title: Plasticity facilitates rapid evolution

abstract: Developmental plasticity enables organisms to cope with new environmental challenges. If deploying such plasticity is costly in terms of time or energy, the same adaptive behavior could subsequently evolve through piecemeal genomic reorganisation that replaces the requirement to acquire that adaptation by individual plasticity. Here we report a new dimension to the way in which plasticity can drive evolutionary change leading to ever greater complexity in biological organization. Our model deploys the concept of partially overlapping functional systems. We found that plasticity accelerated dramatically the evolutionary accumulation of adaptive systems in model organisms with relatively low rates of mutation. The effect of plasticity on the evolutionary growth of complexity was even greater when the number of elements needed to construct a functional system was increased. These results suggest that as the difficulty of challenges from the environment become greater, so plasticity exerts an ever more powerful role in meeting those challenges and in opening up new avenues for the subsequent evolution of complex adaptations.


title: Effects of Body Mass on Leg and Vertical Stiffness in Running Humans

abstract: Numerous cross-species comparisons have examined the scaling of gait parameters with respect to body mass (i.e., allometry), but few have done so within humans. This study examined how leg and vertical stiffness, force, displacement, and leg spring angle scaled in 64 healthy adults of varying body masses during slow and fast leg-length-adjusted running speeds. We calculated scaling patterns for stiffness and its components via kinematic and kinetic data using log-log regressions with 95% confidence/highest density intervals. To determine if the chosen statistical method influenced conclusions about scaling patterns, we compared regression results across three statistical methods, ordinary least squares (OLS) regression, linear mixed models (LMM), and Bayesian linear mixed models (BLMM). We also performed sex-specific analyses to determine if each sex revealed similar scaling patterns as the pooled sample. In the pooled sample, all variables scaled according to the isometric expectations, suggesting that different-sized humans move in a similar manner. Sex-specific analyses revealed similar patterns of isometry in all variables, except for vertical stiffness, which displayed slight negative allometry (i.e., lower than expected stiffness) in both sexes at the slow speed and negative allometry in females during fast running. Model choice did not significantly affect results, and scaling patterns were the same regardless of the statistical method employed.

category: bioengineering


title: FAIRsoft - A practical implementation of FAIR principles for research software

abstract: Software plays a crucial and growing role in research. Unfortunately, the computational component in Life Sciences research is challenging to reproduce and verify most of the time. It could be undocumented, opaque, may even contain unknown errors that affect the outcome, or be directly unavailable, and impossible to use by others. These issues are detrimental to the overall quality of scientific research. One step to address this problem is the formulation of principles that research software in the domain should meet to ensure its quality and sustainability, resembling the FAIR (Findable, Accessible, Interoperable and Reusable) Data Principles. Within the ELIXIR infrastructure, OpenEBench aims to be an open platform providing both support for scientific benchmarking and an active observatory of software quality for the universe of Life Sciences research software. We present our initial proposal to instantiate a FAIR-like framework for assessing software quality as the first step toward the implementation of such an observatory in OpenEBench.

category: bioinformatics


title: A dynamical low-rank approach to solve the chemical master equation for biological reaction networks

abstract: Solving the chemical master equation is an indispensable tool in understanding the behavior of biological and chemical systems. In particular, it is increasingly recognized that commonly used ODE models are not able to capture the stochastic nature of many cellular processes. Solving the chemical master equation directly, however, suffers from the curse of dimensionality. That is, both memory and computational effort scale exponentially in the number of species. In this paper we propose a dynamical low-rank approach that enables the simulation of large biological networks. The approach is guided by partitioning the network into biological relevant subsets and thus avoids the use of single species basis functions that are known to give inaccurate results for biological systems. We use the proposed method to gain insight into the nature of asynchronous vs. synchronous updating in Boolean models and successfully simulate a 41 species apoptosis model on a standard desktop workstation.


title: The effect of motor-induced shaft dynamics on microtubule stability and length

abstract:
Control of microtubule abundance, stability, and length is crucial to regulate intracellular transport as well as cell polarity and division. How microtubule stability depends on tubulin addition or removal at the dynamic ends is well studied. However, microtubule rescue, the event when a microtubule switches from shrinking to growing, occurs at tubulin exchange sites along the shaft. Molecular motors have recently been shown to promote such exchanges. Using a stochastic theoretical description, we study how microtubule stability and length depends on motor-induced tubulin exchange and thus rescue. Our theoretical description matches our in vitro experiments on microtubule dynamics in presence of kinesin-1 molecular motors. Although the average microtubule dynamics can be captured by an effective rescue rate, the dynamics of individual microtubules differs dramatically when rescue occurs only at exchange sites. Furthermore, we study in detail a transition from bounded to unbounded microtubule growth. Our results provide novel insights into how molecular motors imprint information of microtubule stability on the microtubule network.

SIGNIFICANCEThe microtubule network is essential for vital cellular processes like the organization of intracellular transport and division. Although microtubule assembly occurs at its tips, it has recently been reported that tubulin is exchanged along the microtubule shaft. Tubulin exchange plays an essential role in regulating microtubule dynamics and can be induced by molecular motors. Here, we provide the first systematic study of the impact of shaft dynamics on the regulation of rescue events, where a microtubule switches from shrinking to growing. Our results illustrate how the usage of microtubules as tracks for intracellular transport regulates the microtubule network and thus offers a novel perspective on intracellular organization.

category: biophysics


title: Human papilloma virus E6 regulates therapy responses in oropharyngeal cancer by repressing the PGC-1α/ERRα axis

abstract: Therapy with radiation plus cisplatin kills human papilloma virus-related (HPV+) oropharyngeal squamous cell carcinomas (OPSCCs) by increasing reactive oxygen species beyond cellular antioxidant capacity. To explore why some patients fail these standard treatments, we evaluated whether the variation in HPV oncoprotein levels among HPV+ OPSCCs impacts mitochondrial metabolism, a source of antioxidant capacity. In cell line and patient-derived xenograft models, levels of HPV full-length E6 (fl-E6) inversely correlated with oxidative phosphorylation, antioxidant capacity, and therapy resistance, and fl-E6 was the only HPV oncoprotein to display such correlation. Ectopically expressing fl-E6 in models with low levels reduced mitochondrial mass, depleted antioxidant capacity, and sensitized to therapy. In this setting, fl-E6 repressed the PGC-1/ERR pathway for mitochondrial biogenesis by reducing p53-dependent PGC-1 transcription. Concordant observations were made in three clinical cohorts, where expression of mitochondrial components was higher in tumors of patients with reduced survival. These tumors contained the lowest fl-E6 levels, highest p53 target gene expression, and an activated PGC-1/ERR pathway. Our findings demonstrate that E6 can potentiate treatment responses by depleting mitochondrial antioxidant capacity and provide evidence for low E6 negatively impacting patient survival. E6s interaction with the PGC-1/ERR axis has implications for predicting and targeting treatment resistance in OPSCC.

category: cancer biology


title: Lipid droplets are a metabolic vulnerability in melanoma

abstract: Melanoma exhibits numerous transcriptional cell states including neural crest-like cells as well as pigmented melanocytic cells. How these different cell states relate to distinct tumorigenic phenotypes remains unclear. Here, we use a zebrafish melanoma model to identify a transcriptional program linking the pigmented cell state to a dependence on lipid droplets, the specialized organelle responsible for lipid storage. Single-cell RNA-sequencing of these tumors show a concordance between genes regulating pigmentation and those involved in lipid and oxidative metabolism. This state is conserved in human melanoma specimens. This state demonstrates increased fatty acid uptake, an increased number of lipid droplets, and dependence upon oxidative metabolism. Genetic and pharmacologic suppression of lipid droplet production is sufficient to disrupt oxidative metabolism and slow melanoma growth in vivo. Because the pigmented cell state is linked to poor outcomes in patients, these data indicate a metabolic vulnerability in melanoma that depends on the lipid droplet organelle.


title: Hypereosinophilia causes progressive cardiac pathologies in mice

abstract:
Hypereosinophilic syndrome is a progressive disease with extensive eosinophilia that results in organ damage. Cardiac pathologies are the main reason for its high mortality rate. A better understanding of the mechanisms of eosinophil-mediated tissue damage would benefit therapeutic development. Here, we describe the cardiac pathologies that developed in a mouse model of hypereosinophilic syndrome. These IL-5 transgenic mice exhibited decreased left ventricular function at a young age which worsened with age. Mechanistically, we demonstrated infiltration of activated eosinophils into the heart tissue that led to an inflammatory environment. Gene expression signatures showed tissue damage as well as repair and remodeling processes. Cardiomyocytes from IL-5Tg mice exhibited significantly reduced contractility relative to WT controls. This impairment may result from the inflammatory stress experienced by the cardiomyocytes and suggest that dysregulation of contractility and Ca2+ reuptake in cardiomyocytes contributes to cardiac dysfunction at the whole organ level in hypereosinophilic mice.

