Biology subjects

Williams, C. M.

Publications and source records attributed to Williams, C. M..

At least 19 recordsLinked to original sources

bioRxiv2026

Gut-immune signaling drives blood-brain barrier damage in pediatric allogeneic stem cell transplant

Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is a life-saving therapy for children with high-risk hematological diseases. However, allo-HSCT also confers the risk of long-term neurocognitive dysfunction, particularly in pediatric recipients, and the mechanisms underlying this remain poorly understood. While gastrointestinal toxicities and immune responses following allo-HSCT have been well characterized, their contribution to central nervous system toxicities is unknown. Here, using clinical biomarker analysis, we show evidence of blood-brain barrier (BBB) dysfunction in pediatric allo-HSCT, associated with IL-6 signaling and reduced levels of brain-derived neurotrophic factor. Pre-transplant gastrointestinal mucosal barrier injury was associated with post-transplant BBB leakage, implicating disrupted gut-brain-axis signaling. In vitro, gut damage-associated immune activation induced apoptosis and remodeling of brain microvascular endothelial cells (BMECs), with surviving cells exhibiting tight junction disruption and cytoskeletal reorganization. Plasma from allo-HSCT recipients similarly induced BMEC apoptosis. Notably, both immune signaling- and patient plasma-induced BMEC apoptosis were prevented by IL-6 inhibition or supplementation with the gut microbiota-derived metabolite propionate. Together, these findings identify immune signaling as a correlate of BBB damage clinically and a causative driver in vitro in pediatric allo-HSCT.

neuroscience↗

bioRxiv2026

Mapping the genetic architecture of human cortical expansion and its links to neuropsychiatric disorders

Cortical expansion is a defining feature of human evolution and neurodevelopment, involving the tangential growth and gyrification of the cerebral cortex. Although disruptions to the expansion of the cortex are implicated in diverse brain-based disorders, the genetic architecture underlying this process remains undercharacterized. Here, we integrated GWAS data for five neuroanatomical phenotypes measured in up to 73,800 individuals to model a latent genomic factor capturing the shared genetic basis of cortical surface area, folding, curvature, gyrification, and intracranial volume. Using a multivariate framework, we mapped this pleiotropic architecture across biological scales, identifying novel effector genes, neural cell types, and developmental pathways involved in cortical expansion. Functional genomic evidence indicated that a diverse cellular ensemble contributes to the tangential growth and gyrification of the cortex during prenatal neurodevelopment, with progenitor cell lineages prominently involved. Regional analyses further revealed that genetic influences are spatially heterogeneous and organized along canonical anatomical, functional, and developmental gradients. Finally, cortical expansion exhibited substantial genetic overlap with neurodevelopmental, psychiatric, and neurological disorders, with shared genetic influences often concentrated in prefrontal cortical regions. Together, these findings map the genetic architecture of human cortical expansion and implicate it as a common etiological axis linking evolution, neurodevelopment, and health and disease.

genomics↗

bioRxiv2026

From Nuisance to Signal: Leveraging Close Relatives in Biobank-Scale Demographic Inference

Biobank-scale datasets now routinely include hundreds of thousands to millions of individuals, and as sample sizes grow, close relatives become increasingly prevalent. The convention in population genetics has been to remove close relatives prior to inference, effectively treating them as a nuisance parameter. However, the consequences of this practice for demographic inference, and specifically for estimates of recent effective population size (Ne), have not been rigorously evaluated. Here, we benchmark IBDNe and HapNe-IBD, two widely-used methods for inferring recent Ne from identity-by-descent (IBD) segments, under a range of demographic histories and relative sampling schemes. We show that when individuals are randomly ascertained, retaining all relatives produces the least biased Ne estimates; in contrast, removing even second-degree relatives inflates recent Ne and induces oscillatory artifacts that "ripple", leading to biased estimates up to ten generations into the past. We demonstrate that this ripple effect arises because close relatives contribute IBD segments that are assigned by the model to a range of ancestral ages beyond their true TMRCA, meaning their removal creates signal deficits across multiple generations simultaneously. We further show that deliberately oversampling close relatives produces severe downward bias in recent Ne. To support these analyses, we develop an open-source IBD simulation pipeline using msprime that generates realistic IBD segments under arbitrary demographic histories and Wright-Fisher pedigrees. We provide practical guidelines for IBD simulation schemes incorporating pedigrees and argue that, in the biobank era, retaining close relatives is generally the best practice for IBD-based Ne inference.

