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You, Y.

Publications and source records attributed to You, Y..

At least 55 records · Page 3Linked to original sources

Phosphorylation at serine 214 correlates with tau seeding activity in an age-dependent manner in two mouse models for tauopathies and is required for tau transsynaptic propagation.

Pathological aggregation and propagation of hyperphosphorylated and aberrant forms of tau are critical features of the clinical progression of Alzheimers disease and other tauopathies. To better understand the correlation between these pathological tau species and disease progression, we profiled the temporal progression of tau seeding activity and the levels of various phospho- and conformational tau species in the brains of two mouse models of human tauopathies. Our findings indicate that tau seeding is an early event that occurs well before the appearance of AT8-positive NFT. Specifically, we observed that tau phosphorylation in serine 214 (pTau-Ser214) positively correlates to tau seeding activity during disease progression in both mouse models. Furthermore, we found that the histopathology of pTau-Ser214 appears much earlier and has a distinct pattern and compartmentalization compared to the pathology of AT8, demonstrating the diversity of tau species within the same region of the brain. Importantly, we also observed that preventing the phosphorylation of tau at Ser214 significantly decreases tau propagation in mouse primary neurons, and seeding activity in a Drosophila model of tauopathy, suggesting a role for this tau phosphorylation in spreading pathological forms of tau. Together, these results suggest that the diverse spectrum of soluble pathological tau species could be responsible for the distinct pathological properties of tau and that it is critical to dissect the nature of the tau seed in the context of disease progression.

neuroscience↗

Biochar Modulates Wheat Root Metabolome and Rhizosphere Microbiome in a Feedstock-dependent Manner

BackgroundBiochar is a multifunctional soil conditioner capable of enhancing soil health and plant productivity, but the underlying mechanisms remain elusive. Here we tackled this question using wheat as a model plant and through the lens of the rhizosphere, a vital soil-plant interface continuum. We systematically examined the effects of four types of biochar (corn stover, cattle manure, pine sawdust, or wheat straw) applied at two rates (0.25% or 2.5%, w/w). ResultsEmploying untargeted metabolomics and 16S rRNA gene sequencing, we revealed both common and unique modulating effects of the tested biochar treatments on wheat root metabolites and rhizosphere microbiome structure and functioning. Biochar modulated numerous metabolic pathways in wheat roots, where amino acid metabolism was the most common one, leading to cascade effects on the dynamics of a wide range of secondary metabolites, including many plant signaling molecules (e.g., flavonoid compounds, brassinosteroids) that are known to be involved in plant-microbe interactions. All biochar treatments increased rhizosphere microbial diversity, altered community composition, enhanced microbial interactions, and resulted in functional changes. Increased Burkholderiales (denitrifying bacteria) abundance and decreased Thermoplasmata (archaeal methanogens) abundance could explain biochars widely reported effects on nitrous oxide and methane mitigation, respectively. Biochar enhanced positive correlations among microbes and network complexity, particularly modularity, suggesting local adaptation through mutualism and/or synergism and the formation of modules of functionally interrelated taxa. A large number of diverse keystone taxa from both dominant and non-dominant phyla emerged after biochar treatments, including those known to be involved in methane, nitrogen, and sulfur cycling. Besides common alterations, treatment-specific alterations also occurred, and biochar type (i.e., feedstock choice) exerted greater influence than application rate. Wheat biochar applied at a 0.25% rate showed the strongest and distinct modulating effects, resulting in orchestrated changes in both root metabolites and rhizosphere microbiome, especially those relevant to plant-microbe interactions and likely beneficial to the host plant (e.g., upregulated biosynthesis of zeatin and down-regulated limonene degradation). ConclusionsOur work contributes to a mechanistic understanding of how biochar modulates the soil-plant continuum and provides new insights into the potential of top-down rhizosphere microbiome engineering through biochar-based reprogramming of root-microbe interactions.

microbiology↗

Optimization of gene knockout approaches and practical solutions to sgRNA selection challenges in hPSCs with inducible Cas9 system