TeaserToo many eosinophils cause inflammation in the heart and change cardiomyocyte contraction leading to poor heart function.

category: pathology


title: Different combinations of laccase paralogs non-redundantly control the lignin amount and composition of specific cell types and cell wall layers in Arabidopsis

abstract: Vascular plants reinforce the cell walls of the different xylem cell types with lignin, a phenolic polymer. Specific lignin chemistries are conserved between the cell wall layers of each cell type to support their functions. Yet the mechanisms controlling the tight spatial localisation of specific lignin chemistries remain unclear. Current hypotheses focus on a control by monomer biosynthesis and/or export, while their cell wall polymerisation is viewed as random and non-limiting. Here we show that cell wall polymerisation using combinations of multiple different laccases (LACs) non-redundantly and specifically control the lignin chemistry in different cell types and their distinct cell wall layers. We dissected the roles of Arabidopsis thaliana LAC4, 5, 10, 12 and 17 by generating quadruple and quintuple loss-of-function mutants. Different combinatory loss of these LACs lead to specific changes in lignin chemistry affecting both residue ring structures and/or aliphatic tails in specific cell types and cell wall layers. We moreover showed that the LAC-mediated lignification had distinct functions in specific cell types. Altogether, we propose that the spatial control of lignin chemistry depends on different combinations of LACs with non-redundant activities immobilised in specific cell types and cell wall layers.

category: plant biology


title: Introgression of the Triticum timopheevii genome into wheat detected by chromosome-specific KASP markers

abstract: Triticum timopheevii (2n=28, AtAtGG) is a tetraploid wild relative species with great potential to increase the genetic diversity of hexaploid wheat Triticum aestivum (2n=42, AABBDD) for various important agronomic traits. A breeding scheme that propagated advanced backcrossed populations of wheat-T. timopheevii introgression lines through further backcrossing and self-fertilisation resulted in the generation of 99 introgression lines (ILs) that carried 309 homozygous segments from the At and G subgenomes of T. timopheevii. These introgressions contained 89 and 74 unique segments from the At and G subgenomes, respectively. These overlapping segments covered 98.9% of the T. timopheevii genome that has now been introgressed into bread wheat cv. Paragon including the entirety of all T. timopheevii chromosomes via varying sized segments except for chromosomes 3At, 4G and 6G. Homozygous ILs contained between one and eight of these introgressions with an average of three per introgression line. These homozygous introgressions were detected through the development of a set of 480 chromosome-specific Kompetitive allele specific PCR (KASP) markers that are well-distributed across the wheat genome. Of these, 149 were developed in this study based on single nucleotide polymorphisms (SNPs) discovered through whole genome sequencing of T. timopheevii. A majority of these KASP markers were also found to be T. timopheevii subgenome specific with 182 detecting At subgenome and 275 detecting G subgenome segments. These markers showed that 98% of the At segments had recombined with the A genome of wheat and 74% of the G genome segments had recombined with the B genome of wheat with the rest recombining with the D genome of wheat. These results were validated through multi-colour in situ hybridisation analysis. Together these homozygous wheat-T. timopheevii ILs and chromosome-specific KASP markers provide an invaluable resource to wheat breeders for trait discovery to combat biotic and abiotic stress factors affecting wheat production due to climate change.


title: A marked enhancement of a BLOC-1 gene, pallidin, associated with somnolent mouse models deficient in histamine transmission

abstract: Histamine (HA) and orexin (Ox, or hypocretin) neurons act distinctly and synergistically in wake control. A double knock out mouse genotype lacking both HA and Ox shows all sleep disorders of human narcolepsy. We identified in this mouse brain a sharp upregulation of a BLOC-1 gene, pallidin that is associated with dramatic changes in the balance of cholinergic and aminergic systems in mice and an enhanced sleep in drosophila. This study demonstrates potential sleep disorders-associated compensatory mechanisms with pallid as a novel biomarker.

category: neuroscience


title: The effects of physical and temporal certainty on locomotion with discrete underfoot perturbations

abstract:
BackgroundAmbulation over complex terrain requires active control of foot placement to maintain a normal kinematic relationship between the center of mass and base of support. Recent investigations have suggested that foot placement location may be selected to anticipate shifts to the underfoot center of pressure. However, it is unclear whether temporal affordance and physical certainty contribute to the selection of a perturbation-specific anticipatory strategy. This study investigates anticipatory and reactive locomotor strategies for repeated underfoot perturbations with varying levels of temporal certainty, temporal affordance, and physical certainty.

MethodsThirteen healthy adults walked with random underfoot perturbations from a mechanized shoe. Temporal certainty was challenged by presenting the perturbations with or without warning. Temporal affordance was challenged by adjusting the timing of a warning tone before the perturbation. Physical certainty was challenged with conditions that included only eversion perturbations, only inversion perturbations, or both eversion and inversion perturbations. Linear-mixed effects models assessed the effect of each condition on the percent change of margin of stability and step width, respectively.

ResultsFor temporally uncertain perturbations and perturbations with one stride or less of affordance, we observed few changes to step width or margin of stability. As affordance increased to two strides, participants adopted a wider step width in anticipation of the perturbation (p = 0.001). Physical certainty had little effect on gait for the step of the perturbation, but participants recovered normal gait sooner when the physical nature of the perturbation was predictable (p < 0.001).

DiscussionDespite having information about the timing and magnitude of upcoming perturbations, individuals do not develop perturbation specific feedforward strategies but instead rely on feedback control to recover normal gait after a perturbation. However, physical certainty appears to improve the efficiency of the feedback controller and allows individuals to recover normal gait sooner.


title: Katanin is involved in Microtubule Polymerization into Dendritic Spines and regulates Synaptic Plasticity

abstract: Dynamic microtubules transiently polymerize into dendritic spines, however intracellular factors that regulate this process and their functional role at synapses are hardly understood. Using live imaging, electrophysiology, and glutamate uncaging, we show that the microtubule-severing complex katanin is located at individual spine synapses, participates in the activity-dependent process of microtubule polymerization into dendritic spines, and regulates synaptic plasticity. Overexpression of a dominant-negative ATPase-deficient katanin subunit, did not alter microtubule growth velocities or comet density in dendrites, but significantly reduced the activity-dependent invasion of microtubules into dendritic spines. Notably, functional inhibition of katanin significantly affected the potentiation of AMPA-receptor-mediated excitatory currents after chemical induction of long-term potentiation (cLTP). Furthermore, interference with katanin function prevented structural spine remodeling following single spine glutamate uncaging. Our data identify katanin at individual spine synapses in association with PSD-95. Thus, katanin regulates postsynaptic microtubules and modulates synaptic structure and function.


title: Population coding strategies in human tactile afferents

abstract: Sensory information is conveyed by populations of neurons, and coding strategies cannot always be deduced when considering individual neurons. Moreover, information coding depends on the number of neurons available and on the composition of the population when multiple classes with different response properties are available. Here, we study population coding in human tactile afferents by employing a recently developed simulator of mechanoreceptor firing activity. First, we demonstrate that the optimal afferent density for conveying maximal information depends on the tactile feature under consideration and the afferent class coding this feature. Second, we find that information is spread across different classes for all tactile features, such that combining information from multiple afferent classes improves information transmission, and is often more efficient than increasing the density of afferents from the same class. Finally, we test the importance of timing precision and afferent identity in the population code to probe whether temporal and spatial information can be traded against each other. Destroying temporal information turns out to be more destructive than removing spatial information, and the contribution of either cannot be completely recovered from the other. Overall, our results suggest that both optimal afferent innervation densities and the composition of the population depend in complex ways on the tactile features in question, potentially accounting for the variety in which tactile peripheral populations are assembled in different regions across the body.


title: Actin nano-architecture of phagocytic podosomes

abstract: Podosomes are actin-enriched adhesion structures important for multiple cellular processes, including migration, bone remodeling, and phagocytosis. Here, we characterized the structure and organization of phagocytic podosomes using interferometric photoactivated localization microscopy (iPALM), a super-resolution microscopy technique capable of 15-20 nm resolution, together with structured illumination microscopy (SIM) and localization-based superresolution microscopy. Phagocytic podosomes were observed during frustrated phagocytosis, a model in which cells attempt to engulf micro-patterned IgG antibodies. For circular patterns, this resulted in regular arrays of podosomes with well-defined geometry. Using persistent homology, we developed a pipeline for semi-automatic identification and measurement of podosome features. These studies revealed an "hourglass" shape of the podosome actin core, a protruding "knob" at the bottom of the core, and two actin networks extending from the core. Additionally, the distributions of paxillin, talin, myosin II, -actinin, cortactin, and microtubules relative to actin were characterized.

category: cell biology


title: A multiplexed assay of human glucokinase reveals thousands of potential disease variants with both decreased and increased activity

abstract: Diabetes is a complex disease spanning from the heterogeneous etiology of type 1 and type 2 diabetes to monogenic diabetes. A common monogenic form of diabetes is glucokinase (GCK) maturity-onset diabetes of the young (GCK-MODY), which is caused by heterozygous inactivating variants in the gene encoding GCK. GCK is known as the pancreatic glucose sensor, as it regulates insulin secretion to maintain appropriate blood glucose levels. Accordingly, variants that alter GCK activity can cause hypo- and hyperglycemia, associated with hyperinsulinemic hypoglycemia (HH) and GCK-MODY, respectively, affecting up to 10 million people worldwide. Patients with GCK-MODY, in contrast to other people with diabetes, often do not require treatment but are frequently misdiagnosed and treated unnecessarily. Genetic testing can prevent this but is hampered by the challenge of interpreting novel missense variants. To address this, we generated a comprehensive map of GCK variant activity in yeast. The activity map includes 97% of the possible missense and nonsense variants and correlates with in vitro catalytic efficiency, fasting glucose levels in carriers of GCK variants and evolutionary conservation analysis. Activity scores include both hyper- and hypoactive variants. We found that some hyperactive variants shift the conformational equilibrium towards the active state through a relative destabilization of the inactive conformation. As expected, hypoactive variants were concentrated at buried positions, near the active site, and at a partially surface-exposed region involved in GCK conformational dynamics. In conclusion, we provide a comprehensive assessment of GCK variant activity to facilitate variant interpretation and diagnosis, and we expand the mechanistic understanding of hyperactive variants to support development and refinement of drugs targeting GCK.

category: genetics


title: Contributions and synaptic basis of diverse cortical neuron responses to task performance

abstract: Neuronal responses during behavior are diverse, ranging from highly reliable  classical responses to irregular or seemingly-random  non-classically responsive firing. While a continuum of response properties is frequently observed across neural systems, little is known about the synaptic origins and contributions of diverse response profiles to network function, perception, and behavior. Here we use a task-performing, spiking recurrent neural network model incorporating spike-timing-dependent plasticity that captures heterogeneous responses measured from auditory cortex of behaving rodents. Classically responsive and non-classically responsive model units contributed to task performance via output and recurrent connections, respectively. Excitatory and inhibitory plasticity independently shaped spiking responses and task performance. Local patterns of synaptic inputs predicted spiking response properties of network units as well as the responses of auditory cortical neurons from in vivo whole-cell recordings during behavior. Thus a diversity of neural response profiles emerges from synaptic plasticity rules with distinctly important functions for network performance.


