Biology subjects

Ramsey, J.

Publications and source records attributed to Ramsey, J..

8 recordsLinked to original sources

bioRxiv2026

Targeting REV7 exposes a mitotic vulnerability in colorectal cancer cells

Therapeutic resistance remains a barrier to durable treatment of colorectal cancer (CRC), highlighting the need to identify vulnerabilities in resistant tumor cells. REV7 (MAD2L2) is a multifunctional genome-maintenance protein with established roles in REV3-dependent translesion synthesis (TLS) as well as mitotic progression, spindle organization, and chromosome segregation. Although perturbing REV7 dependent DNA damage tolerance has emerged as a strategy to overcome chemoresistance, whether pharmacologic targeting of REV7 exposes vulnerabilities to mitotic disruption remains poorly understood. Here, we investigated the REV7 targeting small molecule inhibitor C10, which disrupts the REV7 and REV3 interaction, and found that C10 sensitized HCT116 and HT29 CRC cells to the microtubule-disrupting agent colchicine, resulting in markedly reduced clonogenic survival. In contrast, C10 did not substantially enhance sensitivity to cisplatin. Genetic loss of REV7 similarly increased sensitivity to colchicine, independently supporting a REV7 dependent vulnerability to microtubule disruption. Combined C10 and colchicine treatment was associated with pronounced alterations in mitotic and post-mitotic nuclear morphology, including condensed/mitotic-like and multinucleated configurations, and increased micronucleus formation. In HT29 cells, combined treatment also increased the frequency of cells containing multiple gamma tubulin positive foci, consistent with disrupted centrosome-associated organization. Together, these findings support a model in which REV7 dependent functions contribute to cellular tolerance and recovery from microtubule mediated mitotic stress, whereas REV7 and REV3 disruption renders CRC cells vulnerable to mitotic perturbation. This study broadens the potential consequences of targeting REV7 beyond its canonical role in TLS and suggests that combining REV7 directed inhibition with mitotic perturbation warrants further investigation as a therapeutic strategy in CRC and potentially other cancers.

cancer biology↗

bioRxiv2025

Phage N4 uses a SAR endolysin-holin system for host cell lysis

Abstract Bacteriophages (phages) cause active host cell lysis to terminate their infection and release progeny into the environment. However, some phages have systems to delay their lysis, and thereby increase progeny yield, in specific conditions: a phenomenon called lysis inhibition (LIN). Two dissimilar phages of Escherichia coli are known to exhibit LIN: T4 and N4. In T4, a multi-protein mechanism stalls lysis and maintains the LIN state in response to superinfection in a high phage population density. However, the lysis proteins responsible for T4 lysis and LIN are not conserved with phage N4. In this study, we characterize the phage N4 proteins involved in lysis by molecular and genetic means. We define the functions of the minimal gene set required for lysis through heterologous expression and complementation. Furthermore, by sequence comparison with a selected mutant library that does not induce LIN, we have identified genomic regions both within and outside the lysis cassette involved in N4 LIN. We propose a model where N4 lysis proteins that execute rapid N4 lysis can be regulated to induce LIN. Despite the lack of conservation with T4 components, our study suggests that direct modulation of lysis initiation may be common and provides a springboard for identifying similar mechanisms in other phages. Importance Phages are viruses that kill only bacteria. To do so, they use lysis proteins to disrupt the structural components of the bacterial envelope. There are commonalities between the phages that infect bacteria with similar structures, but there are also interesting differences we can exploit to learn more about specific phages or their bacterial hosts. In this study, we characterize the lysis proteins of the E. coli phage N4. Our results suggest that lysis regulation controls phage yield in N4 differently than in well-studied phage T4. Future studies on the relationship between lysis proteins and phage yield could provide handles to use this information for optimal large-scale phage production for clinical or industrial applications.

microbiology↗

bioRxiv2023

Representation and Retrieval of Brain Connectivity Information derived from TMS Experiments