RationaleCRISPR/Cas9 has been extensively used to knock out genes, allowing the study of genetic loss-of-function in human pluripotent stem cells (hPSCs). However, the current use of the Cas9-sgRNA plasmid or iCas9 system for gene editing in hPSCs has resulted in limited and inconsistent editing efficiency, as well as labor-intensive work. Additionally, identifying single-guide RNAs (sgRNAs) with high cleavage efficiency and distinguishing them from ineffective ones, which efficiently induce frameshift INDELs (Indels and Deletions) but fail to eliminate target proteins expression, are major challenges in gene knockout experiments. MethodsThis study addresses above issues using an optimized doxycycline-induced spCas9-expressing hPSCs (hPSCs-iCas9) system. We initially developed this system by optimizing a number of parameters to maximize INDELs introducing efficiency in hPSCs-iCas9 cells. The INDELs determined by this system were then compared to predicted scores from three cleavage efficiency scoring algorithms to validate the algorithms accuracy and consistency. Furthermore, we conducted gene knockout using a set of sgRNAs targeting different exons of the ACE2 gene to achieve approximately 80% INDELs for each targeting locus. Western blotting was then performed to detect ACE2 protein expression levels, enabling the identification of potentially ineffective sgRNAs. ResultsSeveral critical factors, including cell tolerance to nucleofection stress, sgRNA stability, nucleofection frequency, and the cell-to-sgRNA ratio, were found to have significant impact on editing efficiency in hPSCs-iCas9. Fine-tuning these parameters markedly improved this efficiency, resulting in up to 93% INDELs for single gene knockout. The three scoring algorithms exhibited significant differences or even conflicts in scoring cleavage efficiency. Through comparing experimental observations to predicted scores, we discovered that the Benchling algorithm outperformed the other two in terms of accuracy and consistency. Furthermore, a sgRNA targeting exon 2 of ACE2 gene was quickly identified as ineffective, as evidenced by the edited cells pool containing 80% INDELs while ACE2 protein expression retained unchanged detected by Western blot. ConclusionThe findings of this study offer valuable insights into the optimal design of gene knockout experiments in hPSCs and provide practical solutions to sgRNA selection challenges for gene editing.

cell biology↗

Early-life Microbiome-Derived HCA Enhances Type 3 Immunity via FXR-dependent m6A RNA methylation

The gut microbiome plays a crucial role in the development of intestinal immunity during early life, but the underlying mechanisms remain largely unknown. Here, we found oxygen consumption in neonatal rats by S. boulardii accelerated the colonization of the microbiome and the development of type 3 immunity, which protected against S. typhimurium. Microbiome maturation increased the abundance of microbiome-encoded bile salt hydrolase (BSH) genes and elevated the levels of Hyocholic acid (HCA). HCA promotes the development of {gamma}{delta}T and type 3 innate lymphoid cell (ILC3) by sustaining the stability of Rorc mRNA via the FXR-WTAP- N6-methyl-adenosine (m6A) axis. L. reuteri, a bacterium encoding BSH, was enriched by oxygen consumption in the intestine and promoted intestinal type 3 immunity. However, inhibition of BSH blocks the L. reuteri-induced development of intestinal type 3 immunity. These results reveal the role of microbiome-derived HCA in the regulation of intestinal type 3 immunity during early life.

microbiology↗

Comprehensive mapping and modelling of the rice regulome landscape unveils the regulatory architecture underlying complex traits

Unraveling the regulatory mechanisms that govern complex traits is pivotal for advancing crop improvement. Here we present a comprehensive regulome atlas for rice (Oryza sativa), charting the chromatin accessibility across 23 distinct tissues from three representative varieties. Our study uncovers 117,176 unique open chromatin regions (OCRs), accounting for [~]15% of the rice genome, a notably higher proportion compared to previous reports in plants. Integrating RNA-seq data from matched tissues, we confidently predict 59,075 OCR-to-gene links, with enhancers constituting 69.54% of these associations, including many known enhancer-to-gene links. Leveraging this resource, we re-evaluate genome-wide association study results and discover a previously unknown function of OsbZIP06 in seed germination, which we subsequently confirm through experimental validation. We optimize deep learning models to decode regulatory grammar, achieving robust modeling of tissue-specific chromatin accessibility. This approach allows to predict cross-variety regulatory dynamics from genomic sequences, shedding light on the genetic underpinnings of cis-regulatory divergence and morphological disparities between varieties. Overall, our study establishes a foundational resource for rice functional genomics and precision molecular breeding, providing valuable insights into regulatory mechanisms governing complex traits.

genomics↗

Spatiotemporally resolved transcriptome atlas of developing mouse placenta reveals mechanisms of embryonic lethality.