title: Airway Basal Cells Show Regionally Distinct Potential to Undergo Metaplastic Differentiation

abstract: Basal cells are multipotent stem cells of a variety of organs, and in the lung are known as crucial components of the airway epithelium. However, it remains unclear how diverse basal cells are and whether distinct subpopulations respond differently to airway challenges. Using single cell RNA-sequencing and functional approaches, we report a significant and previously underappreciated degree of heterogeneity in the basal cell pool, leading to identification of six subpopulations in the murine trachea. Among these we found two major subpopulations comprising the most stem-like progenitor compartment, but with distinct signatures and ability to self-renew and differentiate. Notably, these occupy distinct ventral and dorsal tracheal niches and differ in their ability to initiate an aberrant program of differentiation in response to environmental perturbations in primary cultures and in injury mouse models in vivo. We found that such heterogeneity is acquired prenatally, when the basal cell pool and local niches are being established, and depends on the integrity of these niches, as supported by the altered basal cell phenotype of cartilage-deficient mouse mutants. Lastly, we show that key features that distinguish these progenitor subpopulations in murine airways are conserved in humans. Together, the data provide critical insights into the origin and impact of basal cell heterogeneity on the establishment of regionally distinct responses of the airway epithelium during injury-repair and in disease conditions.

category: developmental biology


title: A Pairwise Imputation Strategy for Retaining Predictive Features When Combining Multiple Datasets

abstract: In the training of predictive models using high-dimensional genomic data, multiple studies worth of data are often combined to increase sample size and improve generalizability. A drawback of this approach is that there may be different sets of features measured in each study due to variations in expression measurement platform or technology. It is often common practice to work only with the intersection of features measured in common across all studies, which results in the blind discarding of potentially useful feature information that is measured only in individual or subsets of all studies. We characterize the loss in predictive performance incurred by using only the intersection of feature information available across all studies when training predictors using gene expression data from microarray and sequencing datasets. We study the properties of linear and polynomial regression for imputing discarded features and demonstrate improvements in the external performance of predictors through simulation and in gene expression data collected on breast cancer patients. We propose and evaluate a pairwise imputation strategy that imputes cross-study missing features in each pair of studies and averages imputed features across pairs. Finally, we provide insights on which subsets of intersected and study-specific features should be used so that missing-feature imputation best promotes cross-study replicability. All code with directions to reproduce results in this paper is available at https://github.com/YujieWuu/Pairwise_imputation


title: Discovery and characterization of a first-in-field transcription factor BRN2 inhibitor for the treatment of neuroendocrine prostate cancer.

abstract: The increased incidence of treatment-emergent neuroendocrine prostate cancer (NEPC) is particularly alarming as this diagnosis is associated with poor prognosis. Despite initial responses to platinum-based chemotherapy, relapses are common and there is no effective second line therapy for NEPC. We previously identified that neuronal transcription factor BRN2 (POU3F2) is a potent driver of neuroendocrine differentiation and an attractive target for NEPC. Utilizing a combination of in silico modeling and X-ray crystallography followed by structure-based lead optimization, we have developed the first potent, specific and orally bioavailable BRN2 inhibitor (B18-94), which inhibits the interaction between BRN2 and DNA. This loss of BRN2 on the chromatin drastically reduces its transcriptional output resulting in downregulation of several known targets in NEPC such as SOX2, ASCL1 and PEG10. Additionally, B18-94 reduces specifically cell proliferation specifically in multiple NEPC models with no effect on adenocarcinoma and other BRN2 negative prostate cancer models. Importantly, the consistency in the transcriptomic changes driven by B18-94 and or CRISPR/Cas9 mediated BRN2 knockout confirmed the on-target specificity, with both methods of BRN2 inhibition downregulating pathways involved in cellular plasticity and proliferation. Finally, we have demonstrated that B18-94, the first-in-field POU-domain transcription factor inhibitor, significantly reduced tumor growth in several NEPC xenograft models with no observable toxicity, suggesting potential for therapeutic intervention of NEPC.


title: bi-axial orientation could explain range expansion in a migratory songbird

abstract: The likelihood of a new migratory route evolving is a function of the associated fitness payoff, and the probability that the route arises in the first place. Cross-breeding studies suggest that young birds migrate in a direction intermediate between their parents, though this would seemingly not explain how highly divergent migratory trajectories arise in apparently sympatric populations. It has been suggested that diametrically opposed  reverse migratory trajectories might be surprisingly common, and if such routes were heritable it follows that they could underlie the rapid evolution of divergent migratory trajectories. Here, we used Eurasian blackcap (Sylvia atricapilla;  blackcap) ringing recoveries and geolocator trajectories to investigate whether a recently-evolved northwards autumn migratory route could be explained by the reversal of each individuals expected southwards migratory direction. We found that northwards migrants were recovered closer to the sites specified by a precise axis reversal than would be expected by chance, consistent with the rapid evolution of new migratory routes via bi-axial variation in orientation. We suggest that the surprisingly high probability of axis reversal might allow birds to expand their wintering ranges rapidly, and hence propose that understanding how direction is encoded is crucial when characterising the genetic basis of migratory direction and how this relates to route evolution.

category: zoology


title: Group A streptococci induce high-affinity M protein-fibronectin interaction when specific human antibodies are bound

abstract: Group A streptococcus (GAS) is a highly adapted, humanspecific pathogen that is known to manipulate the immune system through various mechanisms. GAS M protein constitutes a primary target of the immune system due to its spatial configuration and dominance on the bacterial surface. Antibody responses targeting the M protein have been shown to favor the conserved C region. Such antibodies circumvent antigenic escape and efficiently bind to various M types. The ability of GAS to bind to fibronectin (Fn), a high molecular weight glycoprotein of the extracellular matrix, has long been known to be essential for the pathogens evolutionary success and fitness. However, some strains lack the ability to efficiently bind Fn. Instead, they have been found to inefficiently bind Fn via the M protein A-B domains. Here, we show that human antibodies can induce a high-affinity Fn-binding state in M proteins, likely by enhancing the weak A-B domain binding. The antibodies bind to a conserved region of M proteins, and the high-affinity binding only occurs on the individual M proteins with bound specific antibodies. By allowing the binding of antibodies to a certain region in M, and thereby enhancing Fn-binding, GAS exploits the human humoral immune response to efficiently bind Fn without needing to waste energy on the production of additional proteins - potentially giving such strains an evolutionary advantage.

category: immunology


title: Population Genomics of Stone Age Eurasia

abstract: The transitions from foraging to farming and later to pastoralism in Stone Age Eurasia (c. 11-3 thousand years before present, BP) represent some of the most dramatic lifestyle changes in human evolution. We sequenced 317 genomes of primarily Mesolithic and Neolithic individuals from across Eurasia combined with radiocarbon dates, stable isotope data, and pollen records. Genome imputation and co-analysis with previously published shotgun sequencing data resulted in >1600 complete ancient genome sequences offering fine-grained resolution into the Stone Age populations. We observe that: 1) Hunter-gatherer groups were more genetically diverse than previously known, and deeply divergent between western and eastern Eurasia. 2) We identify hitherto genetically undescribed hunter-gatherers from the Middle Don region that contributed ancestry to the later Yamnaya steppe pastoralists; 3) The genetic impact of the Neolithic transition was highly distinct, east and west of a boundary zone extending from the Black Sea to the Baltic. Large-scale shifts in genetic ancestry occurred to the west of this "Great Divide", including an almost complete replacement of hunter-gatherers in Denmark, while no substantial ancestry shifts took place during the same period to the east. This difference is also reflected in genetic relatedness within the populations, decreasing substantially in the west but not in the east where it remained high until c. 4,000 BP; 4) The second major genetic transformation around 5,000 BP happened at a much faster pace with Steppe-related ancestry reaching most parts of Europe within 1,000-years. Local Neolithic farmers admixed with incoming pastoralists in eastern, western, and southern Europe whereas Scandinavia experienced another near-complete population replacement. Similar dramatic turnover-patterns are evident in western Siberia; 5) Extensive regional differences in the ancestry components involved in these early events remain visible to this day, even within countries. Neolithic farmer ancestry is highest in southern and eastern England while Steppe-related ancestry is highest in the Celtic populations of Scotland, Wales, and Cornwall (this research has been conducted using the UK Biobank resource); 6) Shifts in diet, lifestyle and environment introduced new selection pressures involving at least 21 genomic regions. Most such variants were not universally selected across populations but were only advantageous in particular ancestral backgrounds. Contrary to previous claims, we find that selection on the FADS regions, associated with fatty acid metabolism, began before the Neolithisation of Europe. Similarly, the lactase persistence allele started increasing in frequency before the expansion of Steppe-related groups into Europe and has continued to increase up to the present. Along the genetic cline separating Mesolithic hunter-gatherers from Neolithic farmers, we find significant correlations with trait associations related to skin disorders, diet and lifestyle and mental health status, suggesting marked phenotypic differences between these groups with very different lifestyles. This work provides new insights into major transformations in recent human evolution, elucidating the complex interplay between selection and admixture that shaped patterns of genetic variation in modern populations.

category: evolutionary biology


title: BREEDIT: A novel multiplex genome editing strategy to improve complex quantitative traits in maize (Zea mays L.)

abstract: Ensuring food security for an ever-growing global population while adapting to climate change is the main challenge for agriculture in the 21st century. Though new technologies are being applied to tackle the problem, we are approaching a plateau in crop improvement using conventional breeding. Recent advances in gene engineering via the CRISPR/Cas technology pave the way to accelerate plant breeding and meet this increasing demand. Here, we present a gene discovery pipeline named  BREEDIT that combines multiplex genome editing of whole gene families with crossing schemes to improve complex traits such as yield and drought resistance. We induced gene knockouts in 48 growth-related genes using CRISPR/Cas9 and generated a collection of over 1000 gene-edited maize plants. Edited populations displayed, on average, significant increases of 5 to 10% for leaf length and up to 20% for leaf width compared with controls. For each gene family, edits in subsets of genes could be associated with increased traits, allowing us to reduce the gene space needed to focus on for trait improvement. We propose BREEDIT as a gene discovery pipeline which can be rapidly applied to generate a diverse collection of mutants to identify subsets of promising candidates that could be later incorporated in breeding programs.

