Biology subjects

Yan, X.

Publications and source records attributed to Yan, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

A high-continuity and annotated reference genome of allotetraploid Siberian wildrye (Elymus sibiricus L., Poaceae: Triticeae)

Elymus sibiricus L. (Siberian wildrye, Es), a species belonging to the wheat tribe, is extensively employed as forage and for the reclamation of degraded grasslands within the Qinghai-Tibet Plateau (QTP). This study provides a high-quality reference genome assembly for the allotetraploid Es, which is composed of 14 pseudomolecules with the total genome size of 6.57 Gb. Our finding suggest that large-scale bursts of retrotransposons are critical for the genome expansion of Es. We discovered a translocation event between the Es4H and Es6H chromosomes with a low frequency of combination. Phylogenetic analyses of 90 Es accessions and 25 diploid accessions representing proposed ancestors from various habitats revealed the existence of four distinct populations. We further provided support for the hypothesis that the QTP is the center of origin and genetic diversity for Es. Collectively, our study offers valuable insights into the evolution of Es, as well as providing genomic resources for genetic enhancement in the Elymus genus and wheat tribe.

genomics↗

bioRxiv2024

Instruction Alters The Influence Of Allocentric Landmarks In A Reach Task

Allocentric landmarks have an implicit influence on aiming movements, but it is not clear how an explicit instruction (to aim relative to a landmark) influences reach accuracy and precision. Here, 12 participants performed a task with two instruction conditions (egocentric vs. allocentric), but with similar sensory and motor conditions. Participants fixated gaze near the centre of a display aligned with their right shoulder while a target stimulus briefly appeared alongside a visual landmark in one visual field. After a brief mask/memory delay the landmark then re-appeared at a different location (same or opposite visual field), creating an ego/allocentric conflict. In the egocentric condition, participants were instructed to ignore the landmark and point towards the remembered location of the target. In the allocentric condition, participants were instructed to remember the initial target location relative to the landmark and then reach relative to the shifted landmark (same/opposite visual field). To equalize motor execution between tasks, participants were instructed to anti-point (point to the visual field opposite to the remembered target) on 50 % of the egocentric trials. Participants were more accurate, precise, and quicker to react in the allocentric condition, especially when pointing to the opposite field. We also observed a visual field effect, where performance was worse overall in the right visual field. These results suggest that when egocentric and allocentric cues conflict, explicit use of the visual landmark provides better reach performance than reliance on noisy egocentric signals. Such instructions might aid rehabilitation when the egocentric system is compromised by disease or injury. HighlightsO_LI12 participants reached to remembered targets in the presence of a visual landmark C_LIO_LIParticipants were instructed to ignore, or point relative to, the landmark C_LIO_LIThe landmark instruction improved reaction time, precision, and accuracy C_LIO_LIThese effects were stronger when pointing was cued toward the opposite visual field C_LIO_LIKnowledge of these rules might be used to enhance performance or in rehabilitation C_LI

neuroscience↗

bioRxiv2024

FLASH Irradiation Regulates IFN-β induction by mtDNA via Cytochrome c Leakage

Ultrahigh dose rate radiotherapy (FLASH-RT) is under intensive investigation for its biological benefits. The mechanisms underlying its ability to spare normal tissues while suppress tumor growth still remain controversial. Here we reveal that compared to the low dose rate electron irradiation (0.36 Gy/s), FLASH electron irradiation at 61 or 610 Gy/s enhances the cytochrome c leakage from mitochondria in human breast cells MCF-10A, which elicits substantial caspase activation, suppresses both the cytosolic mitochondrial DNA (mtDNA) accumulation and IFN-{beta} secretion. Besides, the deletion of mtDNA severely decreases the radiation-induced cGAS-STING activation. Conversely, the cytochrome c leakage in carcinoma cells MDA-MB-231 post electron irradiation is limited, especially for the case of FLASH irradiation, resulting in less cytosolic cytochrome c but stronger cGAS-STING activation than those in MCF-10A cells. The enhanced difference of cytochrome c leakage between cancer cells and normal cells post FLASH irradiation indicates a potential mechanism of FLASH effect by regulating the apoptotic and inflammatory pathway.

biophysics↗

bioRxiv2024

Targeting G9a translational mechanism of SARS-CoV-2 pathogenesis for multifaceted therapeutics of COVID-19 and its sequalae