Proper placentation is fundamental to the growth and viability of the maturing embryo. However, a thorough grasp of the spatial organization of cell types, their interactions, and gene expression patterns along the maternal-fetal function during placental development remains incomplete. Here, we utilized Stereo-seq to construct the spatiotemporal transcriptomic atlas of the mouse placenta (STAMP) spanning embryonic (E) days 9.5 to 18.5 at single cell resolution (https://db.cngb.org/stomics/stamp/). This resource delineates spatially resolved cellular dynamics and gene expression patterns across placental and maternal compartments. We identified distinct glycogen trophoblast cell (GC) subclusters, mapped their developmental trajectories, and uncovered transcriptional transitions accompanying their migration from the junctional zone to the maternal decidua from E12.5 onward. In a defective placentation model with perinatal lethality, GCs abnormally persisted at E18.5 with excessive glycogen and reduced degradation metabolites in placenta and fetal liver, indicating impaired glycogen breakdown. Maternal glucose supplementation restored glucose levels and rescued fetal survival, underscoring GC-mediated metabolic support as critical for viability. Together, this study provides a comprehensive spatiotemporal placental atlas and demonstrates that GC-mediated glycogen metabolism is essential for sustaining fetal viability.

developmental biology↗

Reduction of chemokine CXCL9 expression by omega-3 fatty acids via ADP-ribosylhydrolase ARH3 in MIN6 insulin-producing cells

Type 1 diabetes (T1D) results from the autoimmune destruction of the insulin producing {beta} cells of the pancreas. Omega-3 fatty acids protect {beta} cells and reduce the incident of T1D. However, how omega-3 fatty acids act on {beta} cells is not well understood. We have shown that omega-3 fatty acids reduce pro-inflammatory cytokine-mediated {beta}-cell apoptosis by upregulating the expression of the ADP-ribosylhydrolase ARH3. Here, we further investigate the {beta}-cell protection mechanism by ARH3 by performing siRNA of its gene Adprhl2 in MIN6 insulin-producing cells followed by treatment with a cocktail of the pro-inflammatory cytokines IL-1{beta} + IFN-{gamma} + TNF-, and proteomics analysis. ARH3 regulated proteins from several pathways related to the nucleus (splicing, RNA surveillance and nucleocytoplasmic transport), mitochondria (metabolic pathways) and endoplasmic reticulum (protein folding). ARH3 also regulated the levels of cytokine-signaling proteins related to the antigen processing and presentation, and chemokine-signaling pathway. We further studied the role of ARH in regulating the chemokine CXCL9. We confirmed that ARH3 reduces the cytokine-induced expression of CXCL9 by ELISA. We also found that CXCL9 expression is regulated by omega-3 fatty acids. In conclusion, we showed that omega-3 fatty acids regulate CXCL9 expression via ARH3, which might have a role in protecting {beta} cells from immune attack and preventing T1D development.

cell biology↗

Unraveling the role of γδ T cells in the pathogenesis of an oncogenic avian herpesvirus