category: systems biology


title: Development of a Well-Characterized Cynomolgus Macaque Model of Sudan Virus Disease for Support of Product Development

abstract: The primary objective of this study was to characterize the disease course in cynomolgus macaques exposed to Sudan virus (SUDV), to determine if infection in this species is an appropriate model for the evaluation of filovirus countermeasures under the FDA Animal Rule. Sudan virus causes Sudan virus disease (SVD), with an average case fatality rate of approximately 50%, and while research is ongoing, presently there are no approved SUDV vaccines or therapies. Well characterized animal models are crucial for further developing and evaluating countermeasures for SUDV. Twenty (20) cynomolgus macaques were exposed intramuscularly to either SUDV or sterile phosphate buffered saline; 10 SUDV-exposed animals were euthanized on schedule to characterize pathology at defined durations post-exposure and 8 SUDV-exposed animals were not part of the scheduled euthanasia cohort. Survival was assessed, along with clinical observations, body weights, body temperatures, hematology, clinical chemistry, coagulation, viral load (serum and tissues), macroscopic observations, and histopathology. There were statistically significant differences between SUDV-exposed animals and mock-exposed animals for 26 parameters, including telemetry body temperature, clinical chemistry parameters, hematology parameters, activated partial thromboplastin time, serum viremia, and biomarkers that characterize the disease course of SUDV in cynomolgus macaques.

category: microbiology


title: Online Bayesian Analysis with BEAST 2

abstract:
AO_SCPLOWBSTRACTC_SCPLOWThere are a growing number of areas, e.g. epidemiology and within-organism cancer evolution, where re-analysing all available data from scratch every time new data becomes available or old data is refined is no longer feasible. All these and related areas can benefit from online phylogenetic inference that can booster previous data analyses.

Here, we make the case that adding/removing taxa from an analysis can have substantial non-local impact on the tree that is inferred, both in a model based setting, as well as for distance based methods. Consequently, online phylogenetic algorithms may require global updates of the trees and other parameters, a task that in general is highly non-trivial.

Motivated by this observation, we designed an online algorithm that benefits from a parallelism in a Bayesian setting that is substantially more efficient than re-running the analysis from scratch. Furthermore, our algorithm is not sensitive to the number of sequences added, allowing the sequence data to grow/be refined iteratively. We show how this approach can be used in a maximum likelihood setting, and - apart from adding/removing new sequences - demonstrate a number of practical alternative use cases of our algorithm, including how to break up a single (offline) large analysis to get results faster.

An open source implementation is available under GPL3 license as the  online package for BEAST 2 at https://github.com/rbouckaert/online and a tutorial at https://github.com/rbouckaert/online-tutorial.


title: Human collision avoidance behavior against autonomous mobile robot

abstract:
BackgroundAs urban development toward smart cities continues in earnest, pedestrians chances of encountering autonomous mobile robots (AMRs) on the street increase. Although recent studies have discussed how humans avoid collisions with others when passing them, it is still unclear how they would avoid AMRs, which could be common on the streets soon.

Research questionWe investigated humans avoidance strategy against an AMR approaching head-on through an experiment that included recording human-body motions while walking.

MethodThe AMR approached from various starting points, including directly from the participants. The participants were asked to circumvent it by moving rightward or leftward while their walking trajectories were tracked.

ResultWe found no significant bias on either side, suggesting that the avoidance direction is not simply determined by the participants attributes, such as the traffic rules followed in their area of living. The probability of rightward avoidance when the AMR approached head-on indicated that the humans had different avoidance strategy when facing other humans and objects. Moreover, the participants motion analysis revealed that their waists unconsciously twisted in the direction of avoidance before they circumvented.

SignificanceThe results suggest that the human-waist provides an indicator to predict the avoidance direction. Our findings could be adopted in AMRs development to fit them more naturally into our lives.

HighlightsO_LIHuman avoidance strategies against a robot approaching head-on were examined.
C_LIO_LIThe avoidance direction was not simply determined by the participants attributes.
C_LIO_LIHumans used different avoidance strategies when facing other humans and objects.
C_LIO_LIThe human waist provides an indicator to predict the avoidance direction.
C_LI


title: Responses of Model Cortical Neurons to Temporal Interference Stimulation and Other Transcranial Alternating Current Stimulation Modalities

abstract:
Temporal interference stimulation (TIS) has been proposed as a non-invasive, focal, and steerable deep brain stimulation method. TIS is hypothesized to activate neurons via the amplitude-modulated envelope of interference generated by two high-frequency (few kHz) sinusoidal electric fields (E-fields). Existing studies, however, oversimplified TIS and have not represent the full spatial dimensions of E-fields and cortical neurons. The response to TIS and other transcranial alternating current stimulation was simulated using detailed models of layer 5 pyramidal neurons adapted from the Blue Brain Project. We examined a wide range of parameter combinations, including the two E-fields orientations, frequencies, amplitude ratios, amplitude modulation, and phase difference, and obtained thresholds for both activation and inactivation, when stimulus-induced firing stops due to high stimulation amplitude.

TIS has a unique combination of characteristics. At the target region in the cortex, which is generally considered to be where the two E-fields have similar amplitudes, TIS generates an amplitude-modulated total E-field. The TIS E-field also exhibits rotation where the E-field orientations are not aligned, which generally co-localizes with the target. Outside the target region, the TIS E-field is dominated by the high-frequency carrier, with minimal amplitude modulation and/or rotation, and it is less effective at activation with low amplitudes and more effective at inactivation with high amplitudes. TIS activation thresholds are similar to high-frequency stimulation with or without modulation and/or rotation (75-230 V/m). TIS creates inactivation for some combinations of E-field orientations and amplitude ratios at high amplitudes (>1700 V/m), whereas amplitude modulated single-carrier high-frequency stimulation cannot achieve similar effects, regardless of orientation. All observed effects occurred at E-field strengths that are too high to be delivered tolerably through scalp electrodes, limiting the significance of suprathreshold TIS.


title: Involvement of Lateral Habenula Dysfunction in Repetitive Mild Traumatic Brain Injury-Induced Motivational Deficits

abstract: Affective disorders including depression (characterized by reduced motivation, social withdrawal and anhedonia), anxiety and irritability are frequently reported as long-term consequences of mild traumatic brain injury (mTBI)1 in addition to cognitive deficits, suggesting a possible dysregulation within mood/motivational neural circuits. One of the important brain regions that control motivation and mood is the lateral habenula (LHb) whose hyperactivity is associated with depression2. Here we used a repetitive closed head injury mTBI model that is associated with social deficits in adult male mice3 and explored the possible long-term alterations in LHb activity and motivated behavior 10-14 days post-injury. We found that mTBI increased the proportion of spontaneous tonically active LHb neurons while decreased LHb bursting. Additionally, mTBI diminished spontaneous glutamatergic and GABAergic synaptic activity onto LHb neurons, while synaptic excitation and inhibition (E/I) balance was shifted toward excitation through a greater suppression of GABAergic transmission. Behaviorally, mTBI increased the latency in grooming behavior in sucrose splash test suggesting reduced self-care motivated behavior following mTBI. To show whether limiting LHb hyperactivity could restore motivational deficits in grooming behavior, we then tested the effects of Gi (hM4Di)-DREADD-mediated inhibition of LHb activity in sucrose splash test. We found that chemogenetic inhibition of LHb glutamatergic neurons was sufficient to reverse mTBI-induced delays in grooming behavior. Overall, our study provides the first evidence for persistent LHb neuronal dysfunction due to an altered synaptic integration as causal neural correlates of dysregulated motivational states by mTBI.


title: Early structural connectivity within the sensorimotor network: deviations related to prematurity and association to neurodevelopmental outcome

abstract:
The sensorimotor (SM) network is crucial for optimal neurodevelopment. However, undergoing rapid maturation during the perinatal period, it is particularly vulnerable to preterm birth.

Our work explores the prematurity impact on the microstructure and maturation of primary SM white matter (WM) tracts at term-equivalent age (TEA) and evaluates the relationships between these alterations and neurodevelopmental outcome.

We analyzed diffusion MRI data from the developing Human Connectome Project (dHCP) database: 59 preterm (PT) low-risk infants scanned near TEA, compared to a control group of full-term (FT) neonates paired for age at MRI and sex. We dissected pairwise connections between primary SM cortices and subcortical structures using probabilistic tractography and evaluated their microstructure with diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) models. In addition to tract- specific univariate analyses of diffusion metrics, we computed a maturational distance related to prematurity based on a multi-parametric Mahalanobis distance of each PT infant relative to the FT group. Finally, we evaluated the relationships between this distance and Bayley Scales of Infant and Toddler Development (BSID-III) scaled scores at 18 months corrected age.

Our results confirm important microstructural differences in SM tracts between PT and FT infants, with effects increasing with lower gestational age at birth. Additionally, comparisons of maturational distances highlight that prematurity has a differential effect on SM tracts which follows the established WM caudo-rostral developmental pattern. Our results suggest a particular vulnerability of projections involving the primary sensorimotor cortices (S1) and of the most rostral tracts, with cortico-cortical and S1-Lenticular tracts presenting the highest alterations at TEA. Finally, NODDI-derived maturational distances of specific tracts seem related to fine motor and cognitive scores.