genetics↗

bioRxiv2026

Structure-Property-Performance Engineering of Hydrogel Depots for Long-Acting Peptide Delivery

Controlled release systems for subcutaneous peptide delivery often exhibit a pronounced initial burst release followed by inadequate maintenance of therapeutic exposure, limiting depot lifetime and increasing pharmacokinetic variability. Here, we engineer a dynamic, injectable hydrogel depot technology for months-long delivery of lipidated peptides. Using semaglutide as a model, we establish a modular formulation framework integrating: (i) formulation-driven tuning of depot mechanics to control release kinetics, (ii) cargo complexation strategies leveraging hydrophobic and multivalent ion-mediated interactions, and (iii) oxidative stabilization through sacrificial antioxidant excipients. We evaluated depot performance by rheology, in vitro cargo release, and in vivo pharmacokinetic and pharmacodynamic studies in rodents. Optimized formulations sustained semaglutide exposure for over six weeks from a single administration with two-fold reduction in peak-to-trough exposure and comparable total bioavailability relative to daily dosing, resulting in improved glucose control, weight regulation, and preservation of pancreatic islet content. These results suggest potential for quarterly dosing in humans. Together, this work establishes integrated and generalizable structure-property-performance relationships that account for cargo-matrix and cargo-excipient interactions across burst, diffusion, and erosion regimes to inform a practical formulation framework for engineering long-acting depots for sustained peptide delivery.

bioengineering↗

bioRxiv2026

Gradient Multinozzle 3D Printing

Direct ink writing is compatible with an expansive materials palette. While enabling diverse applications, this materials versatility brings significant bottlenecks in ink formulation, often requiring the mixing, printing, and testing of dozens to hundreds of ink compositions over the course of a project. To accelerate ink-space exploration, we introduce gradient embedded multinozzle (GEM) printheads that combine the high-throughput parallelized printing of multinozzles with combinatorial ink mixing. These printheads allow simultaneous mixing of two-, three-, and four-input inks which are distributed to printer nozzles to create complex 3D structures with graded compositions of inks. Using a two-way GEM printhead, we vali-date cell compatibility by printing scaffolds containing various concentrations of fibroblasts and observing non-linear compaction behaviours. We next test a three-way GEM multinozzle to print ten compositions of di- and multi-functionalized poly(ethylene-glycol) diacrylate hydrogel tri-leaflet valves, optimizing for stiffness, swelling ratio, and toughness. Our GEM multinozzles are compatible with open-source printers and either pressure- or volume-driven extrusion systems and promise to accelerate iterative ink design and testing.

bioengineering↗

bioRxiv2026

Quantitative muscle color as a proxy for structural and functional characteristics during muscle remodeling in Gryllus lineaticeps

Understanding the cellular and physiological mechanisms underlying muscle remodeling requires model systems that allow rapid, reliable, and quantitative assessment of muscle state. The cricket Gryllus lineaticeps naturally undergoes non-pathological striated muscle breakdown (histolysis), making it a promising system for studying this process. However, current assessments of muscle state are largely qualitative, subjective, and poorly standardized across experiments. Here, we developed and validated a continuous, quantitative muscle color metric to objectively capture histolysis progression and functional changes in muscle. We show that this metric robustly tracks variation in muscle color across remodeling stages, including the challenging fully transparent stage, and strongly predicts protein content, mitochondrial abundance, and iron content in a muscle- and trait-specific manner. The reproducibility of these relationships across independent datasets demonstrates the generality and robustness of this approach. By providing a rapid, objective, and biologically informative proxy of muscle state, this framework not only advances the utility of G. lineaticeps as a model for muscle remodeling but also offers a strategy for exploring the cellular dynamics underlying age-related muscle diseases and disorders, addressing an increasing public health concern in aging populations.