Mareks disease virus (MDV) is an oncogenic alphaherpesvirus that causes deadly T cell lymphomas in chickens. MDV is highly cell associated which allows the virus to evade antibody-mediated virus neutralization. Therefore, T cell-mediated immune responses are thought to be crucial for combating this deadly pathogen. In chickens, gamma delta ({gamma}{delta}) T cells represent a major population with up to 50% of all peripheral T cells. However, their role in MDV pathogenesis and tumor formation remains poorly understood. To investigate the role of {gamma}{delta} T cells in MDV pathogenesis, we infected genetically modified chickens that lack {gamma}{delta} T cells (TCR C{gamma}-/-) with very virulent MDV. Strikingly, disease and tumor incidence were highly increased in the absence of {gamma}{delta} T cells, indicating that {gamma}{delta} T cells play an important role in the immune response against MDV. In the absence of {gamma}{delta} T cells, virus replication was increased by up to 89-fold in the thymus and spleen, both potential sites of T cell transformation. Taken together, our data provide the first evidence that {gamma}{delta} T cells play an important role in restricting MDV replication, pathogenesis and tumors caused by this deadly pathogen. Author Summary{gamma}{delta} T cells are the most abundant T cells in chickens, but their role in fighting pathogens remains poorly understood. Mareks disease virus (MDV) is an important veterinary pathogen, causes one of the most frequent cancers in animals and is used as a model for virus-induced tumor formation. Our study revealed that {gamma}{delta} T cells play a crucial role in combating MDV, as disease and tumor incidence was drastically increased in the absence of these cells. {gamma}{delta} T cells restricted virus replication in the key lymphoid organs, thereby decreasing the likelihood of causing tumors and disease. This study provides novel insights into the role of {gamma}{delta} T cells in the pathogenesis of this highly oncogenic virus.

microbiology↗

Systematic comparison of sequencing-based spatial transcriptomic methods

Recent advancements of sequencing-based spatial transcriptomics (sST) have catalyzed significant advancements by facilitating transcriptome-scale spatial gene expression measurement. Despite this progress, efforts to comprehensively benchmark different platforms are currently lacking. The extant variability across technologies and datasets poses challenges in formulating standardized evaluation metrics. In this study, we established a collection of reference tissues and regions characterized by well-defined histological architectures, and used them to generate data to compare six sST methods. We highlighted molecular diffusion as a variable parameter across different methods and tissues, significantly impacting the effective resolutions. Furthermore, we observed that spatial transcriptomic data demonstrate unique attributes beyond merely adding a spatial axis to single-cell data, including an enhanced ability to capture patterned rare cell states along with specific markers, albeit being influenced by multiple factors including sequencing depth and resolution. Our study assists biologists in sST platform selection, and helps foster a consensus on evaluation standards and establish a framework for future benchmarking efforts that can be used as a gold standard for the development and benchmarking of computational tools for spatial transcriptomic analysis.

genomics↗

cisDynet: an integrated platform for modeling gene-regulatory dynamics and networks

Chromatin accessibility sequencing has been widely used for uncovering genetic regulatory mechanisms and inferring gene regulatory networks. However, effectively integrating large-scale chromatin accessibility datasets has posed a significant challenge. This is due to the lack of a comprehensive end-to-end solution, as many existing tools primarily emphasize data pre-processing and overlook downstream analyses. To bridge this gap, we have introduced cisDynet, a holistic solution that combines streamlined data pre-processing using Snakemake and R functions with advanced downstream analysis capabilities. cisDynet excels in conventional data analyses, encompassing peak statistics, peak annotation, differential analysis, motif enrichment analysis and more. Additionally, it allows to perform sophisticated data exploration such as tissue-specific peak identification, time-course data fitting, integration of RNA-seq data to establish peak-to-gene associations, constructing regulatory networks, and conducting enrichment analysis of GWAS variants. As a proof of concept, we applied cisDynet to re-analyze the comprehensive ATAC-seq datasets across various tissues from the ENCODE project. The analysis successfully delineated tissue-specific open chromatin regions (OCRs), established connections between OCRs and target genes, and effectively linked these discoveries with 1,861 GWAS variants. Furthermore, cisDynet was instrumental in dissecting the time-course open chromatin data of mouse embryonic development, revealing the dynamic behavior of OCRs over time and identifying key transcription factors governing differentiation trajectories. In summary, cisDynet offers researchers a user-friendly solution that minimizes the need for extensive coding, ensures the reproducibility of results, and greatly simplifies the exploration of epigenomic data. Graphical AbstractcisDynet enables the exploration of the cis-regulatory chromatin dynamics and networks. It offers a streamlined preprocessing pipeline built on Snakemake, along with an R package for advanced downstream data analysis and visualization. It is free to access on GitHub (https://github.com/tzhu-bio/cisDynet). HighlightsO_LIThe cisDynet enables comprehensive and efficient processing of chromatin accessibility data, including pre-processing, advanced downstream data analysis and visualization. C_LIO_LIcisDynet provides a range of analytical features such as processing of time course data, co-accessibility analysis, linking OCRs to genes, building regulatory networks, and GWAS variant enrichment analysis. C_LIO_LIcisDynet simplifies the identification of tissue/cell type-specific OCRs or dynamic OCR changes over time and facilitates the integration of RNA-seq data to depict temporal trajectories. C_LI

