Biology subjects

Ramsey, J. D.

Publications and source records attributed to Ramsey, J. D..

11 recordsLinked to original sources

bioRxiv2026

Synthetic Poly(2-Oxazoline) Chimera 'Lipo-Polymers' as Replacements for Key Lipids in Lipid Nanoparticles

Lipid nanoparticles (LNPs) rely on specialized lipid components, many of which are proprietary and difficult to access or modify. Here, we introduce a polymer-based alternative to key LNP constituents through the development of chimera poly(2-oxazoline) (POx) synthetic lipid polymers (SLPs) and synthetic lipid oligomers (SLOs). These chimeric lipid-mimetic materials are designed for seamless incorporation into existing LNP architectures, enabling direct replacement of PEG-lipid conjugates and ionizable lipids, respectively. Chimeric SLPs comprise hydrophilic shell-forming POx blocks linked to hydrophobic lipid-inserting domains, whereas SLOs consist of hydrophobic POx oligomers terminated with ionizable amine-containing groups. Using mRNA-loaded LNPs, we demonstrate that first-generation POx-Chimera SLPs and SLOs functionally replace industry-standard lipid components while maintaining robust transfection activity in vitro and in vivo. Notably, SLO-containing formulations achieved expression levels comparable to, and in some cases exceeding, those of conventional lipid formulations. Together, these results establish POx-Chimera SLPs and SLOs as a versatile platform for polymer-centric LNP engineering, creating new opportunities to tune nanoparticle composition, biodistribution, and transgene expression while reducing reliance on proprietary lipids.

bioengineering↗

bioRxiv2025

Causal Modeling Reveals Cell-Cell Communication Dynamics in the Tumor Microenvironment During Anti-PD-1 Therapy in Breast Cancer Patients

BackgroundImmune checkpoint blockade (ICB) targeting PD-1/PD-L1 plays a crucial role in breast cancer treatment. Despite clinical success, how ICB reshapes the tumor microenvironment (TME) to enhance anti-tumor activity remains unclear. Anti-PD-1 therapy alters TME cells beyond PD-1+ T cells, with extensive cell-cell communication (CCC) playing a key role. Understanding the dynamic CCC changes upon anti-PD-1 treatment can illuminate ICB mechanisms of action and TME dynamics. MethodsWe analyzed single-cell RNA-seq data from 31 breast cancer patients before and after anti-PD-1 (pembrolizumab) treatment (Bassez et al., 2021). We identified differentially expressed genes (DEGs) induced by treatment in major cell types. We then applied an instrumental variable approach to uncover causal relationships between T-cell and non-T-cell DEGs. We further mapped ligand-receptor interactions mediating signal transduction between cells and constructed a CCC network from T to non-T cells. ResultsAnti-PD-1 therapy induced widespread transcriptional changes across multiple cell populations. Key pathways modulated in T cells included NF-{kappa}B, interferon-{gamma}, and interleukin signaling. CD4+ and CD8+ exhausted T cells engaged in distinct ligand-receptor interactions with tumor-associated macrophages (TAMs) and other types of cells, reshaping the TME. Our results indicated CD4+ exhausted T cells activated M1-like TAMs via TNF-TNFRSF1A and TNFSF14-LTBR, while CD8+ exhausted T cells engaged M1-like TAMs through ICAM1-ITGAL/ITGB2 and CCL8-CCR2, promoting anti-tumor immunity. Conversely, immunosuppressive interactions were also observed, such as TNF-TNFRSF1B (TNFR2) and TNFSF14-TNFRSF14 (HVEM) from CD4 T cells, as well as CSF1-CSF1R and RPS19-C5AR1 from CD8 T cells, which likely promote M2-like tumor-associated macrophage (TAM) polarization and contribute to pro-tumor immune regulation and resistance to therapy. Notably, key receptors in the causal CCC networks, such as C5AR1, TNFR2, and CSF1R, emerged as potential targets to enhance anti-PD-1 efficacy. ConclusionsThese findings elucidate TME remodeling during anti-PD-1 therapy and underscore the pivotal role of CCC in treatment response. Our study identifies critical communication networks that may be biomarkers for immunotherapy responsiveness and highlights novel therapeutic targets, including C5AR1 and HVEM. Furthermore, our application of causal inference methodologies provides a robust framework for dissecting CCC mechanisms in immunotherapy.

bioinformatics↗

bioRxiv2025

PEG-Free Tunable Poly(2-Oxazoline) Lipids Modulate LNP Biodistribution and Expression In Vivo after Intramuscular Administration