By largely unknown mechanism(s), SARS-CoV-2 hijacks the host translation apparatus to promote COVID-19 pathogenesis. We report that the histone methyltransferase G9a noncanonically regulates viral hijacking of the translation machinery to bring about COVID-19 symptoms of hyperinflammation, lymphopenia, and blood coagulation. Chemoproteomic analysis of COVID-19 patient peripheral mononuclear blood cells (PBMC) identified enhanced interactions between SARS-CoV-2-upregulated G9a and distinct translation regulators, particularly the N6-methyladenosine (m6A) RNA methylase METTL3. These interactions with translation regulators implicated G9a in translational regulation of COVID-19. Inhibition of G9a activity suppressed SARS-CoV-2 replication in human alveolar epithelial cells. Accordingly, multi-omics analysis of the same alveolar cells identified SARS-CoV-2-induced changes at the transcriptional, m6A-epitranscriptional, translational, and post-translational (phosphorylation or secretion) levels that were reversed by inhibitor treatment. As suggested by the aforesaid chemoproteomic analysis, these multi-omics-correlated changes revealed a G9a-regulated translational mechanism of COVID-19 pathogenesis in which G9a directs translation of viral and host proteins associated with SARS-CoV-2 replication and with dysregulation of host response. Comparison of proteomic analyses of G9a inhibitor-treated, SARS-CoV-2 infected cells, or ex vivo culture of patient PBMCs, with COVID-19 patient data revealed that G9a inhibition reversed the patient proteomic landscape that correlated with COVID-19 pathology/symptoms. These data also indicated that the G9a-regulated, inhibitor-reversed, translational mechanism outperformed G9a-transcriptional suppression to ultimately determine COVID-19 pathogenesis and to define the inhibitor action, from which biomarkers of serve symptom vulnerability were mechanistically derived. This cell line-to-patient conservation of G9a-translated, COVID-19 proteome suggests that G9a inhibitors can be used to treat patients with COVID-19, particularly patients with long-lasting COVID-19 sequelae.

immunology↗

bioRxiv2024

The blast effector Pwl2 is a virulence factor that modifies the cellular localisation of host protein HIPP43 to suppress immunity.

The rice blast fungus Magnaporthe oryzae secretes a battery of effector proteins to facilitate host infection. Among these effectors, Pwl2 was first identified as a host specificity determinant for infection of weeping lovegrass (Eragrostis curvula) and is also recognised by the barley Mla3 resistance gene. However, its biological activity is not known. Here we show that PWL2 expression is regulated by the Pmk1 MAP kinase during cell-to-cell movement by M. oryzae at plasmodesmata (PD)-containing pit field sites. Consistent with its regulation, we provide evidence that Pwl2 binds to a barley heavy metal-binding isoprenylated protein HIPP43, which results in its displacement from plasmodesmata. Transgenic barley lines overexpressing either PWL2 or HIPP43 exhibit attenuated immune responses and increased disease susceptibility. By contrast, a Pwl2SNDEYWY mutant that does not interact with HIPP43, fails to alter the PD localisation of HIPP43. Targeted deletion of three copies of PWL2 in M. oryzae results in a{Delta} pwl2 mutant showing gain-of-virulence to weeping lovegrass and barley Mla3 lines, but also a reduction in severity of blast disease on susceptible host plants. Taken together, our results provide evidence that Pwl2 is a virulence factor that acts by suppressing host immunity through perturbing the plasmodesmatal deployment of HIPP43.

plant biology↗

bioRxiv2024

Intra-condensate demixing of TDP-43 inside stress granules generates pathological aggregates

Cytosolic aggregation of the nuclear protein TDP-43 is associated with many neurodegenerative diseases, but the triggers for TDP-43 aggregation are still debated. Here, we demonstrate that TDP-43 aggregation requires a double event. One is up-concentration in stress granules beyond a threshold, and the other is oxidative stress. These two events collectively induce intra-condensate demixing, giving rise to a dynamic TDP-43 enriched phase within stress granules, which subsequently transitions into pathological aggregates. Mechanistically, intra-condensate demixing is triggered by local unfolding of the RRM1 domain for intermolecular disulfide bond formation and by increased hydrophobic patch interactions in the C-terminal domain. By engineering TDP-43 variants resistant to intra-condensate demixing, we successfully eliminate pathological TDP-43 aggregates in cells. We conclude that up-concentration inside condensates and simultaneous exposure to environmental stress could be a general pathway for protein aggregation, with intra-condensate demixing constituting a key intermediate step.