physiology↗

bioRxiv2025

Inhibition of BRN2 in Melanoma Reverses Anoikis Resistance and Sensitizes Cells to Killing by Vemurafenib

Anoikis is an apoptotic cell death program triggered upon detachment from surrounding extracellular structures. However, the ability to evade cell death by anoikis in the presence of apoptosis-inducing stimuli is necessary for the formation of malignant tumors and progression to metastasis. Our findings indicate that the BRN2 (POU3F2) transcription factor is associated with anoikis resistance in melanoma cells. However, the BRN2 signaling cascade driving anoikis resistance remains unknown. Herein, we employed genome-wide CRISPR screens to validate BRN2 as a driver of anoikis resistance. Small molecule inhibition of BRN2 in melanoma cell lines with acquired anoikis resistance resensitized to death by anoikis in ultra-low attachment conditions. Our quantitative mass spectrometry analysis revealed that BRN2 functionally impacts oxidative phosphorylation and mitochondrial activity, whereby probes designed to inhibit BRN2 induced apoptosis and mitochondrial fragmentation through the MAPK and NF-{kappa}B signaling pathways and reduction in PPAR{gamma} expression. Our study suggests that inhibition of BRN2 might allow the targeting of metastatic cells in circulation, and sensitizes cells to BRAF-targeted therapy, improving the prognosis for melanoma patients. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=156 SRC="FIGDIR/small/667908v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@12ffd89org.highwire.dtl.DTLVardef@1ae6c8eorg.highwire.dtl.DTLVardef@58e49forg.highwire.dtl.DTLVardef@9b83e_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical Abstract.C_FLOATNO Role of BRN2 in driving anoikis resistance in melanoma. Upon detachment from the extra-cellular matrix (ECM) melanoma cells must evade cell death by anoikis to seed distant metastases. This study expanded the understanding of the role of the BRN2 transcription factor as a driver of resistance to anoikis in melanoma. The use of small molecule inhibitors targeting BRN2 revealed that the transcription factor drives anoikis resistance via the MAPK and NF-{kappa}B signaling pathways, resulting in PPAR{gamma} dysregulation and subsequently driving mitochondrial dysfunction. Green boxes = previously published drivers of anoikis resistance in melanoma. Blue box = changes to mitochondrial function following inhibition of BRN2 as determined by proteomics analysis. C_FIG

cancer biology↗

bioRxiv2025

Long-acting hydrogel-based depot formulations of tirzepatide and semaglutide for the management of type 2 diabetes and weight

Several incretin hormone therapies have been clinically approved and have revolutionized the treatment of diabetes and obesity. Promising therapeutics include semaglutide (Ozempic(R) and Wegovy(R)), an agonist for glucagon-like peptide-1 (GLP-1) receptor, and tirzepatide (Mounjaro(R)), a dual agonist for GLP-1 and glucose-dependent insulinotropic polypeptide (GIP) receptors. These molecules help to regulate blood glucose levels, enhance insulin secretion and sensitivity, and reduce appetite. Currently, these treatments require weekly injections, which can be challenging for patients to adhere to. We recently reported the development of an injectable hydrogel depot technology enabling months-long release of semaglutide (Sema). Here, we further develop this technology for improved prolonged release of both Sema and tirzepatide (TZP). In a rat model of diabetes, we show a single administration of hydrogel-based formulations of either Sema or TZP maintained relevant drug levels for over 6 weeks. In these studies, single administrations of long-acting hydrogel-based therapies of Sema or TZP were similarly effective at regulating blood glucose and weight compared to daily injections of either Sema or TZP in standard aqueous vehicles. This hydrogel depot technology is easy to manufacture, injectable, and exhibits excellent biocompatibility, enabling months-long-acting treatments with the potential to improve management of diabetes and weight.

