BioWorks (United States)

Drug delivery to solid tumors is challenged by multiple physiological barriers arising from the tumor microenvironment, including dense extracellular matrix, cellular heterogeneity, hypoxic gradients, and elevated interstitial fluid pressure. These features hinder the uniform distribution and accumulation of therapeutics, reducing treatment efficacy. Despite their widespread use, conventional two-dimensional monolayer cultures fail to reproduce these complexities, contributing to the poor translational predictability of many preclinical candidates. Three-dimensional multicellular tumor spheroids have emerged as more representative in vitro models that capture essential features of tumor architecture, stromal interactions, and microenvironmental resistance mechanisms. Spheroids exhibit spatially organized regions of proliferation, quiescence, and hypoxia, and can incorporate non-tumor cells to mimic tumor-stroma crosstalk. Advances in spheroid analysis now enable detailed evaluation of drug penetration, cellular migration, cytotoxic response, and molecular gradients using techniques such as optical and confocal imaging, large-particle flow cytometry, biochemical viability assays, and microfluidic integration. By combining physiological relevance with analytical accessibility, spheroid models support mechanistic studies of drug transport and efficacy under tumor-like conditions. Their adoption into routine preclinical workflows has the potential to improve translational accuracy while reducing reliance on animal models.

Abstract Targeted protein degradation (TPD) platforms, including PROTACs and molecular glues, have revolutionized drug discovery as transformative therapeutic strategies. Recent advancements in mass spectrometry-based proteomics have dramatically improved assay speed and sensitivity, providing actionable insights into degradation profiles and drug efficacy on timescales compatible with discovery chemistry. This study evaluates the practical utility of advanced proteomic assays in supporting TPD research, focusing on their role in streamlining drug discovery pipelines. State-of-the-art proteomic workflows were employed to quantify the proteome-wide effects of PROTACs and molecular glues across diverse cellular models. Assay sensitivity, reproducibility, and throughput were rigorously assessed to determine their real-world applicability. Our findings reveal that these enhanced technologies generate robust, high-resolution datasets, capturing the dynamic interplay between target degradation, protein interactions, and cellular responses. This enabled the rapid identification of optimal degrader candidates and informed structure-activity relationship (SAR) studies. Mass spectrometry-based proteomics has emerged as an essential tool for advancing TPD strategies. By combining heightened sensitivity with operational feasibility, these assays offer critical insights that accelerate the development of PROTACs and molecular glues, bridging the gap between foundational research and clinical application. Citation Format: Michael J. Ford, Ravi Amunugama, David L. Allen, Richard C. Jones. Mass spectrometry-based proteomics for accelerating PROTAC and molecular glue drug discovery [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2025; Part 1 (Regular Abstracts); 2025 Apr 25-30; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2025;85(8_Suppl_1):Abstract nr 7027.

Cells must sense and respond to sudden maladaptive environmental changes—stresses—to survive and thrive. Across eukaryotes, stresses such as heat shock trigger conserved responses: growth arrest, a specific transcriptional response, and biomolecular condensation of protein and mRNA into structures known as stress granules under severe stress. The composition, formation mechanism, adaptive significance, and even evolutionary conservation of these condensed structures remain enigmatic. Here we provide a remarkable view into stress-triggered condensation, its evolutionary conservation and tuning, and its integration into other well-studied aspects of the stress response. Using three morphologically near-identical budding yeast species adapted to different thermal environments and diverged by up to 100 million years, we show that proteome-scale biomolecular condensation is tuned to species-specific thermal niches, closely tracking corresponding growth and transcriptional responses. In each species, poly(A)-binding protein—a core marker of stress granules—condenses in isolation at species-specific temperatures, with conserved molecular features and conformational changes modulating condensation. From the ecological to the molecular scale, our results reveal previously unappreciated levels of evolutionary selection in the eukaryotic stress response, while establishing a rich, tractable system for further inquiry.