cell biology↗

bioRxiv2023

PNLDC1 catalysis and postnatal germline function are required for piRNA trimming, LINE1 silencing, and spermatogenesis in mice

PIWI-interacting RNAs (piRNAs) play critical and conserved roles in transposon silencing and gene regulation in the animal germline. Two distinct piRNA populations are present during mouse spermatogenesis: pre-pachytene piRNAs in fetal/neonatal testes and pachytene piRNAs in adult testes. PNLDC1 is required for both pre-pachytene piRNA and pachytene piRNA 3 end maturation in multiple species. However, whether PNLDC1 is the bona fide piRNA trimmer and the physiological role of 3 trimming of two distinct piRNA populations in spermatogenesis remain unclear. Here, by inactivating Pnldc1 exonuclease activity in vitro and in mice, we reveal that PNLDC1 trimmer activity is required for both pre-pachytene piRNA and pachytene piRNA 3 end trimming and male fertility. Furthermore, conditional inactivation of Pnldc1 in postnatal germ cells causes LINE1 transposon de-repression and spermatogenic arrest in mice. This indicates that pachytene piRNA trimming, but not pre-pachytene piRNA trimming, is essential for mouse germ cell development and transposon silencing. Our findings highlight the potential of inhibiting germline piRNA trimmer activity as a potential means for male contraception.

developmental biology↗

bioRxiv2023

DeepEnzyme: a robust deep learning model for improved enzyme turnover number prediction by utilizing features of protein 3D Structures

Turnover numbers (kcat), which indicate an enzymes catalytic efficiency, have a wide range of applications in fields including protein engineering and synthetic biology. Experimentally measuring the enzymes kcat is always time-consuming. Recently, the prediction of kcat using deep learning models has mitigated this problem. However, the accuracy and robustness in kcat prediction still needs to be improved significantly, particularly when dealing with enzymes with low sequence similarity compared to those within the training dataset. Herein, we present DeepEnzyme, a cutting-edge deep learning model that combines the most recent Transformer and Graph Convolutional Network (GCN) architectures. To improve the prediction accuracy, DeepEnzyme was trained by leveraging the integrated features from both sequences and 3D structures. Consequently, our model exhibits remarkable robustness when processing enzymes with low sequence similarity compared to those in the training dataset by utilizing additional features from high-quality protein 3D structures. DeepEnzyme also makes it possible to evaluate how point mutations affect the catalytic activity of the enzyme, which helps identify residue sites that are crucial for the catalytic function. In summary, DeepEnzyme represents a pioneering effort in predicting enzymes kcat values with superior accuracy and robustness compared to previous algorithms. This advancement will significantly contribute to our comprehension of enzyme function and its evolutionary patterns across species.

bioinformatics↗

bioRxiv2023

Distinct functions of the kinesin-9 family in mammalian motile cilia

Ciliary beat and intraflagellar transport (IFT) depend on dynein and kinesin motors. Kinesin-9 family members Kif6 and Kif9 are implicated in ciliary motilities across protists and mammals. How they function and whether they act redundantly, however, remain unclear. Here, we show that they play distinct roles in mammals. Kif6 forms puncta that move bidirectionally without or with IFT-B particles along axonemes, whereas Kif9 is immobilized on ciliary central apparatus. Only Kif6 binds to and glides microtubules, and the activities are self-inhibited. Kif6 deficiency in mice impairs directional ciliary beat across ependymal tissues and cerebrospinal fluid flow, resulting in severe hydrocephalus and high mortality, whereas Kif9 deficiency induces mild hydrocephalus without obviously defective ciliary beat and life span. Both Kif6-/- and Kif9-/- males are infertile but show respectively oligozoospermia with poor sperm motility and defective forward motion of sperms. These results suggest Kif6 as a motile cilia-specific IFT motor and Kif9 as a central apparatus regulator.

