Biology subjects

Craig, A.

Publications and source records attributed to Craig, A..

15 recordsLinked to original sources

bioRxiv2026

Ecdysone Antagonizes Growth and Juvenile Hormone-Dependent Soldier Caste Identity in Camponotus floridanus

From tardigrades to lobsters, ecdysone is the critical steroid hormone regulating ecdysis across Panarthropoda. In insects, the sesquiterpenoid hormone called juvenile hormone (JH) prolongs the juvenile state, and together, ecdysone and JH regulate growth and developmental timing. The complex worker caste system in ants has elaborated multiple times and is composed of individuals exhibiting an array of size and allometry variation. While we have accumulated a great deal of knowledge related to the role of JH in influencing size and caste identity in ants, the role of ecdysone in caste development remains poorly understood. Here we show in Camponotus floridanus that ecdysone negatively regulates size, can block soldier determination, and there is an antagonistic relationship between JH and ecdysone. First, we show that during the worker-soldier switchpoint sensitivity window of development, ecdysone is capable of negatively influencing head size, body size, head-to-body allometry, and unexpectedly extends developmental timing. We then show at the molecular level that as expected, developing soldiers upregulate ecdysone degradation, yet surprisingly, developing soldiers also upregulate ecdysone synthesis and the reception of ecdysone signalling. We next investigated the interaction between JH and ecdysone signaling and found that the two hormones antagonize each other at both the molecular and phenotypic levels. Furthermore, in contrast to other insects, we uncovered that ecdysone signaling is negatively regulated by temperature. Beyond its role in size regulation, we also provide preliminary data suggesting that the interaction of JH and ecdysone may have sex inducing properties, generating male-like anomalies. Altogether, our findings show that ecdysone blocks JH-dependent soldier development and we propose that the dynamic regulation of ecdysone synthesis, reception, and degradation may be the basis for the complex sigmoid-like head-to-body allometry found in this species as well as several others across ants. More generally, the evolutionary tinkering of antagonistic growth hormones, their regulation and interaction, and opposing responses to environmental cues, may be a major source for size diversity across developmentally plastic organisms.

developmental biology↗

bioRxiv2026

A choice disinhibition paradigm to reveal neural correlates of behavioral disinhibition in Frontotemporal dementia

Behavioral disinhibition is a hallmark symptom of behavioral variant frontotemporal dementia (bvFTD). There is no cure or strategy to slow progression, mainly due to little understanding of how disinhibition occurs and the mechanisms underlying self-control. To date, disinhibition has not been demonstrated in an FTD model. We designed a paradigm to assess disinhibition, separating general cognitive capacity, and found that aged mutant mice display increased impulsive choice but have intact cognition, suggestive of early-mid- stage bvFTD-associated symptoms. Further, the neural mechanisms underlying self-control are dissociable from impulsive choice; CaMKIIlower case Greek alpha- and somatostatin-expressing neurons in the medial prefrontal cortex, but not the classical anterior cingulate cortex, were activated during self-control. Together, we demonstrate behavioral disinhibition in mutant mice and identified specific regions and cell types that underlie self-control. This paradigm is viable for future work dissecting neural circuits underling impulsive choice and self-control behavior in bvFTD and other neurological conditions.

neuroscience↗

bioRxiv2025

Isolation of Extracellular Vesicles from Minimal Volume Ascites Fluid Using Strong Anion Exchange Magnetic Beads

Ovarian cancer (OC) remains a leading cause of gynecologic cancer mortality due to late-stage diagnosis and limited early detection strategies. Ascites fluid, a pathological hallmark of OC, is a rich source of tumor-derived extracellular vesicles (EVs) that reflect the tumor microenvironment and hold promise for biomarker discovery. However, isolating EVs from minimal ascites volumes (<100 {micro}L) poses technical challenges using conventional methods like ultracentrifugation or size-exclusion chromatography (SEC). This study explores the application of strong anion exchange (SAX) magnetic beads (Mag-Net) for efficient EV isolation from as little as 2 {micro}L of ascites fluid from both murine models and a human patient with mucinous borderline tumor. We demonstrate that SAX achieves robust EV capture at 10{micro}l of input volume, enabling comprehensive proteomic profiling and single-EV surface-enhanced Raman spectroscopy (SERS) with a >2-fold increase in proteomic depth compared to raw ascites. Notably, this study was able to identify 1000 proteins not previously annotated in Vesiclepedia for OC-derived EVs, alongside distinct SERS signatures, highlighting the potential for multiomic analysis. Comparative analysis with UC revealed enhanced proteomic depth obtained with SAX beads, albeit we also observed differential detection of canonical markers (e.g., CD9, CD81) between input volumes of ascites fluid. These findings establish SAX as a scalable, low-input platform for EV-based biomarker discovery, paving the way for improved early detection and molecular insights into OC progression.

