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Henry, A.

Publications and source records attributed to Henry, A..

18 recordsLinked to original sources

Unique mushroom spine morphology signature in cocaine relapse ensembles in rat nucleus accumbens core

Fos-expressing neuronal ensembles in nucleus accumbens (NAc) are selectively activated by drug-associated cues and shown to play a causal role in drug-cue memories. Many unique molecular and cellular alterations have been identified in these ensembles and thought to be components of an engram encoding the memory; however, spine morphology alterations on these ensembles have rarely been examined. Here, we examined alterations of identified spine types on Fos-expressing neurons in NAc core that were selectively activated by drug-associated cues during cocaine relapse. We combined Fos immunolabeling along with viral-based sparse GFP labeling to identify Fos-positive and Fos-negative neurons with distinguishable dendrites and quantified spine composition, densities and interspine intervals (ISIs) for all spine types, and head and neck diameters of mushroom spines. ISIs and head and neck diameters of mushroom spines were altered on Fos-positive (versus Fos-negative) neurons activated during cue-induced cocaine relapse. Critically, these alterations were not found on Fos-positive neurons activated by exposure to a novel context on relapse test day, despite having identical cocaine self-administration histories. Based on previous work, this suggests these alterations were not simply due to acute activation of a randomly selected set of neurons on test day, but rather they were altered specifically on neurons selectively activated during cocaine self-administration training and then reactivated during relapse. Stubby spines and immature spines, including filopodia and thin spines, were not altered. Altogether, these mushroom spine alterations describe a unique spine morphology signature for a drug-cue memory in NAc neuronal ensembles selectively activated during cocaine relapse.

neuroscience↗

CSF glucosylsphingosine is a central readout of GCase impairment across genetic and sporadic Parkinson’s disease

Parkinsons disease (PD) risk converges on lysosomal biology, including reduced activity of glucocerebrosidase (GCase), encoded by GBA1. Glucosylsphingosine (GlcSph), a toxic deacylated glycosphingolipid and established target engagement biomarker in Gaucher disease, is difficult to quantify in cerebrospinal fluid (CSF) because of low abundance and isomeric interference. We optimized and qualified targeted LC-MS/MS assays for GlcSph in CSF and plasma and measured GlcSph and GCase activity (4-MU assay) in participants from the Parkinsons Progression Markers Initiative (PPMI), including GBA1 and LRRK2 mutation carriers with and without PD, sporadic PD, and healthy controls. Group level analyses showed higher levels of CSF and plasma GlcSph in GBA1 heterozygous variant carriers independent of disease status, [~]120% (p<0.0001) and [~]61% (p<0.0001), respectively, with CSF elevations reflecting allelic dosage and, to a lesser degree, variant severity. Notably, elevated CSF GlcSph was observed not only in carriers of pathogenic GBA1 mutations but also in individuals harboring common GBA1 risk variants. CSF GlcSph was also elevated by [~]30% in sporadic PD (p=0.002) and by [~]40% LRRK2 mutation carriers (p=0.0003), indicating shared central GCase pathway perturbation across PD subtypes. CSF and plasma GlcSph levels showed poor concordance across groups with the exception of the GBA-PD group, supporting the hypothesis that central and peripheral GCase pathway dysfunction arise through distinct biological mechanisms. Together, these findings establish CSF GlcSph as a sensitive biomarker of central GCase pathway impairment and may support its use as a pharmacodynamic and target engagement biomarker for therapeutics targeting GCase in PD. More broadly, CSF GlcSph may enable identification of biologically defined GCase-pathway dysfunction beyond genetically defined GBA1-associated PD, with potential implications for patient stratification in future disease-modifying trials.

Molecular Biology↗

Tomato pollen tube integrity is critical for pollen function at high temperature and is controlled by RALF signaling.