bioengineering↗

bioRxiv2025

Engineering Sustained-Release Broadly Neutralizing Antibody Formulations

Sustained serum levels of broadly neutralizing antibodies (bnAbs) are crucial for effective passive immunization against infectious diseases as protection persists only while these bnAbs remain at adequate concentrations within the body. Current obstacles, such as poor pharmacokinetics (PK) and burdensome administration, must be overcome to make bnAbs a viable option for pre- and post-exposure prophylaxis. In this work, we explore how a polymer-nanoparticle (PNP) hydrogel depot technology can be engineered to prolong protein delivery. In-vivo studies in mice and rats demonstrate prolonged protein release, and modeling efforts predict the impact of both the elimination half-life of the active pharmaceutical ingredient and hydrogel depot volume on overall pharmacokinetics. Moreover, flow cytometry characterization reveals that immune cell infiltration into the hydrogel depot can result in faster-than-expected release of antibody cargo on account of active transport via cellular uptake. We then demonstrate that co-formulation of antibodies with an anti-inflammatory agent reduces cellular infiltration and resulting active transport, further extending delivery and pharmacokinetics. Finally, multicompartmental modeling predicts the human PK profiles of clinically relevant HIV bnAbs delivered via subcutaneous hydrogel injection. These findings aid in the development of next generation hydrogel materials that stabilize and slowly release bnAbs for long-term pre-exposure immunoprophylaxis.

bioengineering↗

bioRxiv2025

Robust inference and widespread genetic correlates from a large-scale genetic association study of human personality

Personality traits describe stable differences in how individuals think, feel, and behave and how they interact with and experience their social and physical environments. We assemble data from 46 cohorts including 611K-1.14M participants with European-like and African-like genomes for genome-wide association studies (GWAS) of the Big Five personality traits (extraversion, agreeableness, conscientiousness, neuroticism, and openness to experience), and data from 51K participants for within-family GWAS. We identify 1,257 lead genetic variants associated with personality, including 823 novel variants. Common genetic variants explain 4.8%-9.3% of the variance in each trait, and 10.5%-16.2% accounting for measurement unreliability. Genetic effects on personality are highly consistent across geography, reporter (self vs. close other), age group, and measurement instrument, and we find minimal spousal assortment for personality in recent history. In stark contrast to many other social and behavioral traits, within-family GWAS and polygenic index analyses indicate little to no shared environmental confounding in genetic associations with personality. Polygenic prediction, genetic correlation, and Mendelian randomization analyses indicate that personality genetics have widespread, potentially causal associations with a wide range of consequential behaviors and life outcomes. The genetic architecture of personality is robust and fundamental to being a human.