biochemistry↗

bioRxiv2025

Juvenile Hormone Signalling Underlies the Switchpoint and Differentiation of Soldiers in Camponotus floridanus

Multicellular organisms are composed of various cell types derived from cellular determination and differentiation, which carry out specialized functions in the individual. Ant societies are composed of various castes of individuals derived from caste determination and differentiation, which divide specialized tasks in the colony. From cells to societies, the underlying mechanisms orchestrating determination and differentiation at different biological levels are fundamental in generating biological diversity. While past work has described the developmental process of caste determination and differentiation in ants, the endocrinological and molecular basis for these processes in the genus Camponotus remains unknown. Here we show that minor worker and soldier development is determined by a Juvenile hormone (JH)-mediated minor-soldier switchpoint in C. floridanus. Hormonal treatments identified a sensitivity period when JH can induce bipotential larvae to become soldiers. Induced soldiers phenocopy natural soldiers in size and soldier-specific head-to-body allometry and this is associated with a heterochronic shift in metamorphosis. Furthermore, we molecularly characterize the activity of the JH pathway at the level of synthesis, degradation, reception, and downstream effectors during caste determination and differentiation. Surprisingly, rather than JH synthesis, we found JH reception and JH degradation are the major signalling processes differentially regulated across castes and RNAi of juvenile hormone degradation enzymes generates soldiers. Finally, our data suggests that the hyperdiverse genus Camponotus has independently evolved a JH-mediated minor-soldier switchpoint similar to that known in Pheidole. More generally, the evolution of plastic hormonal regulation may facilitate the origin of developmental determination and differentiation processes underlying complex adaptive phenotypes. Significance StatementAnts live in complex societies like a superorganism where individuals divide reproductive and various non-reproductive labors, which are analogous to the array of functions of germ cells and highly differentiated somatic cells in an organism. While there are over 1500 species of the hyperdiverse genus Camponotus, a genus whose diversity reflects their complex caste system including minor workers and soldiers, the molecular and endocrinological basis for how these castes develop remains unknown. Here we have identified a juvenile hormone (JH) mediated minor-soldier switchpoint during larval development, and have characterized components of the JH signalling pathway that regulate soldier development. This work enables further understanding of how castes are regulated across ants and social insects more broadly.

developmental biology↗

bioRxiv2025

Challenges and opportunities for drug repurposing in cancers based on synthetic lethality induced by tumor suppressor gene mutations