Reproductive success at high temperature (HT) depends on the ability of pollen to germinate a pollen tube that delivers sperm for double fertilization. We recently found that Solanum lycopersicum (tomato) cultivars capable of setting fruit at HT produce pollen tubes that continue to grow under heat stress. Our present goal is to define the molecular basis of thermotolerant pollen tube growth using quantitative live imaging, transcriptomic and proteomic profiling, and genetic analysis. We found that pollen tube integrity - the ability to maintain an intact tip during germination and elongation - was the pollen performance parameter that distinguished thermotolerant cultivars. We identified the components of the Rapid Alkalinization Factor (RALF) pollen tube integrity signal transduction pathway in tomato and found that RALF peptides repress germination at control temperature and that signaling is antagonized by HT. Loss of a single RALF peptide changes pollen tube cell wall pectin distribution and enhances pollen tube integrity at HT in thermotolerant Heinz, revealing that RALF signaling regulates thermotolerant pollen tube growth and establishing a molecular framework for improving reproductive heat-resilience in crop plants.

plant biology↗

Endothelial Colony-Forming Cell Transcriptomic Profiling in CT-defined Coronary Artery Disease from the BioHEART-CT Study Implicate CCBE1 in Mitochondrial Dysfunction-associated Atherosclerosis

BackgroundEndothelial dysfunction is an early contributor to atherosclerosis. This study combined CT imaging of coronary artery disease (CAD) and patient-dervied endothelial colony-forming cells (ECFCs) transcriptional profiling to investigate potential mechanisms underlying endothelial dysfunction in atherosclerosis. MethodsTwenty-six individuals with CT-defined CAD and eighteen non-CAD controls were included in the Discovery Cohort for bulk RNA sequencing and transcriptomic analysis of ECFCs. Differential gene expression analysis was performed, and candidate genes were selected based on logFC and p-value. Candidate genes were carried forward for gene expression validation using quantitative real-time PCR (qRT-PCR) in a Validation Cohort. Mitochondrial reactive oxygen species (mROS) production and mitochondrial mass were assessed using multi-colour flow cytometry. Functional validation of the top candidate was conducted in using human umbilical vein endothelial cells (HUVECs) using loss-of-function genetic approach. Expression Quantitative Trait Loci (eQTL)-association analysis was conducted using genotype data from the BioHEART-CT cohort. ResultsPairwise analysis identified six differentially expressed protein-coding genes in CAD ECFCs: CCBE1 (Collagen and Calcium Binding EGF Domain-Containing 1), SPINT2, CRISPLD1, PIEZO2, EPB41L3, and AC005943.1. qRT-PCR in the Validation Cohort confirmed significantly higher CCBE1 expression in CAD patients. Individuals with relative CCBE1 fold change expression>10 had a 2.8-fold increase in the log-odds ratio of CT-defined CAD. CAD ECFCs displayed elevated mROS and mitochondrial mass. CCBE1 knockdown in HUVECs reduced mROS and mitochondrial mass without affecting proliferation or permeability, but shifted cells into a metabolically elevated state, marked by increased ATP production, respiration and glycolysis. CCBE1 cis-eQTLs were associated with increased odds of CAD in the BioHEART-CT cohort. ConclusionsCCBE1 expression in ECFCs was higher in patients with CT-defined CAD versus non-CAD. Quantitative assessment of transcript levels supported a causal relationship between greater CCBE1 expression and CAD burden and risk, and functional experiments on CCBE1 knockdown demonstrated improved mitochondrial function in human endothelial cells. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=138 SRC="FIGDIR/small/670989v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@4e609aorg.highwire.dtl.DTLVardef@1a85810org.highwire.dtl.DTLVardef@12d97cdorg.highwire.dtl.DTLVardef@494ab3_HPS_FORMAT_FIGEXP M_FIG C_FIG Novelty and SignificanceO_ST_ABSWhat is Known?C_ST_ABSO_LIThe endothelium plays a critical role in vascular health and susceptibility to atherosclerosis. C_LIO_LIMitochondrial dysfunction has been implicated in atherosclerosis, but its role and mechanism in individual susceptibility to CAD in humans is not known. C_LI What New Information Does This Article Contribute?O_LINovel approach integrating CT imaging with ECFC functional data to link vascular structure with endothelial biology ex vivo. C_LIO_LIPatients with CT-defined CAD had 3.6-fold higher CCBE1 expression compared to non-CAD within the Validation Cohort. C_LIO_LICis-eQTL-association analysis revealed increased odds of CAD. C_LIO_LICCBE1 knockdown improved mitochondrial function in human endothelial cells. C_LIO_LITogether, these 4 lines of evidence point to a novel and causal role for CCBE1 in human CAD. C_LI

cell biology↗

The unfolded protein response in grapevine: abiotic and biotic stresses induce the expression of VvbZIP60, VvbZIP17, VvBIP3, and VvIRE1