genomics↗

bioRxiv2025

Preventing peritendinous adhesions using lubricious supramolecular hydrogels

Of the 1.5 million emergency room visits each year in the United States due to flexor tendon injuries in the hand, over 30-40% result in peritendinous adhesions which can limit range of motion (ROM) and severely impact an individuals quality of life. Adhesions are fibrous scar-like tissues which can form between adjacent tissues in the body in response to injury, inflammation, or during normal healing following surgery. Currently, there is no widespread solution for adhesion prevention in the delicate space of the digit while allowing a patient full ROM quickly after surgery. There is a clear clinical need for a material capable of limiting adhesion formation which is simple to apply, does not impair healing, remains at the application site during motion and initial inflammation (days - weeks), and leaves tendon glide unencumbered. In this work, we developed dynamically crosslinked, bioresorbable supramolecular hydrogels as easy-to-apply lubricious barriers to prevent the formation of peritendinous adhesions. These hydrogels exhibit excellent long-term stability, injectability, and thermally stable viscoelastic properties that allow for simple storage and facile application. We evaluated interactions at the interface of the hydrogels and relevant tissues, including human tendon and skin, in shear and extensional stress modes and demonstrated a unique mechanism of adhesion prevention based on maintenance of a lubricious hydrogel barrier between tissues. Ex vivo studies show that the hydrogels did not impair the gliding behavior nor mechanical properties of tendons when applied in cadaveric human hands following clinically relevant flexor tendon repair. We further applied these hydrogels in a preclinical rat Achilles tendon injury model and observed prolonged local retention at the repair site as well as improved recovery of key functional metrics, including ROM and maximal dorsiflexion. Further, these hydrogels were safe and did not impair tendon strength nor healing compared to the current standard of care. These dynamic, biocompatible hydrogels present a novel solution to the significant problem of peritendinous adhesions with clear translational potential.

bioengineering↗

bioRxiv2024

Phasing millions of samples achieves near perfect accuracy, enabling parent-of-origin classification of variants

Haplotype phasing, the process of determining which genetic variants are physically located on the same chromosome, is crucial for various genetic analyses. In this study, we first benchmark SHAPEIT and Beagle, two state-of-the-art phasing methods, on two large datasets: > 8 million diverse, research-consented 23andMe, Inc. customers and the UK Biobank (UKB). We find that both perform exceptionally well. Beagles median switch error rate (SER) (after excluding single SNP switches) in white British trios from UKB is 0.026% compared to 0.00% for European ancestry 23andMe research participants; 55.6% of European ancestry 23andMe research participants have zero non-single SNP switches, compared to 42.4% of white British trios. South Asian ancestry 23andMe research participants have the highest median SER amongst the 23andMe populations, but it is still remarkably low at 0.46%. We also investigate the relationship between identity-by-descent (IBD) and SER, finding that switch errors tend to occur in regions of little or no IBD segment coverage. SHAPEIT and Beagle excel at intra-chromosomal phasing, but lack the ability to phase across chromosomes, motivating us to develop an inter-chromosomal phasing method, called HAPTIC (HAPlotype TIling and Clustering), that assigns paternal and maternal variants discretely genome-wide. Our approach uses identity-by-descent (IBD) segments to phase blocks of variants on different chromosomes. HAPTIC represents the segments a focal individual shares with their relatives as nodes in a signed graph and performs bipartite clustering on the signed graph using spectral clustering. We test HAPTIC on 1022 UKB trios, yielding a median phase error of 0.08% in regions covered by IBD segments (33.5% of sites). We also ran HAPTIC in the 23andMe database and found a median phase error rate (the rate of mismatching alleles between the inferred and true phase) of 0.92% in Europeans (93.8% of sites) and 0.09% in admixed Africans (92.7% of sites). HAPTICs precision depends heavily on data from relatives, so will increase as datasets grow larger and more diverse. HAPTIC enables analyses that require the parent-of-origin of variants, such as association studies and ancestry inference of untyped parents.

bioinformatics↗

bioRxiv2024

Survival of tardigrades (Hypsibius exemplaris) to subzero temperatures depends on exposure intensity, duration, and ice-nucleation--as shown by large-scale mortality dye-based assays

