Biology subjects

Eward, W. C.

Publications and source records attributed to Eward, W. C..

8 recordsLinked to original sources

bioRxiv2024

A sequence- and structure-based characterization of microbial enzymes identifies P. stutzeri as a plastic-degrading species

Plastic waste has accumulated rapidly in the past century and is now found throughout every ecosystem on Earth. Its ubiquitous presence means that plastic is routinely ingested by countless organisms, with potential negative consequences for organismal health. New solutions are urgently needed to combat plastic pollution. Among the many strategies required to curb the plastic pollution crisis, the bioremediation of plastic via enzymatic activity of microbial species represents a promising approach. Diverse microbes harbor enzymes capable of degrading plastic polymers and utilizing the polymers as a carbon source. Herein, we characterize the landscape of microbial protein-coding sequences with potential plastic degrading capability. Using the two enzyme systems of PETase and MHETase as a guide, we combined sequence motif analysis, phylogenetic inference, and machine learning-guided 3D protein structure prediction to pinpoint potential plastic-degrading enzymes. Our analysis platform identified hundreds of enzymes from diverse microbial taxa with similarity to known PETases, and far fewer enzymes with similarity to known MHETases. Phylogenetic reconstruction revealed that the plastic degrading enzymes formed distinct clades from the sequences of ancestral enzymes. Among the potential candidate sequences, we pinpointed both a PETase-like and MHETase-like enzyme within the bacterium Pseudomonas stutzeri. Using plate clearing assays, we demonstrated that P. stutzeri is capable of degrading both polyurethane (Impranil(R)) and polycaprolactone (PCL). Pseudomonas stutzeri also grew on carbon-free agar supplemented with polystyrene, suggesting this organism can utilize synthetic polymers as a carbon source. Overall, our integrated bioinformatics and experimental approach provides a rapid and low-cost solution to identify and test novel polymer-degrading enzymes for use in the development of plastic bioremediation technologies.

microbiology↗

bioRxiv2023

Toxicogenomic analysis of the carcinogenic potential of plastic additives

Plastics are the most prevalent human-made substance in the world and are ubiquitous throughout all ecosystems. Microscopic plastic particles are routinely ingested and inhaled by humans and other organisms. Despite the frequency of plastic exposures, little is known about their health consequences. Of particular concern are plastic additives -chemical compounds that are mixed into plastics to improve functionality or are unintentionally acquired during plastic production and use. Additives are loosely bound to the plastic polymer and may be released during plastic exposures. These compounds may pose health concerns, such as cancer, but little is known about the potential impact of these chemicals on health. To better understand the health effects of plastic additives, we performed an integrated toxicogenomic analysis on 2,712 additives, focusing on cancer as a well-studied toxicological endpoint. Screening these substances across three chemical databases revealed two key observations: 1) over 150 plastic additives have known carcinogenicity and 2) the majority ([~]90%) of plastic additives lack data on carcinogenic endpoints. Analyses of additive usage patterns pinpointed specific polymers, functions, and products in which carcinogenic additives reside. Based on published chemical-gene interactions, both carcinogenic additives and additives with unknown carcinogenicity impacted similar biological pathways. The predominant pathways involved DNA damage, apoptosis, immune response, viral diseases, and cancer. This study underscores the urgent need for systematic and comprehensive carcinogenicity assessment of plastic additives and regulatory responses to mitigate the potential health risks of plastic exposure.

pharmacology and toxicology↗

bioRxiv2022

Loss of the chromatin remodeler, ATRX, promotes aggressive features of osteosarcoma with increased NF-κB signaling and integrin receptor binding