A wide range of stresses can lead to the accumulation of unfolded or misfolded proteins in the lumen of the endoplasmic reticulum (ER), a condition known as ER stress. To restore proteostasis, eukaryotic cells activate a signaling network called the unfolded protein response (UPR). In Vitis vinifera, two arms of the UPR have been identified: the IRE1/bZIP60 arm and the bZIP17 arm. Notably, no putative ortholog of bZIP28 has been found in V. vinifera, whereas this is the case for Brassicaceae species. We demonstrated that VvbZIP60 undergoes unconventional splicing upon treatment with dithiothreitol (DTT) and tunicamycin (TM), both classical ER stress inducers. Moreover, after testing several abiotic factors, we observed a strong transcriptional activation of UPR-related genes in response to heat and osmotic stresses, as well as copper exposure. Grapevine is also subject to a broad range of microbial challenges, including pathogens such as Plasmopara viticola and Botrytis cinerea. Both pathogens triggered UPR genes activation in grapevine leaves and berries. Interestingly, VvbZIP17 was also upregulated in green berries, a developmental stage associated with strong basal resistance to B. cinerea. Collectively, these findings suggest that the IRE1/bZIP60 and bZIP17 arms of the UPR are not only structurally conserved in grapevine but are also transcriptionally responsive to a variety of abiotic and biotic stresses. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=144 SRC="FIGDIR/small/669611v2_ufig1.gif" ALT="Figure 1"> View larger version (63K): org.highwire.dtl.DTLVardef@13e0b15org.highwire.dtl.DTLVardef@49967dorg.highwire.dtl.DTLVardef@1371bfborg.highwire.dtl.DTLVardef@10e09b2_HPS_FORMAT_FIGEXP M_FIG C_FIG

plant biology↗

Environment-dependent selection impacts heritable developmental stability and trait canalization in rice

Canalization, or the maintenance of trait values regardless of environmental or genetic variability, is fundamentally important for maintaining developmental stability. While this concept was described decades ago, we still know relatively little about how canalization is influenced by environmental stress, how it is shaped by natural selection, and the genetic underpinnings of canalization. In this study, we examined natural selection on microenvironmental canalization in rice (Oryza sativa) in wet and dry field conditions. We measured developmental stability in genetically identical replicates obtained from geographically widespread Indica and Japonica rice accessions, providing precise estimates of canalization in thousands of plants. We found that drought stress decreased canalization, showing that stress can increase instability. We also found evidence that canalization can evolve, given that canalization of several traits was heritable and under selection. We further uncovered specific genes underlying canalization, with genetic mapping and functional genetic experiments showing that the bZIP transcription factor-encoding gene OsTGA5/rTGA2.3, which is part of a module that balances stress response and plant growth, regulates canalization of several traits in an environment-dependent manner. At a genome-wide scale, canalization was associated with lower gene expression stochasticity at an earlier life stage, indicating that expression variation can reduce canalization and increase instability. Trait canalization was also positively correlated to temperature at accessions source environments, suggesting that selection on canalization can vary among environments. Overall, our study provides novel insights into the molecular genetic basis of environmental differences in developmental stability and how it might be shaped by selection. SignificanceMechanisms stabilizing organismal development in response to genetic mutations or environmental stressors (canalization) have been reported for numerous animals and plants, but their underlying genetic basis and whether they may be shaped by selection remain unclear. Here, we report patterns of drought-induced trait decanalization in populations of rice (Oryza sativa) grown in field environments. We determined that trait canalization is heritable and can evolve separately from trait means. We identified the gene OsTGA5, part of a regulatory module shaping trade-offs between growth and stress responses, as impacting trait canalization. Plants with less noisy gene expression and evolving in warmer environments display greater developmental stability, contributing to the notion that canalization in rice may be adaptive.