Although two-thirds of cancers arise from loss-of-function mutations in tumor suppressor genes, there are few approved targeted therapies linked to these alterations. Synthetic lethality offers a promising strategy to treat such cancers by targeting vulnerabilities unique to cancer cells with these mutations. To identify clinically relevant synthetic lethal interactions, we analyzed genome-wide CRISPR/Cas9 knock-out (KO) viability screens from the Cancer Dependency Map and evaluated their clinical relevance in patient tumors through mutual exclusivity, a pattern indicative of synthetic lethality. Indeed, we found significant enrichment of mutual exclusivity for interactions involving cancer driver genes compared to non-driver mutations. To identify therapeutic opportunities, we integrated drug sensitivity data to identify inhibitors that mimic the effects of CRISPR-mediated KO. This approach revealed potential drug repurposing opportunities, including BRD2 inhibitors for bladder cancers with ARID1A mutations and SIN3A-mutated cell lines showing sensitivity to nicotinamide phosphoribosyltransferase (NAMPT) inhibitors. However, we discovered that pharmacological inhibitors often fail to phenocopy KO of matched drug targets, with only a small fraction of drugs inducing similar effects. This discrepancy reveals fundamental differences between pharmacological and genetic perturbations, emphasizing the need for approaches that directly assess the interplay of loss-of-function mutations and drug activity in cancer models. Author SummarySynthetic lethality is an emerging approach for targeting a biological dependency in cancer cells that does not harm normal cells. This strategy is particularly valuable for targeting loss-of-function mutations in tumor suppressor genes, which are more challenging to directly target. In an effort to accelerate treatments for cancer patients, we aimed to map out these dependencies and overlap them with responses to available drugs. We discovered different outcomes when a protein is targeted by a drug versus when that same target is disrupted genetically. Thus, if a drug is to be effectively repurposed as synthetic lethal agent, feasibility studies must capture drug biology, ideally by test the drug empirically in relevant cancer models. A second notable discovery is that in vitro synthetic lethal interactions involving cancer driver genes are significantly more likely to exhibit consistent patterns, such as mutual exclusivity in human tumor samples. This is important since selection of relevant cell lines is often critical in drug development to maximize potential for translation to clinical responses.

cancer biology↗

bioRxiv2024

Genesis: A Modular Protein Language Modelling Approach to Immunogenicity Prediction

Neoantigen immunogenicity prediction is a highly challenging problem in the development of personalised medicines. Low reactivity rates in called neoantigens result in a difficult prediction scenario with limited training datasets. Here we describe Genesis, a modular protein language modelling approach to immunogenicity prediction for CD8+ reactive epitopes. Genesis comprises of a pMHC encoding module trained on three pMHC prediction tasks, an optional TCR encoding module and a set of context specific immunogenicity prediction head modules. Compared with state-of-the-art models for each task, Genesis encoding module performs comparably or better on pMHC binding affinity, eluted ligand prediction and stability tasks. Genesis outperforms all compared models on pMHC immunogenicity prediction (Area under the receiver operating characteristic curve=0.619, average precision: 0.514), with a 7% increase in average precision compared to the next best model. Genesis shows further improved performance on immunogenicity prediction with the integration of TCR context information. Genesis performance is further analysed for interpretability, which locates areas of weakness found across existing immunogenicity models and highlight possible biases in public datasets.

bioinformatics↗

bioRxiv2024

Radiation dermatitis in the hairless mouse model mimics human radiation dermatitis

Over half of all people diagnosed with cancer receive radiation therapy. Moderate to severe radiation dermatitis occurs in most human radiation patients, causing pain, aesthetic distress, and a negative impact on tumor control. No effective prevention or treatment for radiation dermatitis exists. The lack of well-characterized, clinically relevant animal models of human radiation dermatitis contributes to the absence of strategies to mitigate radiation dermatitis. Here, we establish and characterize a hairless SKH-1 mouse model of human radiation dermatitis by correlating temporal stages of clinical and pathological skin injury. We demonstrate that a single ionizing radiation treatment of 30 Gy using 6 MeV electrons induces severe clinical grade 3 peak toxicity at 12 days, defined by marked erythema, desquamation and partial ulceration, with resolution occurring by 25 days. Histopathology reveals that radiation-induced skin injury features temporally unique inflammatory changes. Upregulation of epidermal and dermal TGF-{beta}1 and COX-2 protein expression occurs at peak dermatitis, with sustained epidermal TGF-{beta}1 expression beyond resolution. Specific histopathological variables that remain substantially high at peak toxicity and early clinical resolution, including epidermal thickening, hyperkeratosis and dermal fibroplasia/fibrosis, serve as specific measurable parameters for in vivo interventional preclinical studies that seek to mitigate radiation-induced skin injury.

pathology↗

bioRxiv2024

Fes-deficient macrophages enhance CD8+ T cell priming and tumour control through increased proinflammatory cytokine production and presentation