This study expands the understanding of the impact of early WM alterations in the emerging SM network on long-term neurodevelopment. In the future, related approaches have potential to lead to the development of neuroimaging markers for neurodevelopmental disorders, with special interest for subtle neuromotor impairments frequently observed in preterm-born children.


title: Paired stimulation for spike-timing dependent plasticity quantified with single neuron responses in primate motor cortex

abstract: Spike-timing dependent plasticity (STDP) is an extensively studied topic. Previous studies have demonstrated stimulus induced targeted STDP both in vitro and in vivo, but a more consistent and robust method is required. We hypothesized there were two reasons contributing to the inconsistent results previously reported: 1. the measure of connectivity is poorly understood, and 2. the timing of stimulation is static or has low temporal specificity. To test our hypotheses, we applied paired stimulation to the primary motor cortex of awake primates. Single unit responses to stimulation were used as measures of connectivity, and we applied inter-stimulus intervals (ISIs) from {+/-}0.1 to {+/-}50 ms with sub-millisecond intervals. The excitatory single unit response resulted in very consistent changes after conditioning that was dependent on the ISI. Negative ISIs resulted in depression similar to classic STDP, but positive ISI also often resulted in depression. Normalizing the ISIs to the timing of the excitatory response revealed that potentiation only occurred if the second stimulus arrived before the response. Stimuli occurring around the time of the response often resulted in depression as strong as negative ISIs. We additionally tracked the changes in cortico-cortical evoked potentials (CCEPs), a commonly used measure of connectivity in plasticity experiments. CCEP changes showed a similar but more variable dependence to ISI. These results show that the classic STDP curve may be more difficult to induce due to interactions between excitatory and inhibitory circuitry, and that CCEPs may not be the ideal measure of changes in strength of connectivity.


title: Curation of BIDS (CuBIDS): a workflow and software package for streamlining reproducible curation of large BIDS datasets

abstract:
The Brain Imaging Data Structure (BIDS) is a specification accompanied by a software ecosystem that was designed to create reproducible and automated workflows for processing neuroimaging data. BIDS Apps flexibly build workflows based on the metadata detected in a dataset. However, even BIDS valid metadata can include incorrect values or omissions that result in inconsistent processing across sessions. Additionally, in large-scale, heterogeneous neuroimaging datasets, hidden variability in metadata is difficult to detect and classify. To address these challenges, we created a Python-based software package titled "Curation of BIDS" (CuBIDS), which provides an intuitive workflow that helps users validate and manage the curation of their neuroimaging datasets. CuBIDS includes a robust implementation of BIDS validation that scales to large samples and incorporates DataLad--a version control software package for data--to ensure reproducibility and provenance tracking throughout the entire curation process. CuBIDS provides tools to help users perform quality control on their images metadata and identify unique combinations of imaging parameters. Users can then execute BIDS Apps on a subset of participants that represent the full range of acquisition parameters that are present, accelerating pipeline testing on large datasets.

HIGHLIGHTSO_LICuBIDS is a workflow and software package for curating BIDS data.
C_LIO_LICuBIDS summarizes the heterogeneity in a BIDS dataset.
C_LIO_LICuBIDS prepares BIDS data for successful preprocessing pipeline runs.
C_LIO_LICuBIDS helps users perform metadata-based quality control.
C_LI


title: Common genetic variants in CHRNA5 alter β-amyloid neuropathology and highlight chandelier cells in human aging and Alzheimer's disease

abstract:
Changes in high-affinity nicotinic acetylcholine receptors are intricately connected to cognitive impairment in Alzheimers Disease (AD). While preclinical work suggests a possible protective and cognitive-enhancing role for the auxiliary nicotinic 5 subunit, mRNA expression of the CHRNA5 gene has not been closely examined in the context of human aging and dementia. Here, we investigate the impact of two common SNPs predicted to have different effects on the nicotinic 5 subunit: the function-compromising rs16969968 and the expression-altering rs1979905. We analyzed data from human prefrontal cortex (922 subjects with matched genotypic and post-mortem RNA sequencing, including 22 subjects with single-nucleus data) of elderly participants in the Religious Orders Study and Memory and Aging Project (ROS/MAP). We tested the impact of SNP haplotypes on prefrontal expression of CHRNA5 as well as that of SNPs in its receptor partners: CHRNA4 and CHRNB2. In the context of cognition and neuropathology, we observed a significant negative association between the high CHRNA5-expressing rs1979905A2 genotype and {beta}-amyloid load in the prefrontal cortex. Our analyses revealed that the greatest abundance of CHRNA5 expression was in chandelier neurons, a sparse but disproportionately-powerful set of interneurons, in addition to layer 5 and 6 pyramidal neurons. In subjects with functionally-unaltered CHRNA5, the proportion of chandelier cells in the prefrontal cortex shows resilience to {beta}-amyloid load, but this resilience is diminished in subjects homozygous for the minor allele of the CHRNA5 missense SNP rs16969968. Taken together, these findings urge further investigation into the role of CHRNA5 and chandelier cells in AD neuroprotection.

Significance statementThe nicotinic 5 subunit is important for attention and cognition, however its relationship to aging and neuropathology is unknown. Our findings suggest that polymorphisms affecting CHRNA5 expression associate with altered brain amyloid pathology. Cell type-specific expression of CHRNA5 in the prefrontal cortex implicates chandelier interneurons as a focus of 5-mediated nicotinic signalling, potentially involved in regulating amyloid load. We find that a missense CHRNA5 polymorphism is correlated with increased sensitivity of this class of interneuron to amyloid pathology. A neuroprotective role for CHRNA5 identifies it as a possible target for therapies to improve neuron survival and excitatory/inhibitory balance in AD pathology.


title: Neural correlates for neonicotinoid-induced impairment of olfactory long-term memory

abstract: Reports of olfactory learning and memory deficits in honey bees exposed to neonicotinoid pesticides have been accumulating over the past decades. As agonists of the nicotinic receptors to acetylcholine, neonicotinoids target most of the projection neurons conveying olfactory information to the memory brain centres, the mushroom bodies (MBs). However, the neural mechanisms by which neonicotinoids interfere with memory formation are poorly understood. Here, we investigated the consequences of chronic exposure to the neonicotinoid imidacloprid on the number of projection neuron terminal boutons and on their plasticity in the context of long-term memory formation. Using super-resolution STED microscopy, we also measured the density of synapsin-positive units (SPUs) within boutons, as synapsin is known to be enriched in new boutons following neuronal activation. We show that imidacloprid suppresses the synaptic pruning of projection neurons naturally occurring with age and experience. The resulting excessive number of boutons in the MBs of treated bees was associated with long-term memory deficits. The subset of treated bees that showed successful memory formation had a similar number of boutons as untreated bees, suggesting that synaptic pruning might have been involved in the memorization process. As the SPU density was not affected by the imidacloprid treatment, the high bouton number in the lip of treated bees was not due to synaptogenesis. Altogether, our experiments show that, by altering synaptic pruning, imidacloprid interferes with long-term memory formation.


title: A comprehensive analysis of Usutu virus (USUV) genomes revealed lineage-specific codon usage patterns and host adaptation

abstract: The Usutu virus (USUV) is an emerging arbovirus virus maintained in the environment of Afro-Eurasia via a bird-mosquito-bird enzootic cycle and sporadically infected other vertebrates. Despite primarily asymptomatic or mild symptoms, humans infected by USUV can develop severe neurological diseases such as meningoencephalitis. However, no detailed study has yet been conducted to investigate its evolution from the perspective of codon usage patterns. Codon usage choice of viruses reflects the genetic variations that enable them to reconcile their viability and fitness towards the external environment and new hosts. This study performed a comprehensive evolution and codon usage analysis in USUVs. Our reconstructed phylogenetic tree confirmed the circulation viruses belonging to eight distinct lineages, reaffirmed by principal component analysis based on codon usage patterns. We also found a relatively small codon usage bias and that natural selection, mutation pressure, and evolutionary processes collectively shaped the codon usage of the USUV, with natural selection predominating over the others. Additionally, a complex interaction of codon usage between the USUV and its host was observed. This process could have enabled USUVs to adapt to various hosts and vectors, including humans. Therefore, the USUV may possess a potential risk of cross-species transmission and subsequent outbreaks. In this respect, further epidemiologic surveys, diversity monitoring, and pathogenetic research are warranted.


title: Development of dim-light vision in the nocturnal coral reef fish family, Holocentridae

abstract:
Developmental changes to the visual systems of animals are often associated with ecological shifts. Reef fishes experience a change in habitat between larval life in the shallow open ocean to juvenile and adult life on the reef. Some species also change their lifestyle over this period and become largely nocturnal. While these ecological transitions are well documented, little is known about the ontogeny of nocturnal reef fish vision. Here, we used histology and transcriptomics to investigate visual development in 12 representative species from both subfamilies, Holocentrinae (squirrelfishes) and Myripristinae (soldierfishes), in the nocturnal coral reef fish family, Holocentridae. Results revealed that the visual systems of holocentrids are initially well-adapted to photopic conditions with pre-settlement larvae having high cone densities, high cone opsin gene expression, a broad cone opsin gene repertoire (8 genes) and a multibank retina (i.e., stacked layers of rods) comprising up to two rod banks. At reef settlement, holocentrids started to invest more in their scotopic visual system and upregulated genes involved in cell differentiation/proliferation. By adulthood, they had well-developed scotopic vision with a rod-dominated multibank retina comprising 5-17 rod banks, increased summation of rods onto ganglion cells, high rod opsin gene expression, reduced cone opsin gene expression and repertoire (1-4 genes) and upregulated phototransduction genes. Finally, although the two subfamilies shared similar ecologies across development, their visual systems diverged after settlement, with Myripristinae investing more in scotopic vision than Holocentrinae. Hence, both ecology and phylogeny likely determine the development of the holocentrid visual system.

Summary statementCoral reef fishes in the family Holocentridae remodel their retina at the cellular and molecular levels to adapt to a nocturnal lifestyle during development.


title: Groundfish biodiversity change in northeast Pacific waters under projected warming and deoxygenation

abstract: Projections of how climate change will impact marine species and communities are urgently needed to inform management measures aimed at stemming biodiversity loss. In the coming decades, warming and deoxygenation of marine waters are anticipated to result in shifts in the distribution and abundance of fishes, with consequences for the diversity and composition of fish communities. Most projections to date have focused on temperature, but have not accounted for the confounding influence of oxygen and depth and are limited by the spatial resolution of global climate models. Here, we combine fisheries independent trawl survey data spanning the west coast of the USA and Canada with high resolution regional ocean models to make projections of how 40 groundfish species will be impacted by changes in temperature and oxygen in British Columbia (B.C.) and Washington. By leveraging coast-wide survey data, we quantify how temperature, oxygen, and depth jointly constrain the ranges of species. Then, using two high-resolution regional ocean-biogeochemical models, we make projections of biodiversity change at a high spatial resolution. Our projections suggest that, in B.C. and Washington, the number of species that are projected to decrease in occurrence is roughly balanced by the number that are projected to increase, resulting in considerable compositional turnover. Many, but not all, species are projected to shift to deeper depths as conditions warm, but low oxygen will limit how deep they can go. Thus biodiversity will likely decrease in the shallowest waters (< 100 m) where warming will be greatest, increase at mid depths (100--600 m) as shallow species shift deeper, and remain stable or decrease at depths where oxygen is limited (> 600 m). These results highlight the critical importance of accounting for the joint role of temperature, oxygen, and depth when projecting the impacts of climate change on marine biodiversity.

category: ecology


title: Identifying disease-associated circRNAs based on edge-weighted graph attention and heterogeneous graph neural network

abstract:
MotivationCircular RNAs (circRNAs) with varied biological activities are implicated in pathogenic processes, according to new findings. They are regarded as promising biomarkers for the diagnosis and prognosis due to their structural features. Computational approaches, as opposed to traditional experiments, can identify the circRNA-disease connections at a lower cost. Multi-source pathogenesis data can help to reduce data sparsity and infer probable connections at the system level. The majority of available approaches create a homologous network using multi-source data, but they lose the datas heterogeneity. Effective solutions that make use of the peculiarities of multi-source data are urgently needed.