cell biology↗

bioRxiv2023

Time-dependent Interaction Modification Generated from Plant-soil Feedback

Pairwise interactions between species can be modified by other community members, leading to emergent dynamics contingent on community composition. Despite the prevalence of such higher-order interactions, little is known about how they are linked to the timing and order of species arrival. We generate population dynamics from a mechanistic plant-soil feedback model, then apply a general theoretical framework to show that the modification of a pairwise interaction by a third plant depends on its germination phenology. These time-dependent interaction modifications emerge from concurrent changes in plant and microbe populations and are strengthened by higher overlap between plants associated microbiomes. The interaction between this overlap and the specificity of microbiomes further determines plant coexistence. Our framework is widely applicable to mechanisms in other systems from which similar time-dependent interaction modifications can emerge, highlighting the need to integrate temporal shifts of species interactions to predict the emergent dynamics of natural communities.

ecology↗

bioRxiv2023

Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

Complete characterization of the genetic effects on gene expression is needed to elucidate tissue biology and the etiology of complex traits. Here, we analyzed 2,344 subcutaneous adipose tissue samples and identified 34K conditionally distinct expression quantitative trait locus (eQTL) signals in 18K genes. Over half of eQTL genes exhibited at least two eQTL signals. Compared to primary signals, non-primary signals had lower effect sizes, lower minor allele frequencies, and less promoter enrichment; they corresponded to genes with higher heritability and higher tolerance for loss of function. Colocalization of eQTL with conditionally distinct genome-wide association study signals for 28 cardiometabolic traits identified 3,605 eQTL signals for 1,861 genes. Inclusion of non-primary eQTL signals increased colocalized signals by 46%. Among 30 genes with [≥]2 pairs of colocalized signals, 21 showed a mediating gene dosage effect on the trait. Thus, expanded eQTL identification reveals more mechanisms underlying complex traits and improves understanding of the complexity of gene expression regulation.

genomics↗

bioRxiv2023

Zinc-finger (ZiF) fold secreted effectors form a functionally diverse family across lineages of the blast fungus Magnaporthe oryzae.

Filamentous plant pathogens deliver effector proteins into host cells to suppress host defence responses and manipulate metabolic processes to support colonization. Understanding the evolution and molecular function of these effectors provides knowledge about pathogenesis and can suggest novel strategies to reduce damage caused by pathogens. However, effector proteins are highly variable, share weak sequence similarity and, although they can be grouped according to their structure, only a few structurally conserved effector families have been functionally characterized to date. Here, we demonstrate that Zinc-finger fold (ZiF) secreted proteins form a functionally diverse effector family in the blast fungus Magnaporthe oryzae. This family relies on the Zinc-finger motif for protein stability and is ubiquitously present, forming different effector tribes in blast fungus lineages infecting 13 different host species. Homologs of the canonical ZiF effector, AVR-Pii from rice infecting isolates, are present in multiple M. oryzae lineages, and the wheat infecting strains of the fungus, for example, possess an allele that also binds host Exo70 proteins and activates the immune receptor Pii. Furthermore, ZiF tribes vary in the host Exo70 proteins they bind, indicating functional diversification and an intricate effector/host interactome. Altogether, we uncovered a new effector family with a common protein fold that has functionally diversified in lineages of M. oryzae. This work expands our understanding of the diversity of M. oryzae effectors, the molecular basis of plant pathogenesis and may ultimately facilitate the development of new sources for pathogen resistance. Author SummaryDiseases caused by filamentous plant pathogens impact global food production, leading to severe economic and humanitarian consequences. These pathogens secrete hundreds of effectors inside the host to alter cellular processes and to promote infection and disease. Effector proteins have weak or no sequence similarity but can be grouped in structural families based on conserved protein folds. However, very few conserved effector families have been functionally characterized. We have identified a family of effectors with a shared Zinc-finger protein fold (ZiF) that is present in lineages of the blast fungus Magnaporthe oryzae that can, collectively, infect 13 different grasses. We characterized the binding of a sub-set of these proteins to putative Exo70 host targets and showed they can be recognized by the plant immune system. Furthermore, we show that other ZiF effectors do not bind Exo70 targets, suggesting functional specialization within this effector family for alternative interactors. These findings shed light on the diversity of effectors and their molecular functions, as well as potentially leading to the development of new sources of blast disease resistance in the future.

