Biology subjects

Leonard, A.

Publications and source records attributed to Leonard, A..

10 recordsLinked to original sources

bioRxiv2026

Purinergic signaling promotes gliomagenesis through nuclear calcium transients

Intracellular Ca2+ transients drive key developmental and physiological processes, yet their role in oncogenesis remains incompletely understood. In glioblastoma (GBM), an aggressive brain malignancy, tumor cellular networks exhibit self-sustaining Ca2+ transients that promote tumor growth through unclear mechanisms. Using patient-derived GBM models, we show that these transients depend primarily on intracellular Ca2+ stores and extend to the nucleus to drive tumorigenesis. A neuromodulator screen identified extracellular purines ATP and ADP as potent inducers of both nuclear and cytosolic Ca2+ transients via activation of metabotropic purinergic P2RY1 receptors, whose knockdown attenuates tumorigenicity in vitro and in vivo. Mechanistically, Ca2+ transients promote tumorigenesis via the nuclear Ca2+/calmodulin-dependent kinase CAMK4, which regulates transcriptional and epigenetic programs, as well as ribosomal DNA transcription. From the therapeutic perspective, pharmacologic P2RY1 inhibition suppresses tumor growth in vitro and in vivo. Collectively, these findings reveal a pharmacologically targetable oncogenic mechanism in GBM and possibly other malignancies.

cancer biology↗

bioRxiv2025

Escape from antimicrobial CRISPR-Cas9 in E. coli ST131 depends on the genetic context of the target gene.

Escherichia coli (E. coli) is a common bacterium in the human gut and an important cause of intestinal and extraintestinal infections. Some E. coli sequence types (ST) are associated with high pathogenicity. The Extraintestinal Pathogenic E. coli (ExPEC) ST131 is a globally distributed multidrug-resistant human pathogen associated with urinary tract and bloodstream infections. Antibiotic-resistant infections often lead to antibiotic treatment failure, underscoring the need of developing alternative treatments. The highly selective antimicrobial potential of CRISPR-Cas9 has been demonstrated in a range of model organisms. However, the effectiveness of CRISPR-Cas9 in combating ST131-associated infections and the consequences of CRISPR-Cas9 treatment, such as the emergence of escapers, remains unclear. Here, we investigated the antimicrobial activity of CRISPR-Cas9 against ST131 and assessed the frequency and genetic basis of escape. We conjugatively delivered CRISPR-Cas9 to ST131 isolates which carried cefotaxime-resistance-encoding target gene blaCTX-M-15 in the chromosome and characterized escape subpopulations. Two main types of escapers emerged: blaCTX-M-15-positive escapers carried dysfunctional CRISPR-Cas9 systems and arose at a [~]10-5 frequency. Instead, blaCTX-M-15-negative escapers presented chromosomal deletions involving blaCTX-M-15 loss. The frequency of blaCTX-M-15 loss depended on the blaCTX-M-15 genetic context. Specifically, blaCTX-M-15-negative escapers emerged at low frequency ([~]10-5) in isolates where blaCTX-M-15 was located downstream of insertion sequence (IS) ISEcp1, while escapers emerged with high frequency ([~]10-3) in isolates where blaCTX-M-15 was flanked by IS26. This work emphasizes how the genetic context of target genes can drive the outcome of CRISPR-Cas9 tools, where the presence of IS26 may drive increased frequencies of escape. IMPORTANCEIn the past decade CRISPR-Cas9 has emerged as an efficient antimicrobial tool capable of selective elimination of targeted bacteria. Even though it has been well described that bacteria can evolve to escape targeting by CRISPR-Cas9, the mechanisms of bacterial escape and their consequences remain largely elusive. In this study, we demonstrate the antimicrobial efficacy of CRISPR-Cas9 against natural isolates of Escherichia coli ST131, a clinically relevant pathogen, and elucidate the mechanism of escape from antimicrobial activity. We identify two distinct mechanisms of escape, which involve either dysfunctional CRISPR-Cas9 activity, or loss of the target gene (blaCTX-M-15), with the latter occurring at frequencies that depend on the genetic context of the target gene. These findings provide important insights into the frequency and mechanisms of bacterial escape from CRISPR-Cas9-based antimicrobials and offer a foundation for the development of more effective treatments.

microbiology↗

bioRxiv2025

12/15-Lipoxygenase orchestrates murine wound healing via PPARg-activating oxylipins acting holistically to dampen inflammation.