ResultsIn this paper, we propose a model (CDHGNN) based on edge-weighted graph attention and heterogeneous graph neural networks for discovering probable circRNA-disease correlations prediction. The circRNA network, miRNA network, disease network and heterogeneous network are constructed based on the introduced multi-source data on circRNAs, miRNAs, and diseases. The features for each type of node in the network are then extracted using a designed edge-weighted graph attention network model. Using the revised node features, we learn meta-path contextual information and use heterogeneous neural networks to assign attention weights to different types of edges. CDHGNN outperforms state-of-the-art algorithms with comparable accuracy, according to the findings of the trial. Edge-weighted graph attention networks and heterogeneous graph networks have both improved performance significantly. Furthermore, case studies suggest that CDHGNN is capable of identifying particular molecular connections and can be used to investigate pathogenic pathways.

Contactjxwang@mail.csu.edu.cn


title: Biological age is increased by stress and restored upon recovery

abstract: Aging is classically conceptualized as an ever-increasing trajectory of damage accumulation and loss of function, leading to increases in morbidity and mortality. However, recent in vitro studies have raised the possibility of age reversal. Here, we report that biological age is fluid and exhibits rapid changes in both directions. By applying advanced epigenetic aging clocks, we find that the biological age of young mice is increased by heterochronic parabiosis and restored following surgical detachment of animals. We also identify transient changes in biological age during major surgery, pregnancy, and severe COVID-19 in humans and/or mice. Together, these data show that biological age undergoes a rapid increase in response to diverse forms of stress, which is reversed following recovery from stress. Our study uncovers a new layer of aging dynamics that should be considered in future studies. Elevation of biological age by stress may be a quantifiable and actionable target for future interventions.


title: Microglial expression of the Wnt signalling modulator DKK2 differs between human Alzheimer's disease brains and mouse neurodegeneration models

abstract:
Wnt signalling is crucial for synapse and cognitive function. Indeed, deficient Wnt signalling is causally related to increased expression of DKK1, an endogenous negative Wnt regulator, and synapse loss, both of which likely contribute to cognitive decline in Alzheimers disease (AD). Increasingly, AD research efforts have probed the neuroinflammatory role of microglia, the resident immune cells of the central nervous system (CNS), which have furthermore been shown to be modulated by Wnt signalling.

The DKK1 homologue DKK2 has been previously identified as an activated response and/or disease-associated microglia (DAM/ARM) gene in a mouse model of AD. Here we performed a detailed analysis of DKK2 in mouse models of neurodegeneration, and in human AD brain. In APP/PS1 and APPNL-G-F AD mouse model brains as well as in SOD1G93A ALS mouse model spinal cords, but not in control littermates, we demonstrated significant microgliosis and microglial Dkk2 mRNA upregulation in a disease-stage dependent manner. In the AD models, these DAM/ARM Dkk2+ microglia preferentially accumulated close to {beta}Amyloid plaques. Furthermore, recombinant DKK2 treatment of rat hippocampal primary neurons blocked WNT7a-induced dendritic spine and synapse formation, indicative of an anti-synaptic effect similar to that of DKK1. In stark contrast, no such microglial DKK2 upregulation was detected in the post-mortem human frontal cortex from individuals diagnosed with AD or pathological ageing.

In summary, the difference in microglial expression of the DAM/ARM gene DKK2 between mouse models and human AD brain highlights the increasingly recognised limitations of using mouse models to recapitulate facets of human neurodegenerative disease.

Significance statementThe endogenous negative Wnt regulator Dkk2 is significantly upregulated at the mRNA level in microglia of AD mouse models, implying that microglia derived Dkk2 protein may detrimentally contribute to a reduced Wnt signalling tone in the AD brain, a known pathophysiological manifestation. Indeed, recombinant DKK2 prevented Wnt- dependent synapse formation in cultured neurons. However, DKK2 upregulation was not recapitulated in post-mortem human AD brains.

The success of neurodegeneration animal models has relied on pathophysiology that for the most part correctly modelled human disease. Increasingly however, limitations to the validity of mouse models to recapitulate human neurodegenerative disease have become apparent, as evidenced by the present study by the difference in microglial DKK2 expression between AD mouse models and human AD brain.


title: A parallel channel of state-dependent sensory signaling from the cholinergic basal forebrain to the auditory cortex

abstract: Cholinergic basal forebrain (CBF) signaling exhibits multiple timescales of activity with classic, slow signals related to brain and behavioral states and faster, phasic signals reflecting behavioral events, including movement and reinforcement. Recent evidence suggests that the CBF may also exhibit fast, sensory-evoked responses. It remains unknown, however, whether such sensory signals target the sensory cortex and how they relate to local functional topography. Moreover, the extent to which fast and slow CBF activity interact has been largely unexplored. Here, we used simultaneous two-channel, two-photon imaging of CBF axons and auditory cortical (AC) neurons to reveal that CBF axons project a robust, non-habituating, and stimulus-specific sensory signal to the AC. Individual axon segments exhibited heterogeneous but stable tuning to auditory stimuli allowing stimulus identity to be decoded from the population. However, CBF axons displayed no tonotopy and their frequency tuning was uncoupled from that of nearby cortical neurons. Chemogenetic suppression revealed the auditory thalamus as a principal source of auditory information to the CBF. Finally, slow fluctuations in cholinergic activity modulated the fast, sensory-evoked signals in the same axons, suggesting that a multiplexed combination of fast and slow signals is projected from the CBF to the AC. Taken together, our work demonstrates a novel, non-canonical function of the CBF as a parallel channel of state-dependent sensory signaling to the sensory cortex that provides repeated representations of a broad range of sound stimuli at all points on the tonotopic map.


title: Novel Computational Models of Evoked Dopamine Release In Vivo Measured by Fast Scan Cyclic Voltammetry Quantify the Regulation of Presynaptic Kinetics by Synucleins

abstract: Dopamine neurotransmission in the striatum is central to many normal and disease functions. Ventral midbrain dopamine neurons exhibit ongoing tonic firing that produce low extrasynaptic levels of dopamine below the detection of extrasynaptic electrochemical recordings ([~]10 - 20 nanomolar), with superimposed bursts that can saturate the dopamine uptake transporter and produce transient micromolar concentrations. The bursts have previously been shown to lead to presynaptic plasticity via multiple mechanisms, but analysis methods for these kinetic parameters are limited. To provide a deeper understanding of the mechanics of dopamine neurotransmission, we present three computational models of dopamine release with different levels of spatiotemporal complexity to analyze in vivo fast-scan cyclic voltammetry recordings from the dorsal striatum of mice. The models accurately fit to the cyclic voltammetry data and provide estimates of presynaptic dopamine facilitation/depression kinetics and dopamine transporter reuptake kinetics. We use the models to analyze the role of synuclein proteins in neurotransmission and quantify recent findings linking presynaptic protein -synuclein to the short-term facilitation and long-term depression of dopamine release.


title: Early patterning followed by tissue growth establishes proximo-distal identity in Drosophila Malpighian tubules

abstract:
Specification and elaboration of proximo-distal (P-D) axes for structures or tissues within a body occurs secondarily from that of the main axes of the body. Our understanding of the mechanism(s) that pattern P-D axes is limited to a few examples such as vertebrate and invertebrate limbs. Drosophila Malpighian/renal tubules (MipTs) are simple epithelial tubules, with a defined P-D axis. How this axis is patterned is not known, and provides an ideal context to understand patterning mechanisms of a secondary axis. Furthermore, epithelial tubules are widespread, and their patterning is not well understood. Here, we describe the mechanism that establishes distal tubule and show this is a radically different mechanism to that patterning the proximal MpT. The distal domain is patterned in two steps: distal identity is specified in a small group of cells at the earliest stage of MpT development through Wingless/Wnt signalling. Subsequently, this population is expanded by proliferation to generate the distal MpT domain. This mechanism enables distal identity to be established in the tubule in a domain of cells much wider than the effective range of Wingless.