plant biology↗

bioRxiv2023

Multiunit frontal eye field activity codes the visuomotor transformation, but not gaze prediction or target memory, in a delayed saccade task

Single-unit (SU) activity - action potentials isolated from one neuron -- has traditionally been employed to relate neuronal activity to behavior. However, recent investigations have shown that multi-unit (MU) activity - ensemble neural activity recorded within the vicinity of one microelectrode - may also contain accurate estimations of task-related neural population dynamics. Here, using a well-established model-fitting approach, we compared the spatial codes of SU response fields with corresponding MU response fields recorded from the frontal eye fields (FEF) in head-unrestrained monkeys (Macaca mulatta) during a memory-guided saccade task. We focused on characterizing the visuomotor transformation from Target-in-Eye coordinates to future Gaze-in-Eye coordinates (Sajad et al., 2015). Most SU visual response fields coded targets (with some predicting Gaze), whereas the MU population only coded targets. Most SU motor responses coded Gaze, but many still retained a target code. In contrast, MU motor activity predominantly coded Gaze with very little target coding. Finally, both SU and MU populations showed a progressive transition through intermediate Target-to-Gaze codes during the delay period, but the MU activity showed a smoother transition. These results confirm the theoretical and practical potential of MU activity recordings as a biomarker for fundamental sensorimotor transformations (e.g., Target-to-Gaze coding in the oculomotor system), while also highlighting the importance of SU activity for coding more cognitive (e.g., predictive / memory) aspects of sensorimotor behavior. SIGNIFICANCE STATEMENTMulti-unit recordings (undifferentiated signals from several neurons) are relatively easy to record and provide a simplified estimate of neural dynamics, but it is not clear which single-unit signals are retained, amplified, or lost. Here, we compared single-/multi-unit activity from a well-defined structure (the frontal eye fields) and behavior (memory-delay saccade task), tracking their spatial codes through time. The progressive transformation from target to gaze coding observed in single-unit activity was retained in multi-unit activity, but gaze prediction (in the visual response) and target memory (in the motor response) were lost. This suggests that multi-unit activity provides an excellent biomarker for healthy sensorimotor transformations, at the cost of missing more subtle cognitive signals.

neuroscience↗

bioRxiv2023

Duplication and neofunctionalization of a horizontally-transferred xyloglucanase as a facet of the red queen co-evolutionary dynamic

Oomycetes are heterotrophic protists that share phenotypic similarities with fungi, including the ability to cause plant diseases, but branch in a separate and distant region of the eukaryotic tree of life. It has been suggested that multiple horizontal gene transfers (HGTs) from fungi-to-oomycetes contributed to the evolution of plant-pathogenic traits. These HGTs are predicted to include secreted proteins that degrade plant cell walls. This is a key trait in the pathology of many oomycetes, as the plant cell wall represents a primary barrier to pathogen invasion and a rich source of carbohydrates. Many of the HGT gene families identified have undergone multiple rounds of duplication. Using a combination of phylogenomic analysis and functional assays, we investigate the diversification of a horizontally-transferred xyloglucanase gene family in the model oomycete species Phytophthora sojae. Our analyses detect 11 genes retained in P. sojae among a complex pattern of gene duplications and losses. Using a phenotype assay, based on heterologous expression in yeast, we show that eight of these paralogs have xyloglucanase function, including variants with distinct protein characteristics, such as a long-disordered C-terminal extension that can increase xyloglucanase activity. The functional xyloglucanase variants analysed subtend an ancestral node close to the fungi-oomycetes gene transfer, suggesting the horizontally-transferred gene was a bona fide xyloglucanase. Expression of xyloglucanase paralogs in Nicotiana benthamiana triggers distinct patterns of reactive oxygen species (ROS) generation, demonstrating that enzyme variants differentially stimulate pattern-triggered immunity in plants. Mass spectrometry of detectable enzymatic products demonstrates that some paralogs catalyze production of variant breakdown profiles, suggesting that secretion of multiple xyloglucanase variants increases efficiency of xyloglucan breakdown, as well as potentially diversifying the range of Damage-Associated Molecular Patterns (DAMPs) released during pathogen attack. We suggest that such patterns of protein neofunctionalization, and variant host responses, represent an aspect of the Red Queen host-pathogen co-evolutionary dynamic. Significance StatementThe oomycetes are a diverse group of eukaryotic microbes that include some of the most devastating pathogens of plants. Oomycetes perceive, invade, and colonize plants in similar ways to fungi, in part because they acquired the genes to attack and feed on plants from fungi. These genes are predicted to be useful to oomycete plant pathogens because they have undergone multiple rounds of gene duplication. One key enzyme for attacking plant cell wall structures is called xyloglucanase. Xyloglucanase in the oomycetes has undergone multiple rounds of gene duplication, leading to variants including an enzyme with a C-terminal extension that increases activity. Some xyloglucanase variants trigger unique patterns of reactive oxygen species (ROS) in planta, and generate different profiles of cell wall breakdown products - such outcomes could act to mystify and increase the workload of the plant immune system, allowing successful pathogens to proliferate.