evolutionary biology↗

Modeling and Prediction of Body Segment Inertial Properties of Sheep from Tomographic Imaging

Estimation of body segment inertial properties (BSIPs) is a crucial step in development of inverse dynamics models. The goal of this study was to develop predictive models to estimate the mass, center of mass, and inertia tensor of the hindlimbs of sheep using easily obtainable morphometric data. In addition, this study presents a more comprehensive and repeatable method for defining each hindlimb body segment when calculating BSIPs from CT data. CT scans from 16 sheep of varying age, weight, sex, and phenotype were used to develop predictive models to estimate the BSIPs of the pelvis, thigh, crus, metatarsus, and pastern segments. The predictive models developed enable investigators to create inverse dynamics models of sheep hindlimbs. These models are particularly informative and expand the use of ovine models of human musculoskeletal disease.

bioengineering↗

Genetic basis of an adaptive polymorphism controlling butterfly silver iridescence

Identifying the genes and mutations that drive phenotypic variation and which are subject to selection is crucial for understanding evolutionary processes. Mormon Fritillary butterflies (Speyeria mormonia) exhibit a striking wing color polymorphism throughout their range: typical morphs bear silver spots on their ventral surfaces, and can co-occur with unsilvered morphs displaying a dull coloration1. Through genome-wide association studies in two polymorphic populations, we fine-map this difference in silvering to the 3 region of the transcription factor gene optix. The expression of optix is confined to the unsilvered regions that surround the spots, and these patterns are transformed to a silver identity upon optix RNAi knockdown, implicating optix as a repressor of silver scales in this butterfly. We show that the unsilvered optix haplotype shows signatures of recent selective sweeps, and that this allele is shared with the monomorphic, unsilvered species Speyeria hydaspe, suggesting that introgressions facilitate the exchange of variants of adaptive potential across species. Remarkably, these findings parallel the role of introgressions and cis-regulatory modulation of optix in shaping the aposematic red patterns of Heliconius butterflies2-7, a lineage that separated from Speyeria 45 million years ago8. The genetic basis of adaptive variation can thus be more predictable than often presumed, even for traits that appear divergent across large evolutionary distances. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/628425v1_ufig1.gif" ALT="Figure 1"> View larger version (112K): org.highwire.dtl.DTLVardef@5d2a9borg.highwire.dtl.DTLVardef@982c74org.highwire.dtl.DTLVardef@8e90b3org.highwire.dtl.DTLVardef@1bddf3c_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

evolutionary biology↗

Connecting single neuron transcriptomes to the projectome in mouse visual cortex

The mammalian brain is composed of diverse neuron types that play different functional roles. Recent single-cell RNA sequencing approaches have led to a whole brain taxonomy of transcriptomically-defined cell types, yet cell type definitions that include multiple cellular properties can offer additional insights into a neurons role in brain circuits. While the Patch-seq method can investigate how transcriptomic properties relate to the local morphological and electrophysiological properties of cell types, linking transcriptomic identities to long-range projections is a major unresolved challenge. To address this, we collected coordinated Patch-seq and whole brain morphology data sets of excitatory neurons in mouse visual cortex. From the Patch-seq data, we defined 16 integrated morphoelectric-transcriptomic (MET)-types; in parallel, we reconstructed the complete morphologies of 300 neurons. We unified the two data sets with a multi-step classifier, to integrate cell type assignments and interrogate cross-modality relationships. We find that transcriptomic variations within and across MET-types correspond with morphological and electrophysiological phenotypes. In addition, this variation, along with the anatomical location of the cell, can be used to predict the projection targets of individual neurons. We also shed new light on infragranular cell types and circuits, including cell-type-specific, interhemispheric projections. With this approach, we establish a comprehensive, integrated taxonomy of excitatory neuron types in mouse visual cortex and create a system for integrated, high-dimensional cell type classification that can be extended to the whole brain and potentially across species.