12/15-lipoxygenase (12/15-LOX, Alox15) generates bioactive oxygenated lipids during inflammation, however its homeostatic role(s) in normal healing are unclear. Here, the role of 12/15-LOX in resolving skin wounds was elucidated, focusing on how its lipids act together in physiologically relevant amounts. In mice, wounding caused acute appearance of 12/15-LOX-expressing macrophages and stem cells, coupled to early generation of [~]12 monohydroxy-oxylipins and enzymatically oxygenated phospholipids (eoxPL). Alox15 deletion increased -smooth muscle actin, collagen deposition, stem cell/fibroblast proliferation, IL6/pSTAT3, pSMAD3, and IFN-{gamma} levels. Conversely, CD206 expression, F480+ cells, MMP9 and MMP2 activities were reduced. Alox15-/- skin was deficient in PPAR{gamma}/adiponectin activity. Furthermore, while pro-inflammatory genes were upregulated as normal during wounding, many including Il6, Il1b, ccl4, Cd14, Cd274, Clec4d, Clec4e, Csf3, and Cxcl2 failed to revert to baseline during healing, indicating disruption of an anti-inflammatory brake. Reconstituting Alox15-/- wounds with a physiological mixture of Alox15-derived primary oxylipins generated by healing wounds restored MMP and dampened collagen deposition. The oxylipin mixture activated PPAR{gamma} in vitro, while in vivo, the PPAR{gamma} co-activator, Helz2, was significantly upregulated. Additional inflammatory and proliferative gene networks impacted by Alox15-/-included Elf4, Cebpb and Tcf3, with many of their associated genes significantly dysregulated. In summary, the impact of 12/15-LOX is ascribed to the deficiency of abundantly generated monohydroxy oxylipins acting together via PPAR{gamma}/adiponectin. The identification of multiple gene alterations reveals several new targets for treatment of non-healing wounds. Our studies demonstrate that abundant 12/15-LOX oxylipins act together, dampening inflammation in vivo, revealing a need to consider lipid signaling holistically. Significance statementDefective wound healing is a significant global clinical problem. Macrophage 12/15-lipoxygenase (12/15-LOX, Alox15) generates abundant lipid mediators termed oxylipins during inflammation. However, its physiological role during resolving wound healing is unclear, with studies so far assessing the bioactivity of individual lipids pharmacologically, rather than holistically in physiological amounts. Here, we report that Alox15 deficiency in mice caused a fibrotic response with failure to dampen inflammation, due to a dysregulated PPAR{gamma}/adiponectin axis. Treatment of Alox15-/- wounds with physiological mixtures of PPAR{gamma}-activating 12/15-LOX primary monohydroxy products restored the phenotype. Several transcriptional networks (Elf4, Cebpb and Tcf3) controlled by Alox15 were uncovered, identifying new targets for promoting physiological wound healing.

pharmacology and toxicology↗

bioRxiv2024

One for the road: Bumble bees consume pollen at flowers

Bees are the primary consumers of pollen in many ecosystems, but pollen consumption by adult bees is rarely studied, leaving a gap in our understanding of the nutritional ecology of collective foraging and pollination biology more generally. For example, while eusocial bees feed upon pollen from colony stores, whether they also consume pollen directly from flowers to meet their own needs or to assess its quality for the broader collective is unknown. We therefore captured wild bumble bee colonies (B. bimaculatus and B. griseocollis) and tested whether individual workers consumed pollen directly from flowers in a lab-based foraging assay. After confirming presence of floral pollen in worker crops (i.e., consumption at flowers), in a field setting we tested alternative hypotheses for the function of this behavior using information about the composition, abundance, and diversity of pollen found in the crops vs. pollen baskets of three species of pollen- and nectar-foraging bumble bees (Bombus bimaculatus, B. griseocollis, and B. impatiens). Consistent with the hypothesis that consuming pollen at flowers reflects sampling, total pollen quantity in crops was consistently smaller than in pollen baskets, and basket pollen tended to be a subset of that found in crops. Further, pollen foragers consumed more and different kinds of pollen than nectar foragers. Pollen consumption at flowers is thus unlikely to be purely incidental, or to substantially benefit workers nutritionally. Instead, consuming pollen directly from flowers likely allows foragers to quickly assess pollen quality before collecting it to feed the colony as whole. SIGNIFICANCE STATEMENTWhile nectar-collecting bees are classic models for the study of foraging behavior and plant-pollinator interactions, little is known about how bees assess pollen while foraging. Pollen is a critical source of protein and lipids, offered by many plant species alongside or instead of nectar. Though variation in pollen macronutrient content and secondary chemistry affect bee reproductive performance and health, whether and how foragers evaluate pollen quality is not known. We show that foraging worker bumble bees consume pollen at flowers and suggest this behavior may allow them to sample its nutritional quality. This sheds new light on the nutritional basis of plant-pollinator interactions and adds to our understanding of how bees regulate their collection of this critical resource.