evolutionary biology↗

bioRxiv2023

Asymmetric cortical projections to striatal direct and indirect pathways distinctly control actions

The striatal direct and indirect pathways constitute the core for basal ganglia function in action control. Although both striatal D1- and D2-spiny projection neurons (SPNs) receive excitatory inputs from the cerebral cortex, whether or not they share inputs from the same cortical neurons, and how pathway-specific corticostriatal projections control behavior remain largely unknown. Here using a G-deleted rabies system in mice, we found that more than two-thirds of excitatory inputs to D2-SPNs also target D1-SPNs, while only one-third do so vice versa. Optogenetic stimulation of striatal D1- vs. D2-SPN-projecting cortical neurons differently regulate locomotion, reinforcement learning and sequence behavior, implying the functional dichotomy of pathway-specific corticostriatal subcircuits. These results reveal the partially segregated yet asymmetrically overlapping cortical projections on striatal D1- vs. D2-SPNs, and that the pathway-specific corticostriatal subcircuits distinctly control behavior. It has important implications in a wide range of neurological and psychiatric diseases affecting cortico-basal ganglia circuitry. In BriefKlug, Yan et al. employed a modified rabies system in combination with slice physiology, optogenetics and behavioral tests to reveal that pathway-specific corticostriatal subcircuits distinctly control actions. HighlightsO_LIOne-third of the excitatory inputs to D1-SPNs project to D2-SPNs, while two-third of the excitatory inputs to D2-SPNs also target D1-SPNs C_LIO_LIActivation of D1-SPN projecting cortical neurons triggers behavioral effects in line with postsynaptic striatal direct pathway activation C_LIO_LIActivation of D2-SPN projecting cortical neurons causes behavioral effects similar with co-activation of both direct and indirect pathways C_LIO_LICorticostriatal subcircuits control actions in a brain-region and pathway-specific manner C_LI

neuroscience↗

bioRxiv2023

Nucleolar dynamics are determined by the ordered assembly of the ribosome

Ribosome biogenesis occurs in the nucleolus, a biomolecular condensate whose material properties are thought to be important for function. However, the molecular basis of nucleolar dynamics and their relationship to ribosome assembly remain incompletely understood. We present a platform for high-throughput fluorescence recovery after photobleaching (HiT-FRAP) and use it to screen hundreds of genes for their impact on dynamics of the nucleolar scaffold nucleophosmin (NPM1). We find that NPM1 dynamics and nucleolar morphology are sensitive to ribosome assembly state: accumulation of early preribosomal intermediates slows NPM1 dynamics and compacts the condensate, while accumulation of abortive late precursors accelerates dynamics and disrupts condensate integrity. These opposing biophysical states correlate with the strength of NPM1-pre-ribosome interactions. Importantly, mutations in the NPM1 intrinsically disordered region that alter pre-ribosome binding directly tune nucleolar dynamics. These results establish that ribosomal precursor assembly state determines nucleolar material properties through the valency of scaffold-pre-ribosome interactions and introduce HiT-FRAP as a platform for interrogating condensate dynamics broadly. TOCSheu-Gruttadauria et al. show that the material properties of the nucleolus are shaped by the assembly state of ribosomal precursors, which tune nucleolar dynamics and morphology through their interactions with the nucleolar scaffolding protein NPM1.

molecular biology↗

bioRxiv2023

Peripheral Blood Single-Cell Sequencing Uncovers Common and Specific Immune Aberrations in Fibrotic Lung Diseases

