Biology subjects

Bonham, C. A.

Publications and source records attributed to Bonham, C. A..

9 recordsLinked to original sources

bioRxiv2026

Pannexin 1 Ablation Disrupts Cell Cycle Progression and Compromises the Structure of Melanoma Tumours

Pannexin 1 (PANX1) is a channel-forming glycoprotein that has been implicated in regulating melanoma cell properties such as growth, migration, and invasion. Here we report that the CRISPR-Cas9 mediated ablation of PANX1 or channel inhibition with probenecid shifted A375-P cell cycle distribution towards G2/M, while channel inhibition with spironolactone stalled cell cycle progression at the G1/S checkpoint regardless of PANX1 expression. Bulk RNA sequencing revealed cell cycle related gene expression was downregulated with PANX1 targeting strategies and this was exacerbated when PANX1 deficient cells were treated with spironolactone. When grown as spheroids, we found the deletion and inhibition of PANX1 disrupted spheroid compaction, with spheroids displaying poorly defined borders and reduced circularity. The deletion of PANX1 increased spheroid fragmentation, and this phenotype was intensified when spheroids devoid of PANX1 were treated with spironolactone, highlighting a potential synthetic lethal effect. Using liquid chromatography mass spectrometry, we sought to determine whether PANX1 had binding partners that may act to stabilize spheroid integrity and found that PANX1 co-immunoprecipitated various cell adhesion molecules such as {beta}-actin and F-actin-capping protein subunit -1, suggesting PANX1 and its interacting partners may stabilize cell-cell contacts. When control and PANX1 ablated cells were grown in chick chorioallantoic membrane xenografts to assess their tumour growth characteristics, we discovered that the deletion of PANX1 reduced tumour surface area and viability. Our findings indicate that PANX1 regulates cell cycle progression and the structural architecture of A375-P melanoma tumours, highlighting the therapeutic utility of targeting PANX1 in melanoma.

cancer biology↗

bioRxiv2026

Computational Analysis of Fibroblast Subpopulation Dynamics as a Driver of Fibrotic Foci Formation

Fibroblasts maintain the extracellular matrix (ECM) to support tissue homeostasis and wound healing. In fibrotic diseases, fibroblasts are a primary driver of disease progression through excess collagen secretion and enhanced contractility. Replacing native tissue with a collagen rich fibrotic scar leads to a decline in tissue function. Recent research into idiopathic pulmonary fibrosis (IPF) has identified fibroblast subpopulations that may be primed for the hyper-activation that leads to increased progression of fibrotic disease. Understanding the contribution of these subpopulations to disease progression requires integrating experimental and computational techniques to understand their dynamic contributions to tissue phenotype. Herein, we introduce a framework for modeling subpopulations using a multiscale mechanistic computational model to understand differences within subpopulations, at the intracellular level and how these differences contribute to cell-and tissue-level pathology. We build and validate this framework using two well-defined subpopulations of fibroblasts in IPF. The subpopulations are defined by the presence or absence of Thy-1, a cell-surface protein that regulates fibroblast mechanosensing. We first developed a logic-based network model of a fibroblast. We then applied this model to identify sub-networks that regulate myofibroblast marker expression in the two subpopulations. Coupling this with an agent-based model (ABM) of the lung microenvironment, we observed how different rules regulating cell fate decisions in each subpopulation affected collagen content. Computational image outputs were analyzed with the open-source biological image analysis software QuPath to quantify how changes in subpopulation dynamics change model-predicted foci characteristics such as size and collagen density. We find that the ability for Thy-1+ fibroblasts to transition to Thy-1- fibroblasts significantly increases total collagen content, as well as influences fibrotic foci characteristics. Overall, we present a combined experimental and computational framework for studying how dynamic changes in fibroblast subpopulations lead to tissue-level disease phenotypes. Author SummaryIn wound healing fibroblasts are responsible for rebuilding the scaffolding, called the extracellular matrix (ECM), of the damaged tissue to aid in regeneration. In fibrosis, the normal wound healing processes are hijacked leading to overproduction of ECM proteins, such as collagen, by fibroblasts leading to fibrosis. In fibrotic diseases with no known cause, such as idiopathic pulmonary fibrosis (IPF), subpopulations of fibroblasts have been identified as possible drivers of disease. Herein, we use a multiscale computational model that represents intracellular, cellular, and tissue level signaling to study how the presence or absence of a single protein on a fibroblasts surface, Thy-1, affects the formation of fibrotic scar in IPF. Thy-1 regulates how a fibroblast senses the stiffness of the microenvironment. The absence of Thy-1 impacted intracellular signaling and when combined across many cells led to fibrosis at the tissue level. Additionally, if normal Thy-1+ fibroblasts could dynamically lose Thy-1 expression the amount of collagen they produced correlated with that in end stage IPF lungs. This model presents a framework for studying different fibroblast subpopulations using multiscale computational modeling to understand how changes in a single protein in one cell can, over an entire population, affect the dynamics of disease progression.