bioinformatics↗

ERK signaling drives evolutionary expansion of the mammalian cerebral cortex

The molecular basis for cortical expansion during evolution remains largely unknown. Here, we found that FGF-extracellular signal-regulated kinase (ERK) signaling promotes the self-renewal and expansion of cortical radial glial (RG) cells. Furthermore, FGF-ERK signaling induces Bmp7 expression in cortical RG cells, which increases the length of the neurogenic period. We demonstrate that ERK signaling and SHH signaling mutually inhibit each other in cortical RG cells. We also provide evidence that ERK signaling is elevated in cortical RG cells during development and evolution. We conclude that the evolutionary expansion of the mammalian cortex, notably in human, is driven by ERK-BMP7-GLI3R signaling pathway in cortical RG cells, which participates in a positive feedback loop through antagonizing SHH signaling. We also propose that the molecular basis for cortical evolutionary dwarfism, exemplified by the lissencephalic mouse which originated from a larger and gyrencephalic ancestor, is due to mouse cortical RG cells receiving higher SHH signaling that antagonizes ERK signaling.

neuroscience↗

Enhanced microglial dynamics and paucity of tau seeding in the amyloid plaque microenvironment contributes to cognitive resilience in Alzheimer 's disease

Asymptomatic Alzheimers disease (AsymAD) describes the status of subjects with preserved cognition but with identifiable Alzheimers disease (AD) brain pathology (i.e. A{beta}-amyloid deposits, neuritic plaques, and neurofibrillary tangles) at autopsy. In this study, we investigated the postmortem brains of a cohort of AsymAD cases to gain insight into the underlying mechanisms of resilience to AD pathology and cognitive decline. Our results showed that AsymAD cases exhibit an enrichment of core plaques and decreased filamentous plaque accumulation, as well as an increase in microglia surrounding this last type. In AsymAD cases we found less pathological tau aggregation in dystrophic neurites compared to AD and tau seeding activity comparable to healthy control subjects. We used spatial transcriptomics to further characterize the plaque niche and found autophagy, endocytosis, and phagocytosis within the top upregulated pathways in the AsymAD plaque niche, but not in AD. Furthermore, we found ARP2, an actin-based motility protein crucial to initiate the formation of new actin filaments, increased within microglia in the proximity of amyloid plaques in AsymAD. Our findings support that the amyloid-plaque microenvironment in AsymAD cases is characterized by microglia with highly efficient actin-based cell motility mechanisms and decreased tau seeding compared to AD. These two mechanisms can potentially provide protection against the toxic cascade initiated by A{beta} that preserves brain health and slows down the progression of AD pathology.

neuroscience↗

Regulation of bacterial stringent response by an evolutionary conserved ribosomal protein L11 methylation

Lysine and arginine methylation is an important regulator of enzyme activity and transcription in eukaryotes. However, little is known about this covalent modification in bacteria. In this work, we investigated the role of methylation in bacteria. By reanalyzing a large phyloproteomics dataset from 48 bacterial strains representing 6 phyla, we found that almost a quarter of the bacterial proteome is methylated. Many of these methylated proteins are conserved across diverse bacterial lineages, including those involved in central carbon metabolism and translation. Among the proteins with the most conserved methylation sites is ribosomal protein L11 (bL11). bL11 methylation has been a mystery for five decades, as the deletion of its methyltransferase PrmA causes no cell growth defects. A comparative proteomics analysis combined with a guanosine polyphosphate assay of the {Delta}prmA mutant in Escherichia coli revealed that bL11 methylation is important for stringent response signaling. Moreover, we show that the {Delta}prmA mutant has an abnormal polysome profile, suggesting a role in ribosomal homeostasis during stationary growth phase. Overall, our investigation demonstrates that the evolutionary conserved bL11 methylation is important for stringent response signaling and ribosomal homeostasis. ImportanceProtein methylation in bacteria was first identified over sixty years ago. Since then, its functional role has been identified for only a few proteins. To better understand the functional role of methylation in bacteria, we analyzed a large phyloproteomics dataset encompassing 48 diverse bacteria. Our analysis revealed that ribosomal proteins are often methylated at conserved residues, suggesting that methylation of these sites may have a functional role in translation. Further analysis revealed that methylation of ribosomal protein L11 is important for stringent response signaling and ribosomal homeostasis.