Homeostatic immunoregulatory mechanisms that prevent adverse effects of immune overaction can serve as barriers to successful anti-cancer immunity, representing attractive targets to improve cancer immunotherapy. Here, we demonstrate a novel role of the Fes tyrosine kinase, abundantly expressed in immune cells, as an innate intracellular immune checkpoint. Host Fes-deficiency delays tumour onset in a gene dose-dependent manner and improves murine triple negative breast cancer and melanoma tumour control, survival, doxorubicin efficacy, and anti-PD-1 therapy sensitization. These effects were associated with a shift to an anti-tumourigenic tumour immune microenvironment. In vitro, we observed increased Toll-like receptor signaling, and proinflammatory cytokine production and presentation from antigen presenting cells, leading to increased T cell activation, cancer cell killing and tumour control. This study highlights Fes as a novel innate immune checkpoint with potential as a predictive biomarker for effective immune checkpoint blockade treatment, and a potential therapeutic target to improve anti-cancer immunotherapy.

immunology↗

bioRxiv2024

Impact of Plasmodium falciparum patient-derived isolates on brain endothelium in vitro

A hallmark of cerebral malaria (CM) is sequestration of Plasmodium falciparum infected erythrocytes (IE) within the brain microvasculature. Binding of IE to endothelium reduces microvascular flow and combined with an inflammatory response perturbs endothelial barrier function, resulting in breakdown of the blood- brain barrier (BBB). Cytoadherence leads to activation of the endothelium and alters a range of cell processes affecting signalling pathways, receptor expression, coagulation, and disruption of BBB integrity. Here, we investigated whether CM derived parasites elicit differential effects on human brain microvascular endothelial cells (HBMECs), as compared to uncomplicated malaria (UM) derived parasites. Patient-derived IE from UM and CM clinical cases, as well as non-binding skeleton-binding protein 1 knockout parasites, were overlaid onto TNF-activated HBMECs. Gene expression analysis of endothelial responses was performed using probe-based assays of a panel of genes involved in inflammation, apoptosis, endothelial barrier function, and prostacyclin synthesis pathway. We observed a significant effect on endothelial transcriptional responses in the presence of IE, yet there was no significant correlation between HBMEC responses and type of clinical syndrome (UM or CM). Further, there was no correlation between HBMEC gene expression and both binding itself and level of IE binding to HBMEC, as we detected the same change in endothelial responses when employing both binding and non-binding parasites. Our results suggest that interaction of IE with endothelial cells in this co-culture model induce some endothelial responses that are independent of clinical origin and independent of the expression of the major variant antigen PfEMP1 on the IE surface.

cell biology↗

bioRxiv2023

Synergistic effects of inhibitors targeting PI3K and Aurora Kinase A in preclinical inflammatory breast cancer models

BackgroundInflammatory breast cancer (IBC) is an aggressive clinical subtype of breast cancer often diagnosed in young women. Lymph node and distant metastases are frequently detected at diagnosis of IBC, and improvements in systemic therapies are needed. For IBC that lack hormone or HER2 expression, no targeted therapies are available. Since the phosphatidyl inositol 3 kinase (PI3K) pathway is frequently deregulated in IBC, some studies have tested the pan PI3K inhibitor Buparlisib (BKM120). Although the SUM149 IBC cell line was resistant to Buparlisib, a functional genomic screen showed that silencing of Aurora kinase A (AURKA) sensitized cells to killing by Buparlisib. In this study, we tested whether combination treatments of PI3K and AURKA inhibitors act synergistically to kill IBC cells and tumors. MethodsSUM149 cells were treated with increasing doses of PI3K inhibitor Buparlisib (BKM120) and AURKA inhibitor Alisertib as monotherapies or combination therapies. Effects on target pathways, cytotoxicity, cell cycle, soft agar colony growth and cell migration were analyzed. The individual and combined treatments were also tested in a mammary orthotopic SUM149 tumor xenograft model to measure effects on tumor growth and metastasis ResultsThe SUM149 IBC cell line treated with Buparlisib showed reduced PI3K/AKT activation but no significant skewing of cell cycle progression. Parallel studies of Alisertib treatment showed that AURKA inhibition led to a significant block in G2/M transition in SUM149 cells. In cytotoxicity assays, Buparlisib and Alisertib combination treatments were highly synergistic compared to monotherapy controls. Evidence of synergy between Buparlisib and Alisertib also extended to soft agar colony growth and wound healing motility in SUM149 cells. The combination of Buparlisib and Alisertib also reduced IBC tumor growth in mammary orthotopic xenograft assays and reduced spontaneous metastases development in lung tissue. ConclusionsAlthough SUM149 IBC cells were relatively resistant to killing by the PI3K inhibitor Buparlisib, our study showed that co-targeting the mitotic kinase AURKA with Alisertib synergized to limit IBC cell growth and motility, as well as IBC tumor growth and metastasis.