bioengineering↗

bioRxiv2026

Inhibition of protein tyrosine phosphatase PTP1B function ameliorates pathophysiological deficits in Rett Syndrome

Rett syndrome (RTT) is a severe neurodevelopmental disorder in which current therapeutic strategies remain largely focused on providing symptomatic relief without addressing underlying disease mechanisms. In contrast, we have identified the protein tyrosine phosphatase PTP1B as a mechanism-based therapeutic target and evaluated a class of selective, allosteric small-molecule inhibitors in female murine models of RTT. We show that one of these compounds localizes to brain regions central to motor coordination and cardio-respiratory control, which are core domains of RTT pathology. Pharmacological inhibition of PTP1B produces robust and sustained improvement in multiple disease symptoms, including muscle weakness, motor and coordination deficits, and cardiac and respiratory dysfunction. Concordant results obtained with genetic ablation of PTP1B, with effects maintained for over one year, demonstrate that phenotypic rescue arises from on-target modulation of disease-relevant signaling. Mechanistically, PTP1B inhibition is known to normalize neurotrophic and metabolic pathways, including TRKB and insulin/leptin signaling, thereby restoring circuit-level function. These findings establish PTP1B as a clinically actionable, disease-modifying target and demonstrate that selective, allosteric inhibition of a protein tyrosine phosphatase can achieve durable therapeutic benefit in vivo. This work provides a strong rationale for the clinical evaluation of PTP1B inhibitors as a mechanism-based treatment strategy for RTT. One Sentence SummaryWe have validated inhibition of PTP1B as a mechanism-based therapeutic strategy that alleviates a wide range of symptoms in a mouse model of Rett syndrome.

neuroscience↗

bioRxiv2024

Multi-Scale Computational Model of Microvascular Remodeling in Idiopathic Pulmonary Fibrosis

Investigating the molecular, cellular, and tissue-level changes caused by disease, and the effects of pharmacological treatments across these biological scales, necessitates the use of multiscale computational modeling in combination with experimentation. Many diseases dynamically alter the tissue microenvironment in ways that trigger microvascular network remodeling, which leads to the expansion or regression of microvessel networks. When microvessels undergo remodeling in idiopathic pulmonary fibrosis (IPF), functional gas exchange is impaired due to loss of alveolar structures and lung function declines. Here, we integrated a multiscale computational model with independent experiments to investigate how combinations of biomechanical and biochemical cues in IPF alter cell fate decisions leading to microvascular remodeling. Our computational model predicted that extracellular matrix (ECM) stiffening reduced microvessel area, which was accompanied by physical uncoupling of endothelial cell (ECs) and pericytes, the cells that comprise microvessels. Nintedanib, an FDA-approved drug for treating IPF, was predicted to further potentiate microvessel regression by decreasing the percentage of quiescent pericytes while increasing the percentage of pericytes undergoing pericyte-myofibroblast transition (PMT) in high ECM stiffnesses. Importantly, the model suggested that YAP/TAZ inhibition may overcome the deleterious effects of nintedanib by promoting EC-pericyte coupling and maintaining microvessel homeostasis. Overall, our combination of computational and experimental modeling can explain how cell decisions affect tissue changes during disease and in response to treatments.

bioengineering↗

bioRxiv2022

Cas9-Mediated Knockout of Ndrg2 Enhances the Regenerative Potential of Dendritic Cells for Wound Healing

Chronic wounds impose a significant healthcare burden to a broad patient population. Cell based therapies, while having shown benefits for the treatment of chronic wounds, have not achieved widespread adoption into clinical practice. Here, we developed a novel CRISPR/Cas9 approach to precisely edit dendritic cells (DCs) to enhance their therapeutic potential for healing chronic wounds. Using single-cell RNA sequencing (scRNA-seq) of tolerogenic DCs, we discover N-myc downregulated gene 2 (Ndrg2), which marks a specific population of DC progenitors, as a promising target for CRISPR knockout (KO). Ndrg2-KO alters the transcriptomic profile of DCs and preserves an immature cell state with a strong, pro-angiogenic and regenerative capacity. We then incorporated our CRISPR-based cell engineering within a hydrogel technology for in vivo cell delivery and developed a highly effective translational approach for DC based immunotherapy that accelerated healing of full-thickness wounds in both non-diabetic and diabetic mouse models. These findings could open the door to future clinical trials using safe gene editing in DCs for treating various types of chronic wounds.

cell biology↗

bioRxiv2022

Allometric tissue-scale forces activate mechanoresponsive immune cells to drive pathological foreign body response to biomedical implants