Neuroinflammation plays a crucial role in the development of neurodegenerative protein misfolding disorders. This category of progressive diseases includes, but is not limited to, Alzheimer's disease, Parkinson's disease, and prion diseases. Shared pathogenesis involves the accumulation of misfolded proteins, chronic neuroinflammation, and synaptic dysfunction, ultimately leading to irreversible neuronal loss, measurable cognitive deficits, and death. Presently, there are few to no effective treatments to halt the advancement of neurodegenerative diseases. We hypothesized that directly targeting neuroinflammation by downregulating the transcription factor, NF-κB, and the inflammasome protein, NLRP3, would be neuroprotective. To achieve this, we used a cocktail of RNA targeting therapeutics (SB_NI_112) shown to be brain-penetrant, nontoxic, and effective inhibitors of both NF-κB and NLRP3. We utilized a mouse-adapted prion strain as a model for neurodegenerative diseases to assess the aggregation of misfolded proteins, glial inflammation, neuronal loss, cognitive deficits, and lifespan. Prion-diseased mice were treated either intraperitoneally or intranasally with SB_NI_112. Behavioral and cognitive deficits were significantly protected by this combination of NF-κB and NLRP3 downregulators. Treatment reduced glial inflammation, protected against neuronal loss, prevented spongiotic change, rescued cognitive deficits, and significantly lengthened the lifespan of prion-diseased mice. We have identified a nontoxic, systemic pharmacologic that downregulates NF-κB and NLRP3, prevents neuronal death, and slows the progression of neurodegenerative diseases. Though mouse models do not always predict human patient success and the study was limited due to sample size and number of dosing methods utilized, these findings serve as a proof of principle for continued translation of the therapeutic SB_NI_112 for prion disease and other neurodegenerative diseases. Based on the success in a murine prion model, we will continue testing SB_NI_112 in a variety of neurodegenerative disease models, including Alzheimer's disease and Parkinson's disease.

Sugar substitutes are popular due to their akin taste and low calories. However, excessive use of aspartame and erythritol can have varying effects. While D-allulose is presently deemed a secure alternative to sugar, its excessive consumption is not devoid of cellular stress implications. In this study, the evolution of Escherichia coli Nissle 1917 (EcN) is directed to utilize allulose as sole carbon source through a combination of adaptive laboratory evolution (ALE) and fluorescence-activated droplet sorting (FADS) techniques. Employing whole genome sequencing (WGS) and clustered regularly interspaced short palindromic repeats interference (CRISPRi) in conjunction with compensatory expression displayed those genetic mutations in sugar and amino acid metabolic pathways, including glnP, glpF, gmpA, nagE, pgmB, ybaN, etc., increased allulose assimilation. Enzyme-substrate dynamics simulations and deep learning predict enhanced substrate specificity and catalytic efficiency in nagE A247E and pgmB G12R mutants. The findings evince that these mutations hold considerable promise in enhancing allulose uptake and facilitating its conversion into glycolysis, thus signifying the emergence of a novel metabolic pathway for allulose utilization. These revelations bear immense potential for the sustainable utilization of D-allulose in promoting health and well-being.

Abstract Antimicrobial resistance has emerged as an urgent global public health threat, and development of novel therapeutics for treating infections caused by multi-drug resistant bacteria is urgent.Staphylococcus aureusis a major human and animal pathogen, responsible for high levels of morbidity and mortality worldwide. The intracellular survival ofS. aureusin macrophages contributes to immune evasion, dissemination, and resilience to antibiotic treatment. Here, we present a confocal fluorescence imaging assay for monitoring macrophage infection by GFP-taggedStaphylococcus aureusas a front-line tool to identify antibiotic leads. The assay was employed in combination with nanoscaled chemical analyses to facilitate the discovery of a novel, active rifamycin analogue. Our findings indicate a promising new approach to the identification of anti-microbial compounds with macrophage intracellular activity. The novel antibiotic identified here may represent a useful addition to our armoury in tackling the silent pandemic of antimicrobial resistance.

