relies on partial observations that are theoretically assembled in an ideal life cycle path. To create a more quantitative approach to studying complete eukaryotic life cycles, we generated a deep learning-driven imaging framework to track microorganisms across sexually reproducing generations. Our approach combines microfluidic culturing, life cycle stage-specific segmentation of microscopy images using convolutional neural networks, and a novel cell tracking algorithm, FIEST, based on enhancing the overlap of single cell masks in consecutive images through deep learning video frame interpolation. As proof of principle, we used this approach to quantitatively image and compare cell growth and cell cycle regulation across the sexual life cycle of Saccharomyces cerevisiae. We developed a fluorescent reporter system based on a fluorescently labeled Whi5 protein, the yeast analog of mammalian Rb, and a new High-Cdk1 activity sensor, LiCHI, designed to report during DNA replication, mitosis, meiotic homologous recombination, meiosis I, and meiosis II. We found that cell growth preceded the exit from non-proliferative states such as mitotic G1, pre-meiotic G1, and the G0 spore state during germination. A decrease in the total cell concentration of Whi5 characterized the exit from non-proliferative states, which is consistent with a Whi5 dilution model. The nuclear accumulation of Whi5 was developmentally regulated, being at its highest during meiotic exit and spore formation. The temporal coordination of cell division and growth was not significantly different across three sexually reproducing generations. Our framework could be used to quantitatively characterize other single-cell eukaryotic life cycles that remain incompletely described. An off-the-shelf user interface Yeastvision provides free access to our image processing and single-cell tracking algorithms.

cell biology↗

bioRxiv2024

Efficient CRISPR genome editing and integrative genomic analyses reveal the mosaicism of Cas-induced mutations and pleiotropic effects of scarlet gene in an emerging model system

Despite the revolutionary impacts of CRISPR-Cas gene editing systems, the effective and widespread use of CRISPR technologies in emerging model organisms still faces significant challenges. These include the inefficiency in generating heritable mutations at the organismal level, limited knowledge about the genomic consequences of gene editing, and an inadequate understanding of the inheritance patterns of CRISPR-Cas-induced mutations. This study addresses these issues by 1) developing an efficient microinjection delivery method for CRISPR editing in the microcrustacean Daphnia pulex; 2) assessing the editing efficiency of Cas9 and Cas12a nucleases, examining mutation inheritance patterns, and analyzing the local and global mutation spectrum in the scarlet mutants; and 3) investigating the transcriptomes of scarlet mutants to understand the pleiotropic effects of scarlet underlying their swimming behavior changes. Our reengineered CRISPR microinjection method results in efficient biallelic editing with both nucleases. While indels are dominant in Cas-induced mutations, a few on-site large deletions (>1kb) are observed, most likely caused by microhomology-mediated end joining repair. Knock-in of a stop codon cassette to the scarlet locus was successful, despite complex induced mutations surrounding the target site. Moreover, extensive germline mosaicism exists in some mutants, which unexpectedly produce different phenotypes/genotypes in their asexual progenies. Lastly, our transcriptomic analyses unveil significant gene expression changes associated with scarlet knock-out and altered swimming behavior in mutants, including several genes (e.g., NMDA1, ABAT, CNTNAP2) involved in human neurodegenerative diseases. This study expands our understanding of the dynamics of gene editing in the tractable model organism Daphnia and highlights its promising potential as a neurological disease model.

genomics↗