neuroscience↗

Simplified fecal community transplant restores Clostridioides difficile colonization resistance to antibiotic perturbed murine communities

Fecal communities transplanted into individuals can eliminate recurrent Clostridioides difficile infection (CDI) with high efficacy. However, this treatment is only used once CDI becomes resistant to antibiotics or has recurred multiple times. We sought to investigate whether a fecal community transplant (FCT) pre-treatment could be used to prevent CDI altogether. We treated male C57BL/6 mice with either clindamycin, cefoperazone, or streptomycin, and then inoculated them with the microbial community from untreated mice before challenging with C. difficile. We measured colonization and sequenced the V4 region of the 16S rRNA gene to understand the dynamics of the murine fecal community in response to the FCT and C. difficile challenge. Clindamycin-treated mice became colonized with C. difficile but cleared it naturally and did not benefit from the FCT. Cefoperazone-treated mice became colonized by C. difficile, but the FCT enabled clearance of C. difficile. In streptomycin-treated mice, the FCT was able to prevent C. difficile from colonizing. Then we diluted the FCT and repeated the experiments. Cefoperazone-treated mice no longer cleared C. difficile. However, streptomycin-treated mice colonized with 1:102 dilutions resisted C. difficile colonization. Streptomycin-treated mice that received a FCT diluted 1:103, C. difficile colonized but later was cleared. In streptomycin-treated mice, inhibition of C. difficile was associated with increased relative abundance of a group of bacteria related to Porphyromonadaceae and Lachnospiraceae. These data demonstrate that C. difficile colonization resistance can be restored to a susceptible community with a FCT as long as it complements the missing populations. ImportanceAntibiotic use, ubiquitous with the healthcare environment, is a major risk factor for Clostridioides difficile infection (CDI), the most common nosocomial infection. When C. difficile becomes resistant to antibiotics, a fecal microbiota transplant from a healthy individual can effectively restore the gut bacterial community and eliminate the infection. While this relationship between the gut bacteria and CDI is well established, there are no therapies to treat a perturbed gut community to prevent CDI. This study explored the potential of restoring colonization resistance to antibiotic-induced susceptible gut communities. We described the effect gut bacteria community variation has on the effectiveness of a fecal community transplant for inhibiting CDI. These data demonstrated that communities susceptible to CDI can be supplemented with fecal communities but the effectiveness depended on the structure of the community following the perturbation. Thus, a simplified bacterial community may be able to recover colonization resistance to patients treated with antibiotics.

microbiology↗

Strong genotype by environment interactions in the rice Global MAGIC population across seedling stage drought

Crop adaptation is required to sustainably increase the rate of yield gains to meet projected future needs under the challenging conditions of climate change and competition for resources. Future adaptation will likely need to harness both highly polygenic traits and genotype-by-environment interactions (GxE), the study of which is aided by complex recombinant populations. We used the diverse Oryza sativa Global Multiparent Advanced Generation InterCross (MAGIC) population to study the genetic architecture and contributions of seedling emergence, establishment, and development to yield components under dry-direct seeding and seedling stage drought across three growing seasons. Dry-direct seeding is an establishment practice that has the potential to reduce methane emissions, water use, and labor demands for rice farmers, but increases the possibility of early-season drought conditions. We found substantial evidence for large roles of environmental variation and GxE in controlling trait variation. Maintenance of shoot growth during seedling stage drought was positively correlated with crown root number and both directly and indirectly influenced agronomic traits. Other than the major green revolution locus sd1, most allelic effects were conditionally neutral (affecting trait values in some environments but not others) and most alleles had their strongest effect in an environmental extreme. This discovery is both a challenge and a potential opportunity: with variable genetic architecture, selection in any one environment may not result in stable trait gains across environments. However, conditionally neutral GxE is a potential route to sustainable yield stability through allele pyramiding.