Summary statementHow does proximo-distal patterning occur in the epithelial Malpighian/renal tubules? Cells are patterned early by a mechanism involving Wingless/Wnt, and expand by cell proliferation to generate a distal domain.


title: PKD autoinhibition in trans regulates activation loop autophosphorylation in cis

abstract: Phosphorylation is a ubiquitous mechanism by which signals are transduced in cells. Protein kinases, enzymes that catalyze the phospho-transfer reaction are, themselves, often regulated by phosphorylation. Paradoxically, however, a substantial fraction of the more than 500 human protein kinases are capable of catalyzing their own activation loop phosphorylation. Commonly, these kinases perform this autophosphorylation reaction in trans, whereby transient dimerization leads to the mutual phosphorylation of the activation loop of the opposing protomer. In this study, we demonstrate that Protein Kinase D (PKD) is regulated by the inverse mechanism of dimerization-mediated trans-autoinhibition, followed by activation loop autophosphorylation in cis. We show that PKD forms a stable face-to-face homodimer that is incapable of either auto- or substrate phosphorylation. Dissociation of this trans-autoinhibited dimer results in activation loop autophosphorylation, which occurs exclusively in cis. Phosphorylation serves to increase PKD activity and prevent trans-autoinhibition, thereby switching PKD on. Our findings not only reveal the mechanism of PKD regulation, but have profound implications for the regulation of many other eukaryotic kinases.

category: biochemistry


title: Molecular basis of C9orf72 poly-PR interference with the β-karyopherin family of nuclear transport receptors

abstract: Nucleocytoplasmic transport (NCT) is affected in several neurodegenerative diseases including C9orf72-ALS. It has recently been found that arginine-containing dipeptide repeat proteins (R-DPRs), translated from C9orf72 repeat expansions, directly bind to several importins. To gain insight into how this can affect nucleocytoplasmic transport, we use coarse-grained molecular dynamics simulations to study the molecular interaction of poly-PR, the most toxic DPR, with several Kap{beta}s (importins and exportins). We show that poly-PR-Kap{beta} binding depends on the net charge per residue (NCPR) of the Kap{beta}, salt concentration of the solvent, and poly-PR length. Poly-PR makes contact with the inner surface of most importins, which strongly interferes with Kap{beta} binding to cargo-NLS, IBB, and RanGTP in a poly-PR length-dependent manner. Longer poly-PRs at higher concentrations are also able to make contact with the outer surface of importins that contain several binding sites to FG-Nups. We also show that poly-PR binds to exportins, especially at lower salt concentrations, interacting with several RanGTP and FG-Nup binding sites. Overall, our results suggest that poly-PR might cause length-dependent defects in cargo loading, cargo release, Kap{beta} transport and Ran gradient across the nuclear envelope.


title: Structure of the lysosomal membrane fusion machinery

abstract: Lysosomes are of central importance in cellular recycling, nutrient signaling 1,2 and endocytosis, and are tightly connected to autophagy 3 and the invasion of pathogenic bacteria and viruses 1,4. Lysosomal fusion events are fundamental to cell survival and require HOPS, a conserved heterohexameric tethering complex 5,6. HOPS recognizes and binds small membrane-associated GTPases on lysosomes and organelles, and assembles membrane bound SNAREs for fusion 7,8. Through tethering, HOPS brings membranes in close proximity to each other and significantly increases fusion efficacy by catalysing SNARE assembly. Consequently, different HOPS mutations are causative for severe diseases 6. Despite its fundamental cellular duties, it remained speculative how HOPS fulfils its function as high-resolution structural data were unavailable. Here, we used cryo-electron microscopy to reveal the structure of HOPS. In the complex, two central subunits form the backbone and an assembly hub for the functional domains. Two GTPase binding units extend to opposing ends, while the SNARE binding module points to the side, resulting in a triangular shape of the complex. Unlike previously reported, HOPS is surprisingly rigid and extensive flexibility is confined to its extremities. We show that HOPS complex variants with mutations proximal to the backbone can still tether membranes but fail to efficiently promote fusion indicating, that the observed integrity of HOPS is essential to its function. In our model, the core of HOPS acts as a counter bearing between the flexible GTPase binding domains. This positions the SNARE binding module exactly between the GTPase anchored membranes to promote fusion. Our structural and functional analysis reveals the link between the spectacular architecture of HOPS and its mechanism that couples membrane tethering and SNARE assembly, to catalyse lysosomal fusion.


title: Dual-wavelength stopped-flow analysis of the lateral and longitudinal assembly kinetics of vimentin

abstract:
Vimentin is a highly charged intermediate filament protein that inherently forms extended dimeric coiled-coils, which serve as the basic building blocks of intermediate filaments. Under low ionic strength conditions, vimentin filaments dissociate into uniform tetrameric complexes of two anti-parallel oriented, half-staggered coiled-coil dimers. By addition of salt, vimentin tetramers spontaneously reassemble into filaments in a time-dependent process: i) lateral assembly of tetramers into unit-length filaments (ULFs); ii) longitudinal annealing of ULFs; iii) longitudinal assembly of filaments coupled with subsequent radial compaction. To independently determine the lateral and longitudinal assembly kinetics, we measure with a stopped-flow instrument the static light scattering signal at two different wavelengths (405 and 594 nm) with a temporal resolution of 3 ms, and analyze the signals based on Rayleigh-Gans theory. This theory considers that the intensity of the scattered light depends not only on the molecular weight of the scattering object but also on its shape. This shape-dependence is more pronounced at shorter wavelengths, allowing us to decompose the scattered light signal into its components arising from lateral and longitudinal filament assembly. We demonstrate that both the lateral and longitudinal filament assembly kinetics increase with salt concentration.

Significance statementThe proper formation of intermediate filament (IF) networks in the cytoplasm is important for numerous cell functions. Here, we present a stopped-flow method for measuring the in-vitro assembly kinetics of intermediate filaments with a temporal resolution of 3 ms using static light scattering at two different wavelengths. This allows us to compute the shape factor of the assembly products based on Rayleigh-Gans light scattering theory. From the shape factor, we can separately measure the lateral assembly of tetramers into unit-length filaments (ULFs), and the longitudinal annealing of ULFs and longer filaments. For the IF protein vimentin, we find that with increasing salt concentrations, both the lateral and longitudinal assembly rates increase, and unstable, hyper-aggregated assembly complexes emerge.


title: Host transcriptomic profiling of CD-1 outbred mice with severe clinical outcomes following infection with Orientia tsutsugamushi

abstract:
Orientia tsutsugamushi is an obligately intracellular bacterium with endothelial tropism and can cause mild to lethal scrub typhus in humans. No vaccine is available for this reemerging and severely neglected infection. Previous scrub typhus studies have utilized inbred mice, yet such models have intrinsic limitations. Thus, the development of suitable mouse models that better mimic human diseases is in great need for immunologic investigation and future vaccine studies. This study is aimed at establishing scrub typhus in outbred CD-1 mice and defining immune biomarkers related to disease severity. CD-1 mice received O. tsutsugamushi Karp strain via the i.v. route; major organs were harvested at 2-12 days post-infection for kinetic analyses. We found that for our given infection doses, CD-1 mice were significantly more susceptible (90-100% lethal) than were inbred C57BL/6 mice (0-10% lethal). Gross pathology of infected CD-1 mouse organs revealed features that mimicked human scrub typhus, including pulmonary edema, interstitial pneumonia, perivascular lymphocytic infiltrates, and vasculitis. Alteration in angiopoietin/receptor expression in inflamed lungs implied endothelial dysfunction. Lung immune gene profiling using NanoString analysis displayed a Th1/CD8-skewed, but Th2 repressed profile, including novel biomarkers not previously investigated in other scrub typhus models. Bio-plex analysis revealed a robust inflammatory response in CD-1 mice as evidenced by increased serum cytokine and chemokine levels, correlating with immune cell recruitment during the severe stages of the disease. This study provides an important framework indicating a value of CD-1 mice for delineating host susceptibility to O. tsutsugamushi, immune dysregulation, and disease pathogenesis. This preclinical model is particularly useful for future translational and vaccine studies for severe scrub typhus.

Author SummaryScrub typhus is a severely neglected and potentially fatal disease caused by Orientia tsutsugamushi, a genetically intractable, obligately intracellular bacterium that annually infects at least one million people worldwide. There is no vaccine available, and our current understanding of the host immunological response and mechanisms remains very limited. Appropriate animal models of infection that recapitulate the disease are essential to the development of effective therapeutics and vaccines. In this study, we characterized the immunologic responses by transcriptomics and Bio-plex assays in outbred CD-1 mice with lethal O. tsutsugamushi infection. We found that CD-1 mice were highly susceptible to infection and that the high mortality correlated with a Th1/CD8-skewed, but Th2 repressed, immune profile during the acute phase of disease. This proinflammatory state was further confirmed by elevated cytokine and chemokine levels in the sera. Collectively, this study established CD-1 mice as a practical, preclinical model to define pathogenic mechanisms underlying severe scrub typhus and for future immunologic and translational studies during O. tsutsugamushi infection.


title: Hemodynamic stress activates inflammatory responses and cell death through spectrin-dependent modulation of Store Operated Calcium Entry

abstract: Circulating blood cells, such as leukocytes, experience significant hemodynamic stresses. These stresses are significantly higher when a patient requires mechanical support of the circulation, such as cardiopulmonary bypass. To identify molecular mechanisms by which cells sense these stresses, we utilized genome wide CRISPRi and phosphoproteomics data. These screens identified non-erythroid spectrin 1 (SPTAN1) and RAF1 as effectors of hemodynamic stress in monocytes. We show that fluid stress induces SPTAN1/RAF1 signaling to promote STIM1 and ORAI1 interaction resulting in Store-Operated Calcium Entry (SOCE) thereby driving inflammation and cell death.


title: Gene family expansion and functional diversification of chitinase and chitin synthase genes in Atlantic salmon (Salmo salar)

abstract:
BackgroundChitin is one of the most abundant polysaccharides in nature, forming important structures in insects, crustaceans, and fungal cell walls. Vertebrates on the other hand are generally considered "non-chitinous" organisms, despite having highly conserved chitin metabolism associated genes. Recent work has revealed that the largest group of vertebrates, the teleosts, have the potential to both synthesize and degrade endogenous chitin. Yet little is still known about the genes and proteins responsible for these dynamic processes. Here we used comparative genomics, transcriptomics, and chromatin accessibility data to characterize the repertoire, evolution, and regulation of genes involved in chitin-metabolism in teleosts, with a particular focus on Atlantic salmon.

ResultsReconstruction of gene family phylogenies provide evidence for an expansion of teleost and salmonid chitinase and chitin synthase genes after multiple whole-genome duplications. Analyses of multi-tissue gene expression data demonstrated a strong bias of gastrointestinal tract expression for chitin metabolism genes, but with different spatial and temporal tissue specificities. Finally, we integrated transcriptomes from a developmental time series of the gastrointestinal tract with chromatin accessibility data to identify putative transcription factors responsible for regulating chitin-metabolism gene expression (CDX1 and CDX2) as well as tissue-specific divergence in the regulation of gene duplicates (FOXJ2). These transcription factors are also potential regulators of multiple glycosyltransferases being co-expressed with the chitin remodeling genes.

ConclusionThe findings presented here add support to the hypothesis that chitin metabolism genes in teleosts play a role in developing and maintaining a chitin-based barrier in the teleost gut and provide a basis for further investigations into the molecular basis of this barrier.


title: The role of dynamic DNA methylation in liver transplant rejection in children

abstract:
BackgroundTranscriptional regulation of liver transplant (LT) rejection may reveal novel predictive and therapeutic targets.