Tardigrades are an emerging model system for understanding a diversity of environmental stress responses, yet few studies describe the physiology of cold tolerance in hydrated, active tardigrades. Here, we develop methods to screen tardigrades for survival in a high-throughput manner, to investigate the impacts of several key environmental conditions on survival. The visualization of dye uptake (SYTOX Green) in hydrated, cold-exposed Hypsibius exemplaris allows us to quickly and accurately quantify the survival of thousands of animals, under a range of ecologically-relevant low temperatures, exposure times, conditions, and thermal acclimations. As a proof-of-concept, we show that SYTOX Green uptake more accurately predicts 2-week survival outcomes of tardigrades post-cold exposure, compared to previous methods of scoring survival (locomotion). We show that hydrated, active tardigrades survive mild cold exposures of - 10{degrees}C at high rates of [~]98%. Survival of tardigrades to exposures of -15{degrees}C depends on environmental freezing in pure mineral water, and survival decreased exponentially with exposure time at -20{degrees}C (to 45% after 24 hours; with freezing occurring at nearly all -20{degrees}C timepoints). To investigate the role of environmental ice-formation on tardigrade survival vs. temperature, we incubated unacclimated tardigrades with ice-nucleating bacteria--which initiate environmental freezing at higher temperatures (-1.8 to 3.8{degrees}C). Surprisingly, we found a significant increase in survival of tardigrades frozen at -20{degrees}C (p-value = 0.0152) with the addition of Pseudomonas syringae compared to non-inoculated controls, as well as observing high-survival of tardigrades in ice-nucleated samples exposed to -10{degrees}C and -15{degrees}C. This indicates the species tolerance to environmental ice formation and exposure to our lowest temperature (-20{degrees}C), under certain conditions of controlled environmental ice formation. A 3-week acclimation of tardigrades to mild cold (1{degrees}C and 4{degrees}C) in constant darkness did not significantly improve survival after acute exposure to low temperature, but acclimating animals to 15{degrees}C did. Overall, we find that H. exemplaris--an emerging tardigrade model species--has a range of cold tolerance capabilities, dependent on time, temperature, environmental ice-formation, and culturing conditions. This work offers a framework with new tools for performing large-scale physiological assays in numerous species, establishing tardigrades as a tractable and uniquely informative model system in comparative physiology and the study of environmental stress. Key Findings- Active, hydrated tardigrades--with no prior acclimation to cold--have high survival of temperatures above -15{degrees}C, even in response to prolonged exposures. - Below -15{degrees}C, tardigrade survival declines exponentially with increasing exposure time. - Incubating tardigrades with ice-nucleating bacteria significantly improves survival after cold exposure, illustrating the importance of ice-formation dynamics and environmental microbes. - A 3-week acclimation of tardigrades to mild cold (1{degrees}C & 4{degrees}C) does not significantly improve survival to low temperature, while acclimation to 15{degrees}C (vs the standard culture condition of 20{degrees}C) does. - Uptake of the dye SYTOX Green is a more accurate metric of tardigrade mortality in response to cold exposure, compared to the traditional method of scoring lack of locomotion during recovery.

physiology↗

bioRxiv2024

Spatiotemporal dynamics of NF-κB/Dorsal inhibitor IκBα/Cactus in Drosophila blastoderm embryos

The NF-{kappa}B signaling pathway is a key regulatory network in mammals that controls many cellular processes, including immunity and inflammation. Of particular note is the relationship between NF-{kappa}B and its inhibitor I{kappa}B, which sequesters NF-{kappa}B to the cytoplasm of cells until needed. It is also known that I{kappa}B can enter nuclei, disrupt NF-{kappa}B binding to DNA, and shuttle it out to again sequester NF-{kappa}B in the cytoplasm. In Drosophila melanogaster, a homologous system between the proteins Dorsal (homologous to NF-{kappa}B) and Cactus (homologous to I{kappa}B) is important in embryo development, specifically in establishment of the Dorsal nuclear concentration gradient. Previous work suggests Cactus also enters the nucleus; mathematical models of the Dorsal gradient fail to accurately predict the normal range of the gradient without nuclear Cactus. However, direct, in vivo visualization of Cactus spatiotemporal dynamics, including its localization to the nuclei, has been difficult to gather. Previously, imaging Cactus in live embryos was complicated by rapid protein turnover, preventing fluorescent protein fusions from fully maturing. To address this, we used the CRISPR/Cas9 system to tag Cactus with the recently developed "LlamaTag" (LT), a genetically encodable nanobody from llamas that dynamically binds to GFP in vivo. We then employed standard confocal imaging, as well as advanced optical techniques such as raster image correlation spectroscopy (RICS) and fluorescent recovery after photobleaching (FRAP) to investigate the spatiotemporal distribution of Cactus-LlamaTag in Drosophila embryos at the blastoderm stage. Our results demonstrate that Cactus can be found in the nuclei of early embryos, consistent with its role as a transcription factor regulator. Moreover, by using the data from FRAP and RICS, we were able to estimate biophysical parameters of Cactus dynamics in vivo, including its nuclear transport rate constants and fraction bound to GFP. These data were further used to constrain a mathematical model that allowed us to infer experimentally inaccessible biophysical parameters, such as the concentration of Cact protein and the dissociation constant of LT and GFP. Our study provides new insights into the regulation of the NF-{kappa}B pathway in early Drosophila embryos and highlights the power of advanced optical techniques for investigating complex biological dynamics.