systems biology↗

Microbial Responses to Biochar Soil Amendment and Influential Factors: A Three-level Meta-analysis

Biochar is a multifunctional soil conditioner capable of enhancing soil health and crop production while reducing greenhouse gas emissions. Understanding how soil microbes respond to biochar amendment is a vital step towards precision biochar application. Here, we synthesized 3899 observations of 24 microbial responses from 61 primary studies, applied a three-level mixed-effects model to estimate biochar effects, and evaluated the importance of biochar characteristics (feedstock, pyrolysis temperature), soil properties (pH, C:N, cation exchange capacity, bulk or rhizosphere), and treatment protocols (application rate, fertilization, duration, field or laboratory). Biochar significantly boosts microbial abundance (microbial biomass carbon > CFU), nitrite reductase gene (nirS), the activity of C- and N-cycling enzymes (dehydrogenase > cellulase > urease > invertase), and potential nitrification rate. Biochar characteristics, soil properties, and treatment protocols strongly determine the direction and extent of microbial response changes. Feedstock, pyrolysis temperature, application rate, and soil pH are important predictors most frequently included in the final models. Our study highlights the promise of purpose-driven biochar production and application such that biochar production parameters can be tuned to elicit the desired microbial responses and application protocols could be optimized to invoke multiple benefits. It also underlines current knowledge gaps and future research needs. SynopsisMeta-analysis reveals overall effect sizes of soil microbial responses to biochar amendment and the most influential factors, highlighting the potential of purpose-driven precision biochar towards sustainable agriculture.

ecology↗

Multi-omics and Pharmacological Characterization of Patient-derived Glioma Cell Lines

Glioblastoma (GBM) is the most common brain tumor and is currently incurable. Primary GBM cultures are widely used tools for screening potentially therapeutic drugs; however, there is a lack of genomic and pharmacological characterization of these primary GBM cultures. Here, we collected 52 patient-derived glioma cell (PDGC) lines and characterized them through whole- genome sequencing (WGS), RNA-seq, and drug response screening. We identified three molecular subtypes among PDGCs: mesenchymal (MES), proneural (PN), and oxidative phosphorylation (OXPHOS). Upon profiling the responses of PDGCs to 214 drugs, we found that the PN subtype PDGCs were sensitive to tyrosine kinase inhibitors, whereas the OXPHOS subtype PDGCs were sensitive to histone deacetylase inhibitors, oxidative phosphorylation inhibitors, and HMG-CoA reductase inhibitors. PN and OXPHOS subtype PDGCs stably formed tumors in vivo upon intracranial transplantation into immunodeficient mice, while most MES subtype PDGCs were incapable of tumorigenesis in vivo. In addition, profiling and follow-up investigations showed that the serum-free culture system used for PDGCs enriched and propagated rare MYC/MYCN- amplified glioma cells. Our study provides a resource for understanding primary glioma cell cultures and aiding clinical translation. SignificanceOur study provides a resource for patient-derived glioma cell lines (PDGCs) on transcriptome, genome, drug response, and tumorigenic abilities. PDGCs are categorized into PN, MES, and OXPHOS subtypes, with MES-subtype PDGCs incapable of tumorigenesis in vivo. Notably, the serum-free culture system for PDGCs enriches glioma cells with MYC/MYCN amplification.