PurposeTo test the role of differential DNA methylation in children with biopsy-proven acute cellular rejection (rejectors, R) after LT.

MethodsPaired peripheral blood DNA samples were obtained before and after LT from 17 children, including 4R and 13 non-rejector (NR), and assayed with MethylC capture sequencing (MCC-Seq) approach covering 5 million CpGs in immune-cell specific regulatory elements. Differentially methylated CpGs (DMCs) were identified using generalized linear regression models adjusting for sex and age and merged into differentially methylated regions (DMR) comprising 3 or more DMCs.

ResultsContrasting R vs NR, we identified 2238 DMCs in post-LT and 2620 DMCs in pre-LT samples, which clustered in 216 and 282 DMRs respectively. DMCs associated with R were enriched in enhancers and depleted in promoters. The proportion of hypomethylated versus hypermethylated DMRs increased from 22% to 48% (p<0.0001) in pre-LT vs. post-LT DMCs, respectively. The highest-ranked biological processes enriched in post-LT DMCs were antigen processing and presentation via MHC class I, MHC class I complex, and peptide binding (p<7.92E-17), respectively. Top-ranked DMRs mapped to genes which mediate B-cell receptor signaling (ADAP1) or regulate several immune cells (ARRB2) (p<3.75E-08). DMRs in MHC class I genes were enriched for SNPs which bind TFs, affect gene expression and splicing, or alter peptide-binding amino acid sequences.

ConclusionsDynamic methylation in distal regulatory regions reveals known transplant-relevant MHC-dependent rejection pathways, and identifies novel loci for future mechanistic evaluations in pediatric transplant subcohorts.

category: genomics


title: Structure of the RAF1-HSP90-CDC37 complex reveals the basis of RAF1 regulation

abstract: RAF kinases are RAS-activated enzymes that initiate signalling through the MAPK cascade to control cellular proliferation, differentiation, and survival. Here, we describe the structure of the full-length RAF1 protein in complex with HSP90 and CDC37 obtained by cryo-electron microscopy. The reconstruction reveals a RAF1 kinase with an unfolded N-lobe separated from its C-lobe. The hydrophobic core of the N-lobe is trapped in the HSP90 dimer while CDC37 wraps around the chaperone and interacts with the N- and C-lobes of the kinase. The structure indicates how CDC37 can discriminate between the different members of the RAF family. Our structural analysis also reveals that the folded RAF1 assembles with 14-3-3 dimers, suggesting that after folding follows a similar activation as B-RAF. Finally, disruption of the interaction between CDC37 and the DFG segment of RAF1 unveils potential vulnerabilities to attempt the pharmacological degradation of RAF1 for therapeutic purposes.


title: An Entropy Approach for Choosing Gene Expression Cutoff

abstract: Annotating cell types using single-cell transcriptome data usually requires binarizing the expression data to distinguish between the background noise vs. real expression or low expression vs. high expression cases. A common approach is choosing a "reasonable" cutoff value, but it remains unclear how to choose it. In this work, we describe a simple yet effective approach for finding this threshold value.

category: bioinformatics


title: Genomic patterns of malignant peripheral nerve sheath tumour (MPNST) evolution correlate with clinical outcome and are detectable in cell-free DNA

abstract: Malignant peripheral nerve sheath tumour (MPNST) is an aggressive soft-tissue sarcoma that arises in peripheral nerves. MPNST occurs either sporadically or in people with neurofibromatosis type 1 (NF1), a common cancer predisposition syndrome caused by germline pathogenic variants in NF1. Although MPNST is the most common cause of death and morbidity for individuals with NF1, the molecular underpinnings of MPNST pathogenesis remain unclear. Here, we report the analysis of whole-genome sequencing, multi-regional exome sequencing, transcriptomic and methylation profiling data for 95 MPNSTs and precursor lesions (64 NF1-related; 31 sporadic) from 77 individuals. Early events in tumour evolution include biallelic inactivation of NF1 followed by inactivation of CDKN2A and in some cases also TP53 and polycomb repressive complex 2 (PRC2) genes. Subsequently, both sporadic and NF1-related MPNSTs acquire a high burden of somatic copy number alterations (SCNAs). Our analysis revealed distinct pathways of tumour evolution and immune infiltration associated with inactivation of PRC2 genes and H3K27 trimethylation (H3K27me3) status. Tumours with loss of H3K27me3 evolve through extensive chromosomal losses with retention of chromosome 8 heterozygosity followed by whole genome doubling and chromosome 8 amplification. These tumours show lower levels of immune cell infiltration with low cytotoxic activity and low expression of immune checkpoints. In contrast, tumours with retention of H3K27me3 evolve through extensive genomic instability in the absence of recurrent alterations and exhibit an immune cell-rich phenotype. Specific SCNAs detected in both tumour samples and cell-free DNA (cfDNA) act as a surrogate for loss of H3K27me3 and immune infiltration, and predict prognosis. Our results suggest that SCNA profiling of tumour or cfDNA could serve as a biomarker for early diagnosis and to stratify patients into prognostic and treatment-related subgroups.


title: Testing the link between isoaspartate and Alzheimer's disease etiology

abstract:
Isoaspartate (isoAsp) is a damaging amino acid residue formed in proteins as a result of spontaneous deamidation. IsoAsp disrupts the secondary and higher order structures of proteins, damaging their functions and making them prone to aggregation. An association has been suggested between isoAsp and Alzheimers Disease (AD). Here we strengthened the link between isoAsp and AD by novel approaches to isoAsp analysis in blood human serum albumin (HSA), the most abundant blood protein, a major carrier of amyloid beta (A{beta}) peptide and phosphorylated tau (pTau) protein in blood and a key participant in their clearance pathway. We discovered a reduced amount of anti-isoAsp antibodies (P < .0001), an elevated isoAsp level in HSA (P < .001), more HSA aggregates (P < .0001) and increased levels of free A{beta} (P < .01) in AD blood compared to healthy controls. We also found that deamidation significantly reduces HSA capacity to bind with A{beta} and pTau (P < .05). These findings support the presence in AD of a bottleneck in clearance of A{beta} and pTau leading to their increased concentrations in brain and facilitating their aggregations there.

RESEARCH IN CONTEXTO_LISystematic review: We reviewed the evidence that associates isoaspartate (isoAsp) residue in blood proteins with the etiology of Alzheimers disease (AD). However, the link between isoAsp in blood and aggregation of amyloid beta (A{beta}) peptide and phosphorylated tau (pTau) protein in brain remained unclear.
C_LIO_LIInterpretation: For the first time we demonstrate that isoAsp-containing human serum albumin (HSA) forms aggregates with reduced binding capacity toward A{beta} peptide and pTau protein. Using a novel ELISA, we discovered in AD blood elevated levels of isoAsp in HSA, together with reduced endogenous anti-isoAsp antibody levels, suggesting hampered A{beta} and pTau clearance in AD.
C_LIO_LIFuture directions: As degradation of the innate anti-isoAsp defenses may take years to develop, investigation of the isoAsp role in early stages of AD is warranted. And enrollment of different neurodegenerative disease cohorts will illustrate if isoAsp is AD-specific or universal to diseases related to aging.
C_LI

O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY


title: Neutrophil-Mediated Stromal-Tumor IL-6/STAT-3 Signaling Underlies the Association between Neutrophil-to-Lymphocyte Ratio Dynamics and Chemotherapy Response in Localized Pancreatic Cancer: A Hybrid Clinical-Preclinical Study

abstract:
BackgroundPartial/complete pathologic response following neoadjuvant chemotherapy (NAC) in pancreatic cancer (PDAC) patients undergoing pancreatectomy is associated with improved survival. We sought to determine whether neutrophil-to-lymphocyte ratio (NLR) dynamics predict pathologic response following chemotherapy in PDAC, and if manipulating NLR impacts chemosensitivity in preclinical models and uncovers potential mechanistic underpinnings underlying these effects.

MethodsPathologic response in PDAC patients (n=94) undergoing NAC and pancreatectomy (7/2015-12/2019) was dichotomized as partial/complete or poor/absent (case-cohort design). Bootstrap-validated multivariable models assessed associations between pre-chemotherapy NLR (%neutrophils/%lymphocytes) or NLR dynamics during chemotherapy ({Delta}NLR=pre-surgery--pre-chemotherapy NLR) and pathologic response, disease-free survival (DFS), and overall survival (OS). To preclinically model effects of NLR attenuation on chemosensitivity, C57BL/6 mice (n=8-10/arm) were orthotopically injected with KrasG12D/+;Trp53fl/+;PdxCre(KPC)cells and randomized to vehicle, NLR-attenuating anti-Ly6G, gemcitabine/paclitaxel, or gemcitabine/paclitaxel+anti-Ly6G treatments.

ResultsIn 94 PDAC patients undergoing NAC (median:4 months), pre-chemotherapy NLR (P<0.001) and {Delta}NLR attenuation during NAC (P=0.002) were independently associated with partial/complete pathologic response. An NLR score=pre-chemotherapy NLR+{Delta}NLR correlated with DFS (P=0.006) and OS (P=0.002). Upon preclinical modeling, combining NLR-attenuating anti-Ly6G treatment with gemcitabine/paclitaxel--compared with gemcitabine/paclitaxel or anti-Ly6G alone--not only significantly reduced tumor burden and metastatic outgrowth, but also augmented tumor-infiltrating CD107a+-degranulating CD8+ T-cells (P<0.01) while dampening inflammatory cancer-associated fibroblast (CAF) polarization (P=0.006) and chemoresistant IL-6/STAT-3 signaling in vivo. Neutrophil-derived IL-1{beta} emerged as a novel mediator of stromal inflammation, inducing inflammatory CAF polarization and CAF-tumor cell IL-6/STAT-3 signaling in ex vivo co-cultures.

ConclusionsTherapeutic strategies to mitigate neutrophil-CAF-tumor cell IL-1{beta}/IL-6/STAT-3 signaling during NAC may improve pathologic responses and/or survival in PDAC.