Osteosarcoma (OS) is a lethal disease with few known targeted therapies. Here we show that decreased ATRX expression is associated with more aggressive tumor cell phenotypes, including increased growth, migration, invasion, and metastasis. These phenotypic changes correspond with activation of NF-{kappa}B signaling, extracellular matrix remodeling, increased integrin v{beta}3 expression, and ETS family transcription factor binding. Here we characterize these changes in vitro, in vivo, and in a dataset of human OS patients. This increased aggression substantially sensitizes ATRX-deficient OS cells to integrin signaling inhibition. Thus, ATRX plays an important tumor suppression role in OS, and loss of function of this gene may underlie new therapeutic vulnerabilities. The relationship between ATRX expression and integrin binding, NF-{kappa}B activation, and ETS family transcription factor binding has not been described in previous studies and may impact the pathophysiology of other diseases with ATRX loss, including other cancers and the ATR-X alpha thalassemia mental retardation syndrome.

cancer biology↗

bioRxiv2021

Atrx deletion impairs cGAS-STING signaling and increases response to radiation and oncolytic herpesvirus in sarcoma

ATRX is one of the most frequently altered genes in solid tumors, and mutation is especially frequent in soft tissue sarcomas. However, the role of ATRX in tumor development and response to cancer therapies remains poorly understood. Here, we developed a primary mouse model of soft tissue sarcoma and showed that Atrx deleted tumors are more sensitive to radiation therapy. In the absence of Atrx, irradiated sarcomas have increased persistent DNA damage, telomere dysfunction, and mitotic catastrophe. We find that Atrx deleted sarcomas have a reduced adaptive immune response, impaired cGAS-STING signaling, and increased sensitivity to an oncolytic herpesvirus therapy. Translation of these results to patients with ATRX mutant cancers could enable genomically-guided cancer therapeutic approaches that improve patient outcomes.

cancer biology↗

bioRxiv2021

An integrated comparative physiology and molecular approach pinpoints mediators of breath-hold capacity in dolphins

Ischemic events, such as ischemic heart disease and ischemic stroke, are the number one cause of death globally. Ischemia prevents blood, carrying essential nutrients and oxygen, from reaching tissues and organ systems, leading to cell and tissue death, and eventual organ failure. While humans are relatively intolerant to these ischemic events, other species, such as marine mammals, have evolved remarkable tolerance to chronic ischemia/reperfusion during diving. Here we capitalized on the unique adaptations of bottlenose dolphins (Tursiops truncatus) as a comparative model of ischemic stress and hypoxia tolerance to identify molecular features associated with breath-holding. Using RNA-Seq we observed time-dependent upregulation of the arachidonate 5-lipoxygenase (ALOX5) gene during breath-holding. Consistent with the RNA-Seq data, we also observed increased ALOX5 enzymatic activity in the serum of dolphins undergoing breath holds. ALOX5 has previously been shown to be activated during hypoxia in rodent models, and its metabolites, leukotrienes, induce vasoconstriction. The upregulation of ALOX5 occurred within the estimated aerobic dive limit of the species, suggesting that ALOX5 enzymatic activity may promote tolerance to ischemic stress through sustained vasoconstriction in dolphins during diving. These observations pinpoint a potential molecular mechanism by which dolphins, and perhaps other marine mammals, have adapted to the prolonged breath-holds associated with diving.

physiology↗

bioRxiv2019

From the clinic to the bench and back again in one dog year: identifying new treatments for sarcoma using a cross-species personalized medicine pipeline

Cancer drug discovery is an inefficient process, with more than 90% of newly-discovered therapies failing to gain regulatory approval. Patient-derived models of cancer offer a promising new approach to identifying personalized treatments; however, for rare cancers, such as sarcomas, access to patient samples can be extremely limited, which precludes development of patient-derived models. To address the limited access to patient samples, we have turned to pet dogs with naturally-occurring sarcomas. Although sarcomas make up less than 1% of all cancers in humans, sarcomas represent at least 15% of all cancers in dogs. Dogs with naturally-occurring sarcomas also have intact immune systems, an accelerated pace of cancer progression, and share the same environment as humans, making them ideal models that bridge key gaps between mouse models and human sarcomas.\n\nHere, we develop a framework for a personalized medicine pipeline that integrates drug screening, validation, and genomics to identify new therapies. We tested this paradigm through the study of a pet dog, Teddy, who presented with six synchronous leiomyosarcomas. By integrating patient-derived cancer models, in vitro drug screens, and in vivo validation we identified proteasome inhibitors as a potential therapy for Teddy. After showing an initial response to the proteasome inhibitor, bortezomib, Teddy developed rapid resistance, and tumor growth resumed. Whole exome sequencing revealed substantial genetic heterogeneity across Teddys multiple recurrent tumors and metastases, suggesting that intra-patient heterogeneity was responsible for the heterogeneous clinical response. Ubiquitin proteomics coupled with exome sequencing revealed multiple candidate driver mutations in proteins related to the proteasome pathway. Together, our results demonstrate how the comparative study of canine sarcomas can offer rapid insights into the process of developing personalized medicine approaches that can lead to new treatments for sarcomas in both humans and canines.