developmental biology↗

bioRxiv2023

Guidelines for Evaluating the Comparability of Down-Sampled GWAS Summary Statistics

Proprietary genetic datasets are valuable for boosting the statistical power of genome-wide association studies (GWASs), but their use can restrict investigators from publicly sharing the resulting summary statistics. Although researchers can resort to sharing down-sampled versions that exclude restricted data, down-sampling reduces power and might change the genetic etiology of the phenotype being studied. These problems are further complicated when using multivariate GWAS methods, such as genomic structural equation modeling (Genomic SEM), that model genetic correlations across multiple traits. Here, we propose a systematic approach to assess the comparability of GWAS summary statistics that include versus exclude restricted data. Illustrating this approach with a multivariate GWAS of an externalizing factor, we assessed the impact of down-sampling on (1) the strength of the genetic signal in univariate GWASs, (2) the factor loadings and model fit in multivariate Genomic SEM, (3) the strength of the genetic signal at the factor level, (4) insights from gene-property analyses, (5) the pattern of genetic correlations with other traits, and (6) polygenic score analyses in independent samples. For the externalizing GWAS, down-sampling resulted in a loss of genetic signal and fewer genome-wide significant loci, while the factor loadings and model fit, gene-property analyses, genetic correlations, and polygenic score analyses are robust. Given the importance of data sharing for the advancement of open science, we recommend that investigators who share down-sampled summary statistics report these analyses as accompanying documentation to support other researchers use of the summary statistics.

genetics↗

bioRxiv2022

Dynamics of BMP signaling in the early Drosophila embryo

In developing tissues, morphogen gradients are thought to initialize gene expression patterns. However, the relationship between the dynamics of morphogen-encoded signals and gene expression decisions are largely unknown. Here we examine the dynamics of the Bone Morphogenetic Protein (BMP) pathway in Drosophila blastoderm-stage embryos. In this tissue, the BMP pathway is highly dynamic: it begins as a broad and weak signal on the dorsal half of the embryo, then 20-30 min later refines into a narrow, intense peak centered on the dorsal midline. This dynamical progression of the BMP signal raises questions of how it stably activates target genes. Therefore, we performed live imaging of the BMP signal and found that dorsal-lateral cells experience only a short transient in BMP signaling, after which the signal is lost completely. Moreover, we measured the transcriptional response of the BMP target gene pannier in live embryos and found it to remain activated in dorsal-lateral cells, even after the BMP signal is lost. Our findings may suggest that the BMP pathway activates a memory, or "ratchet" mechanism that may sustain gene expression.

developmental biology↗

bioRxiv2022

Alterations in platelet proteome signature and impaired platelet integrin αIIbβ3 activation in patients with COVID-19