cancer biology↗

Regional vulnerability in a neurodegenerative disease: Delineating SCA1 CNS and muscle therapeutic targets using a conditional mutant ATXN1 mouse

Spinocerebellar ataxia type 1 (SCA1) is a fatal neurodegenerative disease caused by an expanded polyglutamine tract in the widely expressed ATXN1 protein. To elucidate anatomical regions and cell types that underlie mutant ATXN1-induced disease phenotypes, we developed a floxed conditional knockout mouse model (f-ATXN1146Q/2Q) having mouse Atxn1 coding exons replaced by human exons encoding 146 glutamines. F-ATXN1146Q/2Q mice manifest SCA1-like phenotypes including motor and cognitive deficits, wasting, and decreased survival. CNS contributions to disease were revealed using ATXN1146Q/2Q;Nestin-Cre mice, that showed improved rotarod, open field and Barnes maze performances. Striatal contributions to motor deficits were examined using f-ATXN1146Q/2Q;Rgs9-Cre mice. Mice lacking striatal ATXN1146Q/2Q had improved rotarod performance late in disease. Muscle contributions to disease were revealed in f-ATXN1146Q/2Q;ACTA1-Cre mice which lacked muscle pathology and kyphosis seen in f-ATXN1146Q/2Q mice. Kyphosis was not improved in f-ATXN1146Q/2Q;Nestin-Cre mice. Thus, optimal SCA1 therapeutics will require targeting mutant ATXN1 toxic actions in multiple brain regions and muscle.

neuroscience↗

Network analysis reveals strain-dependent response to misfolded tau aggregates

Mouse genetic backgrounds have been shown to modulate amyloid accumulation and propagation of tau aggregates. Previous research into these effects has highlighted the importance of studying the impact of genetic heterogeneity on modeling Alzheimers disease. However, it is unknown what mechanisms underly these effects of genetic background on modeling Alzheimers disease, specifically tau aggregate-driven pathogenicity. In this study, we induced tau aggregation in wild-derived mice by expressing MAPT (P301L). To investigate the effect of genetic background on the action of tau aggregates, we performed RNA sequencing with brains of 6-month-old C57BL/6J, CAST/EiJ, PWK/PhJ, and WSB/EiJ mice (n=64). We also measured tau seeding activity in the cortex of these mice. We identified three gene signatures: core transcriptional signature, unique signature for each wild-derived genetic background, and tau seeding-associated signature. Our data suggest that microglial response to tau seeds is elevated in CAST/EiJ and PWK/PhJ mice. Together, our study provides the first evidence that mouse genetic context influences the seeding of tau. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/526029v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1c99217org.highwire.dtl.DTLVardef@965522org.highwire.dtl.DTLVardef@1af4105org.highwire.dtl.DTLVardef@d5ea98_HPS_FORMAT_FIGEXP M_FIG C_FIG SUMMARYSeeding of tau predates the phosphorylation and spreading of tau aggregates. Acri and colleagues report transcriptomic responses to tau and elevated tau seeds in wild-derived mice. This paper creates a rich resource by combining genetics, tau biosensor assays, and transcriptomics.

neuroscience↗

Establishment of cell transcriptional identity during seed germination

Germination involves highly dynamic transcriptional programs as the cells of seeds reactivate and express the functions necessary to establish in the environment. Individual cell types have distinct roles within the embryo, so must therefore have cell-type specific gene expression and gene regulatory networks. We can better understand how the functions of different cell types are established and contribute to the embryo by determining how cell-type specific transcription begins and changes through germination. Here we describe a temporal analysis of the germinating Arabidopsis embryo at single-cell resolution. We define the highly dynamic cell-type specific patterns of gene expression and how these relate to changing cellular function as germination progresses. Underlying these are unique gene regulatory networks and transcription factor activity. We unexpectedly discover that most embryo cells transition through the same initial transcriptional state early in germination, after which cell-type specific gene expression is established. Furthermore, our analyses support previous findings that the earliest events leading to the induction of embryo growth take place in the vasculature. Overall, our study constitutes a general framework to characterise Arabidopsis cell states through embryo growth, allowing investigation of different genotypes and other plant species whose seed strategies may differ.

plant biology↗