cancer biology↗

bioRxiv2018

An integrative systems biology and experimental approach identifies convergence of epithelial plasticity, metabolism, and autophagy to promote chemoresistance

The evolution of therapeutic resistance is a major cause of death for patients with solid tumors. The development of therapy resistance is shaped by the ecological dynamics within the tumor microenvironment and the selective pressure induced by the host immune system. These ecological and selective forces often lead to evolutionary convergence on one or more pathways or hallmarks that drive progression. These hallmarks are, in turn, intimately linked to each other through gene expression networks. Thus, a deeper understanding of the evolutionary convergences that occur at the gene expression level could reveal vulnerabilities that could be targeted to treat therapy-resistant cancer. To this end, we used a combination of phylogenetic clustering, systems biology analyses, and wet-bench molecular experimentation to identify convergences in gene expression data onto common signaling pathways. We applied these methods to derive new insights about the networks at play during TGF-{beta}-mediated epithelial-mesenchymal transition in a lung cancer model system. Phylogenetics analyses of gene expression data from TGF-{beta} treated cells revealed evolutionary convergence of cells toward amine-metabolic pathways and autophagy during TGF-{beta} treatment. Using high-throughput drug screens, we found that knockdown of the autophagy regulatory, ATG16L1, re-sensitized lung cancer cells to cancer therapies following TGF-{beta}-induced resistance, implicating autophagy as a TGF-{beta}-mediated chemoresistance mechanism. Analysis of publicly-available clinical data sets validated the adverse prognostic importance of ATG16L expression in multiple cancer types including kidney, lung, and colon cancer patients. These analyses reveal the usefulness of combining evolutionary and systems biology methods with experimental validation to illuminate new therapeutic vulnerabilities.

cancer biology↗

bioRxiv2018

E-cadherin represses anoikis resistance in sarcomas through both signaling and mechanical mechanisms

E-cadherin, an epithelial-specific cell-cell adhesion molecule, plays multiple roles in maintaining adherens junctions, regulating migration and invasion, and mediating intracellular signaling. Downregulation of E-cadherin is a hallmark of epithelial-mesenchymal transition (EMT) and correlates with poor prognosis in multiple carcinomas. Conversely, upregulation of E-cadherin is prognostic for improved survival in sarcomas. Yet, despite the prognostic benefit of E-cadherin expression in sarcoma, the mechanistic significance of E-cadherin in sarcomas remains poorly understood. Here, by combining mathematical models with wet-bench experiments, we identify the core regulatory networks mediated by E-cadherin in sarcomas, and decipher their functional consequences. Unlike in carcinomas, E-cadherin overexpression in sarcomas does not induce a mesenchymal-epithelial transition (MET). However, E-cadherin acts to reduce both anchorage-independent growth and spheroid formation of sarcoma cells. Ectopic E-cadherin expression acts to downregulate phosphorylated CREB (p-CREB) and the transcription factor, TBX2, to inhibit anoikis resistance. RNAi-mediated knockdown of TBX2 phenocopies the effect of E-cadherin on p-CREB levels and restores anoikis sensitivity to sarcoma cells. Beyond its signaling role, E-cadherin expression in sarcoma cells can also strengthen cell-cell adhesion and restricts spheroid growth through mechanical action. Together, our results demonstrate that E-cadherin inhibits sarcoma aggressiveness by inducing anoikis and restricting colony growth.

cancer biology↗