cancer biology↗

bioRxiv2020

Power-law scaling of brain wave activity associated with mental fatigue

This paper investigates the cause and detection of power-law scaling of brain wave activity due to the heterogeneity of the brain cortex, considered as a complex system, and the initial condition such as the alert or fatigue state of the brain. Our starting point is the construction of a mathematical model of global brain wave activity based on EEG measurements on the cortical surface. The model takes the form of a stochastic delay-differential equation (SDDE). Its fractional diffusion operator and delay operator capture the responses due to the heterogeneous medium and the initial condition. The analytical solution of the model is obtained in the form of a Karhunen-Loeve expansion. A method to estimate the key parameters of the model and the corresponding numerical schemes are given. Real EEG data on driver fatigue at 32 channels measured on 50 participants are used to estimate these parameters. Interpretation of the results is given by comparing and contrasting the alert and fatigue states of the brain. The EEG time series at each electrode on the scalp display power-law scaling, as indicated by their spectral slopes in the low-frequency range. The diffusion of the EEG random field is non-Gaussian, reflecting the heterogeneity of the brain cortex. This non-Gaussianity is more pronounced for the alert state than the fatigue state. The response of the system to the initial condition is also more significant for the alert state than the fatigue state. These results demonstrate the usefulness of global SDDE modelling complementing the time series approach for EEG analysis.

bioinformatics↗

bioRxiv2020

Unannotated small RNA clusters in circulating extracellular vesicles detect early stage liver cancer

BackgroundHepatocellular carcinoma (HCC) is among the deadliest malignancies and surveillance tools for early detection are suboptimal. Extracellular vesicles (EVs) have gained increasing scientific interest due to their involvement in tumor initiation and metastasis, however, most extracellular RNA (exRNA) biomarker studies are limited to annotated genomic regions. MethodsEVs were isolated with ultracentrifugation and nanoDLD and quality assessed by electron microscopy, immunoblotting, nanoparticle tracking, and deconvolution analysis. We performed genome-wide small exRNA sequencing, including unannotated transcripts. We identified small RNA clusters (smRCs) and delineated their key genomic features across biospecimens (blood, urine, tissue) and EV isolation techniques. A 3-smRC signature for early HCC detection was trained and validated in two independent cohorts. ResultsEV-derived smRCs were dominated by uncharacterized, unannotated small RNA and uniformly tiled across the genome with a consensus sequence of 20bp. A 3-smRC signature was significantly overexpressed in circulating EVs of HCC patients compared to controls at risk or patients with non-HCC malignancies (p<0.01, n=157). An independent validation in a phase 2 biomarker study revealed 86% sensitivity and 91% specificity for the detection of early HCC from controls at risk (i.e. cirrhosis or chronic liver disease, n=209) (positive predictive value (PPV): 89%, area under the ROC curve [AUC]: 0.87). The 3-smRC signature was independent of alpha-fetoprotein (p<0.0001) and a composite model yielded an increased AUC of 0.93 (sensitivity: 85%, specificity: 94%, PPV: 95%). ConclusionAn exRNA-based 3-smRC signature from plasma detects early stage HCC, which directly leads to the prospect of a minimally-invasive, blood-only, operator-independent surveillance biomarker. One sentence summaryWe employ a novel, data-driven approach to identify and characterize small RNA clusters from unannotated loci in extracellular vesicle-derived RNA across different cancer types, isolation techniques, and biofluids, facilitating discovery of a robust biomarker for detection of early stage liver cancer.