BackgroundPatients with coronavirus disease-19 (COVID-19) are at increased risk of thrombosis, which is associated with altered platelet function and coagulopathy, contributing to excess mortality. ObjectivesWe aimed to characterise the mechanism of altered platelet function in COVID-19 patients. MethodsThe platelet proteome, platelet functional responses and platelet-neutrophil aggregates were compared between patients hospitalised with COVID-19 and healthy control subjects using Tandem Mass Tag (TMT) proteomic analysis, Western blotting and flow cytometry. ResultsCOVID-19 patients showed a different profile of platelet protein expression (858 altered out of 5773 quantified). Levels of COVID-19 plasma markers were enhanced in COVID-19 platelets. Gene ontology (GO) pathway analysis demonstrated that levels of granule secretory proteins were raised, whereas some platelet activation proteins, such as the thrombopoietin receptor and PKC, were lowered. Basally, COVID-19 platelets showed enhanced phosphatidylserine (PS) exposure, with unaltered integrin IIb{beta}3 activation and P-selectin expression. Agonist-stimulated integrin IIb{beta}3 activation and PS exposure, but not P-selectin expression, were significantly decreased in COVID-19 patients. COVID-19 patients had high levels of platelet-neutrophil aggregates, even under basal conditions, compared to controls. This interaction was disrupted by blocking P-selectin, demonstrating that platelet P-selectin is critical for the interaction. ConclusionsOverall, our data suggests the presence of two platelet populations in patients with COVID-19: one with circulating platelets with an altered proteome and reduced functional responses and another with P-selectin expressing neutrophil-associated platelets. Platelet driven thromboinflammation may therefore be one of the key factors enhancing the risk of thrombosis in COVID-19 patients. Essentials- COVID-19 patient platelet function and platelet proteins were compared with healthy controls - Proteomic analysis of platelets indicated that COVID-19 decreased platelet activation proteins - Agonist induced PS exposure and integrin IIb{beta}3 activation were impaired in COVID-19 - COVID-19 led to maximal levels of P-selectin dependent platelet-neutrophil aggregates

cell biology↗

bioRxiv2022

Brain Volumes, Thicknesses, and Surface Areas as Mediators of Genetic Factors and Childhood Adversity on Intelligence

Although genetic and environmental factors influence general intelligence (g-factor), few studies examined the neuroanatomical measures mediating environmental and genetic effects on intelligence. Therefore, we investigate the brain volumes, cortical mean thicknesses, and cortical surface areas mediating the effects of the g-factor polygenic score (gPGS) and childhood adversity on the g-factor in the UK Biobank. We first identified the global and regional brain measures for the mediation models that contribute to the g-factor independently of global brain size and regional associations. Most regions contributed to the g-factor through global brain size. Parieto-Frontal Integration Theory (P-FIT) regions were not more associated with the g-factor than non-PFIT regions. Adjusting for global brain size and regional associations, only a few regions, such as the right olfactory sulcus and the right mediodorsal thalamic nuclei volumes, the right orbital inferior frontal gyrus surface area, and the anterior cingulate gyrus mean thicknesses, predicted intelligence and were included in the mediation analyses. We conducted mediation analyses on global measures, regional volumes, mean thicknesses, and surface areas, separately. Total brain volume mediated 7.04% of the gPGS effect on the g-factor and 2.50% of childhood adversitys effect on the g-factor. In comparison, the fraction of the gPGS and childhood adversitys effects mediated by individual regional volumes, surfaces, and mean thicknesses was 10-15 times smaller. Our findings suggest that genetic and environmental effects on general intelligence must be mediated to a larger extent by other structural brain properties. Significance StatementGenes and environmental factors, such as childhood adversity, influence our cognitive abilities via the brain. Our results show that genetic and environmental effects on intelligence are mediated to some extent by neuroanatomical properties. However, we find that global brain measures (e.g., total brain volume) are the largest mediators and that regional volumes, surfaces, and mean thicknesses only mediated a fraction of a persons genetic predisposition to intelligence and childhood adversitys effect on intelligence. This suggests that genetic and environmental effects on general intelligence are to a large extent mediated by other kinds of brain structural properties.

neuroscience↗