Rationale and ObjectivesThe extent and commonality of peripheral blood immune aberrations in fibrotic interstitial lung diseases are not well characterized. In this study, we aimed to identify common and distinct immune aberrations in patients with idiopathic pulmonary fibrosis (IPF) and fibrotic hypersensitivity pneumonitis (FHP) using cutting-edge single-cell profiling technologies. MethodsSingle-cell RNA sequencing was performed on patients and healthy controls peripheral blood and bronchoalveolar lavage samples using 10X Genomics 5 gene expression and V(D)J profiling. Cell type composition, transcriptional profiles, cellular trajectories and signaling, and T and B cell receptor repertoires were studied. The standard Seurat R pipeline was followed for cell type composition and differential gene expression analyses. Transcription factor activity was imputed using the DoRothEA-VIPER algorithm. Pseudotime analyses were conducted using Monocle3, while RNA velocity analyses were performed with Velocyto, scVelo, and CellRank. Cell-cell connectomics were assessed using the Connectome R package. V(D)J analyses were conducted using CellRanger and Immcantation frameworks. Across all analyses, disease group differences were assessed using the Wilcoxon rank-sum test. Measurements and Main Results327,990 cells from 83 samples were profiled. Overall, changes in monocytes were common to IPF and FHP, whereas lymphocytes exhibited disease-specific aberrations. Both diseases displayed enrichment of CCL3hi/CCL4hi CD14+ monocytes (p<2.2e-16) and S100Ahi CD14+ monocytes (p<2.2e-16) versus controls. Trajectory and RNA velocity analysis suggested that pro-fibrotic macrophages observed in BAL originated from peripheral blood monocytes. Lymphocytes exhibited disease-specific aberrations, with CD8+ GZMKhi T cells and activated B cells primarily enriched in FHP patients. V(D)J analyses revealed unique T and B cell receptor complementarity-determining region 3 (CDR3) amino acid compositions (p<0.05) in FHP and significant IgA enrichment in IPF (p<5.2e-7). ConclusionsWe identified common and disease-specific immune mechanisms in IPF and FHP; S100Ahi monocytes and SPP1hi macrophages are common to IPF and FHP, whereas GMZKhi T lymphocytes and T and B cell receptor repertoires were unique in FHP. Our findings open novel strategies for the diagnosis and treatment of IPF and FHP.

genomics↗

bioRxiv2023

Influence of Gaze, Vision, and Memory on Hand Kinematics in a Placement Task

People usually reach for objects to place them in some position and orientation, but the placement component of this sequence is often ignored. For example, reaches are influenced by gaze position, visual feedback, and memory delays, but their influence on object placement is unclear. Here, we tested these factors in a task where participants placed and oriented a trapezoidal block against 2D visual templates displayed on a frontally located computer screen. In Experiment 1, participants matched the block to three possible orientations: 0{degrees} (horizontal), +45{degrees} and -45{degrees}, with gaze fixated 10{degrees} to the left/right. The hand and template either remained illuminated (closed-loop), or visual feedback was removed (open-loop). In Experiment 2, a memory delay was added, and participants sometimes performed saccades (centripetal, centrifugal, or opposite side). In Experiment 1, the hand consistently overshot the template relative to gaze (similar to reaching), especially in the open-loop task. After a memory delay, location errors were influenced by both template orientation and gaze position. Based on previous reach experiments, we expected these errors to be independent of the previous eye position, but placement overshoot also depended on previous saccade metrics. Hand orientation over-rotated relative to template orientation (all conditions). Orientation was influenced by gaze position in Experiment 1, but this vanished in the presence of a memory delay. These results demonstrate interactions between gaze, location, and orientation signals in the planning and execution of hand placement and suggest different neural mechanisms for closed-loop, open-loop, and memory delay placement. NEW & NOTEWORTHYEye-hand coordination studies usually focus on object acquisition, but placement is equally important. Here, we investigated how gaze position influences object placement toward a 2D template, with different levels of visual feedback. Like reach, placement overestimated goal location relative to gaze, but was also influenced by previous saccade metrics. Gaze also modulated hand orientation, which generally overestimated template orientation. Gaze influence was feedback-dependent, with location errors increasing but orientation errors decreasing after a memory delay.

neuroscience↗