cancer biology↗

bioRxiv2019

Developing a xenograft model of human vasculature in the mouse ear pinna

Humanised xenograft models allow for the analysis of human tissue within a physiological environment in vivo. However, current models often rely on the angiogenesis and ingrowth of recipient vasculature to perfuse tissues, preventing analysis of biological processes and diseases involving human blood vessels. This limits the effectiveness of xenografts in replicating human physiology and may lead to issues with translating findings into human research. We have designed a xenograft model of human vasculature to address this issue. Human subcutaneous fat was cultured in vitro to promote blood vessel outgrowth prior to implantation into immunocompromised mice. We demonstrate that implants survived, retained human vasculature and anastomosed with the circulatory system of the recipient mouse. Significantly, by performing transplants into the ear pinna, this system enabled intravital observation of xenografts by multiphoton microscopy, allowing us to visualise the steps leading to vascular cytoadherence of erythrocytes infected with the human parasite Plasmodium falciparum. This model represents a useful tool for imaging the interactions that occur within human tissues in vivo and permits visualization of blood flow and cellular recruitment in a system which is amenable to intervention for various studies in basic biology together with drug evaluation and mechanism of action studies.

pathology↗

bioRxiv2019

Parasite histones mediate leak and coagulopathy in cerebral malaria

Coagulopathy and leak, specific to the brain vasculature, are central pathogenetic components of cerebral malaria (CM). It is unclear how the parasite, Plasmodium falciparum, triggers these processes. Extracellular histones, released from damaged host cells, bind to cell membranes and cause coagulation activation, platelet aggregation and vascular leak in diverse critical illnesses. In CM patients with P. falciparum, serum histones correlate with fibrin formation, thrombocytopenia, and endothelial activation and predict brain swelling on magnetic resonance imaging and fatal outcome. Post-mortem, histones bind to the luminal vascular surface, co-localizing with P. falciparum-infected erythrocytes (IE), and with thrombosis and leak. Purified P. falciparum histones cause toxicity and barrier disruption in cultured human brain microvascular endothelial cells, as does serum from CM patients, reversed by anti-histone antibodies and non-anticoagulant heparin. These data implicate parasite histones as a key trigger of fatal brain swelling in CM. Neutralizing histones with agents such as non-anticoagulant heparin warrant exploration to prevent brain swelling and improve outcome.

microbiology↗

bioRxiv2018

Aberrant mast cell activation promotes chronic recurrent multifocal osteomyelitis

Chronic nonbacterial osteomyelitis (CNO) is an autoinflammatory bone disease. While some patients exhibit bone lesions at single sites, most patients develop chronically active or recurrent bone inflammation at multiple sites, and are then diagnosed with recurrent multifocal osteomyelitis (CRMO). Chronic multifocal osteomyelitis (CMO) mice develop IL-1{beta}-driven sterile bone lesions reminscent of severe CRMO. Mechanistically, CMO disease arises due to loss of PSTPIP2, a negative regulator of macrophages, osteoclasts and neutrophils. The goal of this study was to evaluate the potential involvement of mast cells in CMO/CRMO disease pathophysiology. Here, we show that mast cells accumulate in the inflamed tissues from CMO mice, and mast cell protease Mcpt1 was detected in the peripheral blood. The role of mast cells in CMO disease was investigated using a transgenic model of connective tissue mast cell depletion (Mcpt5-Cre:Rosa26-Stopfl/fl-DTa) that was crossed with CMO mice. The resulting CMO/MC-mice showed a significant delay in disease onset compared to age-matched CMO mice. At 5-6 months of age, CMO/MC- mice had fewer bone lesions and immune infiltration in the popliteal lymph nodes that drain the affected tail and paw tissues. To test the relevance of mast cells to human CRMO, we tested serum samples from a cohort of healthy controls or CRMO patients at diagnosis. Interestingly, mast cell chymase was elevated in CRMO patients as well as patients with oligoclonal juvenile arthritis. Tryptase-positive mast cells were also detected in bone lesions from CRMO patients as well as patients with bacterial osteomyelitis. Taken together, our results identify mast cells as cellular contributors to bone inflammation in CMO/CRMO. Observations of this study promise potential for mast cells and derived mediators as future biomarkers and/or therapeutic targets.

immunology↗