animal behavior and cognition↗

bioRxiv2024

Coleoid Cephalopods Demonstrate Asocial Path to the Evolution of Big Brains

Social factors have been argued to be the main selection pressure for the evolution of large brains and complex behavior on the basis of data from mammals and birds. Coleoid cephalopods (octopuses, squid, and cuttlefish) have large brains, complex nervous systems and show signs of intelligent behavior comparable to that of primates, cetaceans, and birds. However, many cephalopods live largely solitary, semelparous, short lives, and many are cannibalistic, leaving little to no opportunity for parental care, complex group dynamics, or social learning. This suggests that the large brains found in cephalopods are not the result of social selection pressures. Here, motivated by the predictions of the "Asocial Brain Hypothesis", a yet untested regime of the Cultural Brain Hypothesis formal model, we compare the relationships between brain size and social, ecological, and other factors in cephalopods. Consistent with the prediction that ecological factors should be the primary selection pressure with larger brains in more calorie-rich complex ecologies, we find that shallower and benthic (seafloor) habitats--arguably more complex environments than open-ocean (pelagic) habitats--are associated with larger brain sizes, and that measures of sociality are not. Our findings from these highly divergent evolutionary lineages, which diverged from vertebrates over 500 million years ago are not causal, but are consistent with the "Asocial Brain Hypothesis" mechanistic model that describes how ecological selection pressures can also produce large, complex brains.

evolutionary biology↗

bioRxiv2021

Black Dots: Microcontact-Printed, Reference-Free Traction Force Microscopy

Measuring the traction forces produced by cells provides insight into their behavior and physiological function. Here, we developed a technique (dubbed black dots) that microcontact prints a fluorescent micropattern onto a flexible substrate to measure cellular traction forces without constraining cell shape or needing to detach the cells. To demonstrate our technique, we assessed human platelets, which can generate a large range of forces within a population. We find platelets that exert more force have more spread area, are more circular, and have more uniformly distributed F-actin filaments. As a result of the high yield of data obtainable by this technique, we were able to evaluate multivariate mixed effects models with interaction terms and conduct a clustering analysis to identify clusters within our data. These statistical techniques demonstrated a complex relationship between spread area, circularity, F-actin dispersion, and platelet force, including cooperative effects that significantly associate with platelet traction forces. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=79 SRC="FIGDIR/small/454500v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1da5eeeorg.highwire.dtl.DTLVardef@18e939aorg.highwire.dtl.DTLVardef@17c7198org.highwire.dtl.DTLVardef@105c97c_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2021

C-STEM: ENGINEERING NICHE-LIKE MICRO-COMPARTMENTS FOR OPTIMAL AND SCALE-INDEPENDENT EXPANSION OF HUMAN PLURIPOTENT STEM CELLS IN BIOREACTORS

Human pluripotent stem cells (hPSCs) have emerged as the most promising cellular source for cell therapies. To overcome scale up limitations of classical 2D culture systems, suspension cultures have been developed to meet the need of large-scale culture in regenerative medicine. Despite constant improvements, current protocols relying on the generation of micro-carriers or cell aggregates only achieve moderate amplification performance. Here, guided by reports showing that hPSCs can self-organize in vitro into cysts reminiscent of the epiblast stage in embryo development, we developed a physio-mimetic approach for hPSC culture. We engineered stem cell niche microenvironments inside microfluidics-assisted core-shell microcapsules. We demonstrate that lumenized three-dimensional colonies maximize viability and expansion rates while maintaining pluripotency. By optimizing capsule size and culture conditions, we scale-up this method to industrial scale stirred tank bioreactors and achieve an unprecedented hPSC amplification rate of 282-fold in 6.5 days. TEASEROptimizing human pluripotent stem cells amplification by recapitulating and protecting biomimetic colonies in a bioreactor

bioengineering↗

bioRxiv2019

Functional Maturation of Human iPSC-based Cardiac Microphysiological Systems with Tunable Electroconductive Decellularized Extracellular Matrices

Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) offer tremendous potential for use in engineering human tissues for regenerative therapy and drug screening. However, differentiated cardiomyocytes are phenotypically immature, reducing assay reliability when translating in vitro results to clinical studies and precluding hiPSC-derived cardiac tissues from therapeutic use in vivo. To address this, we have developed hybrid hydrogels comprised of decellularized porcine myocardial extracellular matrix (dECM) and reduced graphene oxide (rGO) to provide a more instructive microenvironment for proper cellular and tissue development. A tissue-specific protein profile was preserved post-decellularization, and through the modulation of rGO content and degree of reduction, the mechanical and electrical properties of the hydrogels could be tuned. Engineered heart tissues (EHTs) generated using dECM-rGO hydrogel scaffolds and hiPSC-derived cardiomyocytes exhibited significantly increased twitch forces at 14 days of culture and had increased the expression of genes that regulate contractile function. Similar improvements in various aspects of electrophysiological function, such as calcium-handling, action potential duration, and conduction velocity, were also induced by the hybrid biomaterial. We also demonstrate that dECM-rGO hydrogels can be used as a bioink to print cardiac tissues in a high-throughput manner, and these tissues were utilized to assess the proarrhythmic potential of cisapride. Action potential prolongation and beat interval irregularities was observed in dECM-rGO tissues at clinical doses of cisapride, indicating that the enhanced maturation of these tissues corresponded well with a capability to produce physiologically relevant drug responses.

bioengineering↗

bioRxiv2019

Chromatin compartment dynamics in a haploinsufficient model of cardiac laminopathy

Pathogenic mutations in A-type nuclear lamins cause dilated cardiomyopathy, which is postulated to result from dysregulated gene expression due to changes in chromatin organization into active and inactive compartments. To test this, we performed genome-wide chromosome conformation analyses (Hi-C) in human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) with a haploinsufficient mutation for lamin A/C. Compared to gene-corrected cells, mutant hiPSC-CMs have marked electrophysiological and contractile alterations, with modest gene expression changes. While large-scale changes in chromosomal topology are evident, differences in chromatin compartmentalization are limited to a few hotspots that escape inactivation during cardiogenesis. These regions exhibit upregulation of multiple non-cardiac genes including CACNA1A, encoding for neuronal P/Q-type calcium channels. Pharmacological inhibition of the resulting current partially mitigates the electrical alterations. On the other hand, A/B compartment changes do not explain most gene expression alterations in mutant hiPSC-CMs. We conclude that global errors in chromosomal compartmentation are not the primary pathogenic mechanism in heart failure due to lamin A/C haploinsufficiency. SummaryBertero et al. observe that lamin A/C haploinsufficiency in human cardiomyocytes markedly alters electrophysiology, contractility, gene expression, and chromosomal topology. Contrary to expectations, however, changes in chromatin compartments involve just few regions, and most dysregulated genes lie outside these hotspots. Condensed titleGenomic effects of lamin A/C haploinsufficiency

genomics↗

bioRxiv2018

A total synthetic approach to CRISPR/Cas9 genome editing and homology directed repair

CRISPR/Cas9 has become a powerful tool for genome editing in zebrafish that permits the rapid generation of loss of function mutations and the knock-in of specific alleles using DNA templates and homology directed repair (HDR). We compared synthetic, chemically modified sgRNAs to in vitro transcribed sgRNAs and demonstrate the increased activity of synthetic sgRNAs in combination with recombinant Cas9 protein. We developed an in vivo genetic assay to measure HDR efficiency and we utilized this assay to optimize the design of synthetic DNA templates to promote HDR. Utilizing these principles, we successfully performed knock-in of fluorophores at multiple genomic loci and demonstrate transmission through the germline at high efficiency. We demonstrate that synthetic HDR templates can be used to knock-in bacterial nitroreductase (ntr) to facilitate lineage ablation of specific cell types. Collectively, our data demonstrate the utility of combining synthetic sgRNAs and dsDNA templates to perform homology directed repair and genome editing in vivo.

molecular biology↗