genetics↗

Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation

The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Inter-individual differences in microbial composition are found to be much larger than intra-individual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples may be of environmental origin, showing the importance of including environmental controls or several lines of biomolecular evidence.

microbiology↗

Evolutionary systems biology reveals patterns of rice adaptation to drought-prone agro-ecosystems

Rice was domesticated around 10,000 years ago and has developed into a staple for half of humanity. The crop evolved and is currently grown in stably wet and intermittently dry agro-ecosystems, but patterns of adaptation to differences in water availability remain poorly understood. While previous field studies have evaluated plant developmental adaptations to water deficit, adaptive variation in functional and hydraulic components, particularly in relation to gene expression, has received less attention. Here, we take an evolutionary systems biology approach to characterize adaptive drought resistance traits across roots and shoots. We find that rice harbors heritable variation in molecular, physiological, and morphological traits that is linked to higher fitness under drought. We identify modules of co-expressed genes that are associated with adaptive drought avoidance and tolerance mechanisms. These expression modules showed evidence of polygenic adaptation in rice subgroups harboring accessions that evolved in drought-prone agro-ecosystems. Fitness-linked expression patterns had predictive value and allowed us to identify the drought-adaptive nature of optimizing photosynthesis and interactions with arbuscular mycorrhizal fungi. Taken together, our study provides an unprecedented, integrative view of rice adaptation to water-limited field conditions.

plant biology↗

Coupled myovascular expansion directs growth and regeneration of the neonatal mouse heart

BackgroundHeart regeneration requires multiple cell types to enable cardiomyocyte (CM) proliferation. How these cells interact to create growth niches is unclear. Here we profile proliferation kinetics of cardiac endothelial cells (CECs) and CMs in the neonatal mouse heart and find that they are spatiotemporally coupled. Methods and ResultsWe show that coupled myovascular expansion during cardiac growth or regeneration is dependent upon VEGF-VEGFR2 signaling, as genetic deletion of Vegfr2 from CECs or inhibition of VEGFA abrogates both CEC and CM proliferation. Repair of cryoinjury displays poor spatial coupling of CEC and CM proliferation. Boosting CEC density after cryoinjury with virus encoding Vegfa enhances regeneration. Using Mendelian randomization, we demonstrate that circulating VEGFA levels are positively linked with human myocardial mass, suggesting that Vegfa can stimulate human cardiac growth. ConclusionsOur work demonstrates the importance of coupled CEC and CM expansion and reveals a myovascular niche that may be therapeutically targeted for heart regeneration.

developmental biology↗

Genome-wide association study provides new insights into the genetic architecture and pathogenesis of heart failure

Heart failure (HF) is a leading cause of morbidity and mortality worldwide1. A small proportion of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide association studies (GWAS) have yielded only limited insights, leaving the observed heritability of HF largely unexplained2-4. We report the largest GWAS meta-analysis of HF to-date, comprising 47,309 cases and 930,014 controls. We identify 12 independent variant associations with HF at 11 genomic loci, all of which demonstrate one or more associations with coronary artery disease (CAD), atrial fibrillation, or reduced left ventricular function suggesting shared genetic aetiology. Expression quantitative trait analysis of non-CAD-associated loci implicate genes involved in cardiac development (MYOZ1, SYNPO2L), protein homeostasis (BAG3), and cellular senescence (CDKN1A). Using Mendelian randomisation analysis we provide new evidence supporting previously equivocal causal roles for several HF risk factors identified in observational studies, and demonstrate CAD-independent effects for atrial fibrillation, body mass index, hypertension and triglycerides. These findings extend our knowledge of the genes and pathways underlying HF and may inform the development of new therapeutic approaches.

genetics↗

LRRK2 kinase inhibitors induce a reversible effect in the lungs of non-human primates with no measurable pulmonary deficits