For decades, it has been assumed that the foreign body response (FBR) to biomedical implants is primarily a reaction to the chemical and mechanical properties of the implant. Here, we show for the first time that a third independent variable, allometric tissue-scale forces (which increase exponentially with body size), can drive the biology of FBR in humans. We first demonstrate that pathological FBR in humans is mediated by immune cell-specific Rac2 mechanotransduction signaling, independent of implant chemistry or mechanical properties. We then show that mice, which are typically poor models of human FBR, can be made to induce a strikingly human-like pathological FBR by altering these extrinsic tissue forces. Altering these extrinsic tissue forces alone activates Rac2 signaling in a unique subpopulation of immune cells and results in a human-like pathological FBR at the molecular, cellular, and local tissue levels. Finally, we demonstrate that blocking Rac2 signaling negates the effect of increased tissue forces, dramatically reducing FBR. These findings highlight a previously unsuspected mechanism for pathological FBR and may have profound implications for the design and safety of all implantable devices in humans. One-Sentence SummaryAllometric tissue-scale forces at the implant-tissue interface drive pathological foreign body response.

bioengineering↗

bioRxiv2021

Xenogeneic Skin Transplantation Promotes Angiogenesis and Tissue Regeneration Through Vitamin D-Activated Trem2+ Macrophages

Skin allo- and xenotransplantation are the standard treatment for major burns when donor sites for autografts are not available and have been shown to significantly accelerate wound healing. Although the cellular elements of foreign grafts are rejected, the extracellular matrix components integrate into the wound and may underlie their beneficial effects on wound healing. The molecular mechanisms defining the relationship between the immune response to foreign grafts and their impact on wound healing have not been fully elucidated. Here, we investigated changes in collagen architecture after xenogeneic implantation of clinically available human biologic scaffolds. We show that collagen deposition in response to the implantation of human split-thickness skin grafts (hSTSG) containing live cells recapitulates normal skin architecture, whereas human acellular dermal matrix (ADM) grafts led to highly aligned collagen deposition, characteristic of fibrosis and scar. Using single-cell RNA-sequencing, we show that macrophage differentiation in response to hSTSG is driven by vitamin D (VD) signaling toward Trem2+ subpopulations with an enrichment of pro-angiogenic and anti-fibrotic transcriptomic programs. We subsequently induced this regenerative subpopulation in vitro by treating bone marrow-derived cells with vitamin D3 and found that hydrogel delivery of Trem2+ macrophages significantly accelerated wound closure in a human-like murine excisional wound model. Our study identifies the preclinical therapeutic potential of Trem2+ macrophages to mitigate fibrosis and promote wound healing and provides a novel effective strategy to develop advanced cell therapies for complex wounds. One Sentence SummaryVitamin D-activated Trem2+ macrophages promote angiogenesis and mitigate fibrosis, providing a novel effective strategy to develop advanced cell therapies for complex wounds.

immunology↗

bioRxiv2020

Divergent molecular signatures of regeneration and fibrosis during wound repair

Regeneration is the "holy grail" of tissue repair, but skin injury typically yields fibrotic, non-functional scars. Developing pro-regenerative therapies requires rigorous understanding of the molecular progression from injury to fibrosis or regeneration. Here, we report the divergent molecular events driving skin wound cells toward either scarring or regenerative fates. We profile scarring versus YAP inhibition-induced wound regeneration at the transcriptional (single-cell RNA-sequencing), protein (timsTOF proteomics), and tissue (extracellular matrix ultrastructural analysis) levels. Using cell surface barcoding, we integrate these data to reveal fibrotic and regenerative "molecular trajectories" of healing. We show that disrupting YAP mechanical signaling yields regenerative repair orchestrated by fibroblasts with activated Trps1 and Wnt signaling. Our findings serve as a multimodal map of wound regeneration and could have therapeutic implications for pathologic fibroses.

cell biology↗

bioRxiv2018

Single-Cell Transcriptomic Analysis of Human Lung Reveals Complex Multicellular Changes During Pulmonary Fibrosis

Pulmonary fibrosis is a devastating disorder that results in the progressive replacement of normal lung tissue with fibrotic scar. Available therapies slow disease progression, but most patients go on to die or require lung transplantation. Single-cell RNA-seq is a powerful tool that can reveal cellular identity via analysis of the transcriptome, but its ability to provide biologically or clinically meaningful insights in a disease context is largely unexplored. Accordingly, we performed single-cell RNA-seq on lung tissue obtained from eight transplant donors and eight recipients with pulmonary fibrosis and one bronchoscopic cryobiospy sample. Integrated single-cell transcriptomic analysis of donors and patients with pulmonary fibrosis identified the emergence of distinct populations of epithelial cells and macrophages that were common to all patients with lung fibrosis. Analysis of transcripts in the Wnt pathway suggested that within the same cell type, Wnt secretion and response are restricted to distinct non-overlapping cells, which was confirmed using in situ RNA hybridization. Single-cell RNA-seq revealed heterogeneity within alveolar macrophages from individual patients, which was confirmed by immunohistochemistry. These results support the feasibility of discovery-based approaches applying next generation sequencing technologies to clinically obtained samples with a goal of developing personalized therapies.\n\nOne Sentence SummarySingle-cell RNA-seq applied to tissue from diseased and donor lungs and a living patient with pulmonary fibrosis identifies cell type-specific disease-associated molecular pathways.

systems biology↗