ABSTRACTWe present a net-shaped DNA nanostructure (called “DNA Net” herein) design strategy for selective recognition and high-affinity capture of the intact SARS-CoV-2 virions through spatial pattern-matching and multivalent interactions between the aptamers (targeting wild type spike-RBD) positioned on the DNA Net and the trimeric spike glycoproteins displayed on the viral outer surface. Carrying a designer nanoswitch, the DNA Net-aptamers releases fluorescent signal upon virus binding that is easily read by a hand-held fluorimeter for a rapid (in 10 mins), simple (mix- and-read), sensitive (PCR equivalent), room temperature compatible, and inexpensive (∼ $1.26/test) COVID-19 test assay. The DNA Net-aptamers also impede authentic wild-type SARS-CoV-2 infection in cell culture with a near 1×103-fold enhancement of the monomeric aptamer. Furthermore, our DNA Net design principle and strategy can be customized to tackle other life-threatening and economically influential viruses like influenza and HIV, whose surfaces carry class-I viral envelope glycoproteins like the SARS-CoV-2 spikes in trimeric forms.

Simple SummaryThe foxglove aphid (FGA), Aulacorthum solani (Keltenbach), feeds on many important greenhouse crops in Canada. Currently, biological control of this pest is difficult as existing biocontrol agents are only moderately effective. Access to a generalist predator would strengthen biocontrol programs for this and other similarly challenging pests. Anystis baccarum (L.) is a globally distributed generalist predatory mite. We assessed the predatory efficacy of A. baccarum against FGA in a series of laboratory and small-scale greenhouse trials. The laboratory trials showed that A. baccarum readily consumed all FGA life stages and was particularly effective against first instars. In a greenhouse trial on sweet peppers, working together with Aphidius ervi Haliday, an aphid-specific parasitoid wasp, A. baccarum successfully eradicated the aphids and higher fruit yields were obtained compared to plants protected by the parasitoids only. Pepper plants also became naturally infested with western flower thrips during the trial, which caused feeding damage to the fruits. The fruits were likely to have less thrips’ feeding damage on plants carrying A. baccarum as the predator also fed on these pests. The results demonstrate that A. baccarum could be a useful addition to greenhouse IPM programs for hard-to-control pests like FGA, especially when they occur together with other pest species.A generalist predatory mite, Anystis baccarum (L.), has been identified as a key predator of small, soft-bodied pest species in various agroecosystems around the world. The foxglove aphid Aulacorthum solani (Keltenbach) is a new problematic pest in Canadian greenhouses. Laboratory colonies of A. baccarum were established and its predatory efficacy against A. solani was assessed. In laboratory trials, A. baccarum ate approximately one adult aphid or seven first instar aphids in 24 h. In a greenhouse bench trial on sweet peppers with the free-flying aphid parasitoid, Aphidius ervi Haliday, the population dynamics of A. solani in the presence or absence of A. baccarum was evaluated. Although the parasitoid alone successfully eradicated A. solani, when A. baccarum were present on the plants, the aphid population was eradicated more rapidly. Fruit yield was also 15% higher from plants where A. baccarum was released than the control (without A. baccarum). Furthermore, plants were naturally infested by Frankliniella occidentalis (Pergande) during the trial, which caused visible feeding damage to the fruits. Anystis baccarum also predates on thrips and thrips’ feeding damage to the fruits was reduced on plants where A. baccarum was released. Anystis baccarum was able to establish in sweet peppers and was determined to be complementary to the current practice of using A. ervi for the biological control of A. solani.

Activating RAS missense mutations are among the most prevalent genomic alterations observed in human cancers and drive oncogenesis in the three most lethal tumor types. Emerging evidence suggests mutant KRAS (mKRAS) may be targeted immunologically, but mKRAS epitopes remain poorly defined. Here we employ a multi-omics approach to characterize HLA class I-restricted mKRAS epitopes. We provide proteomic evidence of mKRAS epitope processing and presentation by high prevalence HLA class I alleles. Select epitopes are immunogenic enabling mKRAS-specific TCRαβ isolation. TCR transfer to primary CD8+ T cells confers cytotoxicity against mKRAS tumor cell lines independent of histologic origin, and the kinetics of lytic activity correlates with mKRAS peptide-HLA class I complex abundance. Adoptive transfer of mKRAS-TCR engineered CD8+ T cells leads to tumor eradication in a xenograft model of metastatic lung cancer. This study validates mKRAS peptides as bona fide epitopes facilitating the development of immune therapies targeting this oncoprotein.