BackgroundTranscranial magnetic stimulation (TMS) is a painless non-invasive method that allows focal activation or deactivation of a human brain region in order to assess effects on other brain regions. As such, it has a unique role in elucidating brain connectivity during behavior and at rest. Information regarding brain connectivity derived from TMS experiments has been published in hundreds of papers but is not accessible in aggregate. ObjectiveOur objective was to identify, extract, and represent TMS-connectivity data in a graph database. This approach uses nodes connected by edges to capture the directed nature of interregional communication in the brain while also being flexible enough to contain other information about the connections, such as the source of information and details about the experiments that produced them. MethodsData related to interregional brain connectivity is first extracted from full-text publications, with creation of a table-like structure that list data of multiple types, principally the source and target brain regions, sign (excitatory/inhibitory) and latency. While machine-reading methods were explored, so far human experts have had to extract and verify data. These data are used to populate a neo4j graph database. A graphical user interface coupled with a query system allows users to search for networks and display information about connections between any two brain regions of interest. ResultsExperiments involving two TMS stimulating coils, in which one is over a putative source region and the other is over another region with a measurable effect in the body (such as the primary motor cortex) are the most straightforward to represent in the database. Even in those experiments, differing conventions for naming regions, and differing experimental parameters such as stimulation intensity and coil position, create issues for representing data from multiple studies in the same database. Other types of experiments, such a neuromodulatory stimulation such as rTMS, can provide information regarding connectivity, but are harder to represent. But we have, thus far, stored information about 100 connections in the database and demonstrated its utility in exploring direct and indirect connections between brain regions. We have also explored adding a causal inference method to those connections, allowing information about latency to shape the connections retrieved given latency limits. ConclusionA graph database can flexibly store information about interregional brain connectivity and is particularly useful for exploring the temporal aspects of brain networks.

neuroscience↗

bioRxiv2021

Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)

Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource for studying gene function, especially within model organisms. Unprecedented expansion of the scientific literature and validation of the predicted proteins have increased both data value and the challenges of keeping pace. Capturing literature-based functional annotations is limited by the ability of biocurators to handle the massive and rapidly growing scientific literature. Within the community-oriented wiki framework for GO annotation called the Gene Ontology Normal Usage Tracking System (GONUTS), we describe an approach to expand biocuration through crowdsourcing with undergraduates. This multiplies the number of high-quality annotations in international databases, enriches our coverage of the literature on normal gene function, and pushes the field in new directions. From an intercollegiate competition judged by experienced biocurators, Community Assessment of Community Annotation with Ontologies (CACAO), we have contributed nearly 5000 literature-based annotations. Many of those annotations are to organisms not currently well-represented within GO. Over a ten-year history, our community contributors have spurred changes to the ontology not traditionally covered by professional biocurators. The CACAO principle of relying on community members to participate in and shape the future of biocuration in GO is a powerful and scalable model used to promote the scientific enterprise. It also provides undergraduate students with a unique and enriching introduction to critical reading of primary literature and acquisition of marketable skills. Significance StatementThe primary scientific literature catalogs the results from publicly funded scientific research about gene function in human-readable format. Information captured from those studies in a widely adopted, machine-readable standard format comes in the form of Gene Ontology annotations about gene functions from all domains of life. Manual annotations based on inferences directly from the scientific literature, including the evidence used to make such inferences, represents the best return on investment by improving data accessibility across the biological sciences. To supplement professional curation, our CACAO project enabled annotation of the scientific literature by community annotators, in this case undergraduates, which resulted in contribution of thousands of validated entries to public resources. These annotations are now being used by scientists worldwide.

bioinformatics↗

bioRxiv2020

Poly(2-oxazoline) nanoparticle delivery enhances the therapeutic potential of vismodegib for medulloblastoma by improving CNS pharmacokinetics and reducing systemic toxicity

We report a novel, nanoparticle formulation of the SHH pathway inhibitor vismodegib that improves efficacy for medulloblastoma treatment while reducing toxicity. Systemic therapies for brain tumors are complicated by restricted blood-brain barrier (BBB) permeability and dose-limiting extraneural toxicity, therefore improved delivery approached are needed. Here we show how a nanoparticle delivery system addresses these obstacles, bringing new efficacy to previously ineffective therapy. Vismodegib has been a promising agent for patients with SHH- subgroup medulloblastoma and is FDA-approved for basal cell carcinoma. However, vismodegib has limited benefit for patients with SHH-driven medulloblastoma, due to off-target toxicities and the development of resistance during therapy. We encapsulated vismodegib in polyoxazoline block copolymer micelles (POx-vismo). We then evaluated POx-vismo using transgenic mice engineered to develop endogenous medulloblastomas, testing the novel agent in a preclinical model with native vasculature and tumor microenvironment. POx-vismo showed improved CNS pharmacokinetics and reduced systemic and bone toxicity. Mechanistic studies show that POx nanoparticles did not enter the CNS, but rather acted within the vascular compartment to improve drug delivery by decreasing drug binding to serum proteins and reducing the volume of distribution. POx-vismo demonstrated improved efficacy, extending the survival of medulloblastoma-bearing mice. Our results show the potential for a simple, non-targeted nanoparticle formulation to improve systemic brain tumor therapy, and specifically to enhance vismodegib therapy for SHH-driven cancers.