Putative gain-of-function mutations in leucine-rich repeat kinase 2 (LRRK2), resulting in increased kinase activity and cellular toxicity, are a leading genetic cause of Parkinsons disease (PD). Hence, there is strong interest in developing LRRK2 kinase inhibitors as a disease-modifying therapy. Published reports that repeat dosing with two LRRK2 kinase inhibitors (GNE-7915 and GNE-0877) induce histopathological changes in the lung of non-human primates Fuji et al. 2015 (1) raised concerns about potential safety liability of LRRK2 kinase inhibitors. In the present study, we sought to determine whether previously observed effects in the lung: (a) represent on-target pharmacology, but with the potential for margin of safety, (b) are reversible upon drug withdrawal, and (c) are associated with pulmonary function deficits. To this end, we evaluated the histopathological effects, toxicokinetics and target inhibition of three structurally diverse LRRK2 kinase inhibitors, GNE-7915 (30 mg/kg, BID, as a positive control), MLi-2 (15 and 50 mg/kg, QD) and PFE-360 (3 and 6 mg/kg, QD) following 2 weeks of dosing in non-human primates. Subsets of animals dosed with GNE-7915 or MLi-2 were evaluated after 2-week dose-free periods. All three LRRK2 kinase inhibitors induced mild cytoplasmic vacuolation of type II pneumocytes, as reported previously, confirming an on-target effect of these compounds. Interestingly, despite lower doses of both PFE-360 and MLi-2 producing nearly complete inhibition of LRRK2 kinase activity in the brain as assessed by levels of pS935-LRRK2, histopathological changes in lung were absent in animals treated with low-dose PFE-360 and observed only sporadically in the low-dose MLi-2 group. The lung effect was fully reversible at 2 weeks post-dosing of GNE-7915. In a second study of identical dosing with MLi-2 and GNE-7915, no deficits were observed in a battery of translational pulmonary functional tests. In aggregate, these results do not preclude the development of LRRK2 kinase inhibitors for clinical investigation in Parkinsons disease.

pharmacology and toxicology↗

Classification of electrophysiological and morphological types in mouse visual cortex

Understanding the diversity of cell types in the brain has been an enduring challenge and requires detailed characterization of individual neurons in multiple dimensions. To profile morpho-electric properties of mammalian neurons systematically, we established a single cell characterization pipeline using standardized patch clamp recordings in brain slices and biocytin-based neuronal reconstructions. We built a publicly-accessible online database, the Allen Cell Types Database, to display these data sets. Intrinsic physiological and morphological properties were measured from over 1,800 neurons from the adult laboratory mouse visual cortex. Quantitative features were used to classify neurons into distinct types using unsupervised methods. We establish a taxonomy of morphologically- and electrophysiologically-defined cell types for this region of cortex with 17 e-types and 35 m-types, as well as an initial correspondence with previously-defined transcriptomic cell types using the same transgenic mouse lines.

neuroscience↗

The organization of intracortical connections by layer and cell class in the mouse brain

The mammalian cortex is a laminar structure composed of many cell types densely interconnected in complex ways. Recent systematic efforts to map the mouse mesoscale connectome provide comprehensive projection data on interareal connections, but not at the level of specific cell classes or layers within cortical areas. We present here a significant expansion of the Allen Mouse Brain Connectivity Atlas, with [~]1,000 new axonal projection mapping experiments across nearly all isocortical areas in 49 Cre driver lines. Using 13 lines selective for cortical layer-specific projection neuron classes, we identify the differential contribution of each layer/class to the overall intracortical connectivity patterns. We find layer 5 (L5) projection neurons account for essentially all intracortical outputs. L2/3, L4, and L6 neurons contact a subset of the L5 cortical targets. We also describe the most common axon lamination patterns in cortical targets. Most patterns are consistent with previous anatomical rules used to determine hierarchical position between cortical areas (feedforward, feedback), with notable exceptions. While diverse target lamination patterns arise from every source layer/class, L2/3 and L4 neurons are primarily associated with feedforward type projection patterns and L6 with feedback. L5 has both feedforward and feedback projection patterns. Finally, network analyses revealed a modular organization of the intracortical connectome. By labeling interareal and intermodule connections as feedforward or feedback, we present an integrated view of the intracortical connectome as a hierarchical network.

neuroscience↗