neuroscience↗

bioRxiv2019

Phage-encoded cationic antimicrobial peptide used for outer membrane disruption in lysis

Spanins are required for the last step in bacteriophage lysis: the disruption of the outer membrane. Bioinformatic analysis has shown that ~15% of phages lack a spanin gene, which suggests an alternate mechanism of outer membrane disruption. To address this, we selected virulent podophage {phi}KT as a spaninless exemplar and tested {phi}KT genes for outer membrane disruption during lysis. Hypothetical novel gene 28 causes outer membrane disruption when co-expressed with {phi}KT lysis genes and complements the lysis defect of a {lambda} spanin mutant. Gp28 is a 56 aa cationic peptide with predicted amphipathic helical structure and is associated with the particulate fraction after lysis. Urea and KCl washes did not release gp28 from the particulate, suggesting a strong hydrophobic interaction with the membrane. Super high-resolution microscopy supports a primarily outer membrane localization for the peptide. Additionally, holin function is not required for gp28-mediated lysis. Gp28 is similar in size, charge, predicted fold, and membrane association to the human cathelicidin antimicrobial peptide LL-37. In standard assays to measure bactericidal and inhibitory effects of antimicrobial peptides on bacterial cells, synthesized gp28 performed equivalently to LL-37. The studies presented here suggest that {phi}KT Gp28 disrupts bacterial outer membranes during lysis in a manner akin to antimicrobial peptides.\n\nSignificanceHere we provide evidence that {phi}KT produces an antimicrobial peptide for outer membrane disruption during lysis. The disruptin is a new paradigm for phage lysis, and has no similarities to other known lysis genes. Many mechanisms have been proposed for the function of antimicrobial peptides, however there is not a consensus on the molecular basis of membrane disruption. Additionally, there is no established genetic selection system to support such studies. Therefore, the {phi}KT disruptin may represent the first genetically tractable antimicrobial peptide.

microbiology↗

bioRxiv2018

Domains of the TF protein important in regulating its own palmitoylation

Sindbis virus particles contain the viral proteins capsid, E1 and E2, and low levels of a small membrane protein called TF. TF is produced during a (-1) programmed ribosomal frameshifting event during the translation of the structural polyprotein. TF from Sindbis virus-infected cells is present in two palmitoylated states, basal and maximal; unpalmitoylated TF is not detectable. Mutagenesis studies demonstrated that without palmitoylation, TF is not incorporated into released virions, suggesting palmitoylation of TF is a regulated step in virus assembly. In this work, we identified Domains within the TF protein that regulate its palmitoylation state. Mutations and insertions in Domain III, a region proposed to be in the cytoplasmic loop of TF, increase levels of unpalmitoylated TF found during an infection and even allow incorporation of unpalmitoylated TF into virions. Mutations in Domain IV, the TF unique region, are likely to impact the balance between basal and maximal palmitoylation.

molecular biology↗

bioRxiv2018

RUNX1 suppresses breast cancer stemness and tumor growth

Recent studies have revealed that mutations in the transcription factor Runx1 are prevalent in breast tumors. Yet, how loss of Runx1 contributes to breast cancer (BCa) remains unresolved. We demonstrate for the first time that Runx1 represses the breast cancer stem cell (BCSC) phenotype and consequently, functions as a tumor suppressor in breast cancer. Runx1 ectopic expression in MCF10AT1 and MCF10CA1a BCa cells reduces (60%) migration, invasion and in vivo tumor growth in mouse mammary fat pad (P<0.05). Runx1 is decreased in BCSCs, and overexpression of Runx1 suppresses tumorsphere formation and reduces the BCSC population. Furthermore, Runx1 inhibits Zeb1 expression, while Runx1 depletion activates Zeb1 and the epithelial-mesenchymal transition. Mechanistically Runx1 functions as a tumor suppressor in breast cancer through repression of cancer stem cell activity. This key regulation of BCSCs by Runx1 may be shared in other epithelial carcinomas, highlighting the importance of Runx1 in solid tumors.

cancer biology↗