Over the past decade, lipid nanoparticles (LNPs) have emerged as a transformative delivery platform, particularly in the field of mRNA vaccines, by enabling the stabilization and efficient intracellular delivery of nucleic acids. Importantly, the FDA approved LNPs used in the Pfizer-BioNTech and Moderna COVID-19 vaccines, rely on polyethylene glycol (PEG) to stabilize the nanoparticle in vivo. However, recent studies revealed that anti-PEG antibodies are ubiquitous in the population and are known to be a major cause of anaphylaxis and reduced therapeutic efficacy by accelerating blood clearance of PEGylated products. In this study, we report the development of novel poly(2-oxazoline) (POx) "stealth" lipids as PEG alternatives for LNP formulation. POx polymers are known to be poorly immunogenic and mitigate accelerated blood clearance. Upon varying polymer hydrophilicity and molecular weight, we screened transfection efficiency in multiple cell lines and evaluated top candidates in vivo by intramuscular administration. Our findings demonstrate that POx-lipids incorporating shorter hydrophilic methyl- and ethyl-oxazoline POx chains enhance transfection both in vitro and in vivo, while concurrently reducing liver accumulation and improving dendritic cell uptake - key features for effective vaccine delivery. These POx-lipids boost expression in muscle tissue by up to threefold, and greatly increase accumulation in extrahepatic tissues, including lymph nodes and spleen - critical sites for immune priming in the in the context of vaccination. Altogether, this work marks a notable advancement toward replacing PEG in LNP-based therapies and provides a clear path to optimizing POx-lipids for targeted vaccine and therapeutic applications.

bioengineering↗

bioRxiv2023

Combination of Polymeric Micelle Formulation of TGFβ Receptor Inhibitors and Paclitaxel Produce Consistent Response Across Different Mouse Models of TNBC

Triple-negative breast cancer (TNBC) is notoriously difficult to treat due to the lack of targetable receptors and sometimes poor response to chemotherapy. The transforming growth factor-beta (TGF{beta}) family of proteins and their receptors (TGFR) are highly expressed in TNBC and implicated in chemotherapy-induced cancer stemness. Here we evaluated combination treatments using experimental TGFR inhibitors (TGF{beta}i), SB525334 (SB), and LY2109761 (LY) with Paclitaxel (PTX) chemotherapy. These TGF{beta}i target TGFR-I (SB) or both TGFR-I&II (LY). Due to the poor water solubility of these drugs, we incorporated each of them in poly(2-oxazoline) (POx) high-capacity polymeric micelles (SB-POx and LY-POx). We assessed their anti-cancer effect as single agents and in combination with micellar Paclitaxel (PTX-POx) using multiple immunocompetent TNBC mouse models that mimic human subtypes (4T1, T11-Apobec and T11-UV). While either TGF{beta}i or PTX showed a differential effect in each model as single agents, the combinations were consistently effective against all three models. Genetic profiling of the tumors revealed differences in the expression levels of genes associated with TGF{beta}, EMT, TLR-4, and Bcl2 signaling, alluding to the susceptibility to specific gene signatures to the treatment. Taken together, our study suggests that TGF{beta}i and PTX combination therapy using high-capacity POx micelle delivery provides a robust anti-tumor response in multiple TNBC subtype mouse models. Translational Impact StatementPaclitaxel is a widely used chemotherapy in breast cancer. However, response to single-agent chemotherapy is short-lived in a metastatic setting. This study shows the broad applicability of the therapeutic combination of TGF{beta} inhibitors with Paclitaxel across different TNBC subtypes.

cancer biology↗

bioRxiv2022

High-Dose Paclitaxel and its Combination with CSF1R Inhibitor in Polymeric Micelles for Chemoimmunotherapy of Triple Negative Breast Cancer

The presence of immunosuppressive immune cells in cancer is a significant barrier to the generation of therapeutic immune responses. Similarly, in vivo triple-negative breast cancer (TNBC) models often contain prevalent tumor-associated macrophages in the tumor microenvironment (TME), resulting in breast cancer initiation, invasion, and metastasis by generating immunosuppressive environment. Here, we test systemic chemoimmunotherapy using small-molecule agents, paclitaxel (PTX), and colony-stimulating factor 1 receptor (CSF1R) inhibitor, PLX3397, to enhance the adaptive T cell immunity against TNBCs in immunocompetent mouse TNBC models. PTX and PLX3397 are very poorly soluble in water and shown poor therapeutic outcomes in TNBC animal models in conventional formulation. To address the challenge for the delivery of insoluble drugs to TNBC, we use high-capacity poly(2-oxazoline) (POx)-based polymeric micelles to greatly improve the solubility and widen the therapeutic index of such drugs. The results demonstrate that high-dose PTX in POx, even as a single agent, exerts strong effects on TME and induces the long-term immune memory. In addition, we demonstrate that the PTX and PLX3397 combination provides consistent therapeutic improvement across several TNBC models, resulting from the repolarization of the immunosuppressive TME and enhanced T cell immune response that suppress both the primary tumor growth and metastasis. Overall, the work emphasizes the benefit of drug reformulation and outlines potential translational path for both PTX and PTX with PLX3397 combination therapy using POx polymeric micelles for the treatment of TNBC.

cancer biology↗

bioRxiv2022

Nanoformulated Remdesivir with Extremely Low Content of Poly(2-oxazoline) - Based Stabilizer for Aerosol Treatment of COVID-19

The rise of the novel virus SARS-CoV2 which causes the disease known as COVID-19 has led to a global pandemic claiming millions of lives. With no clinically approved treatment for COVID-19, physicians initially struggled to treat the disease and there is still need for improved anti-viral therapies in this area. We conceived early in the pandemic that an inhalable formulation of the drug Remdesivir which directly targets the virus at the initial site of infection could improve therapeutic outcomes in COVID-19. We developed a set of requirements that would be conducive to rapid drug approval: 1) try to use GRAS or GRAS similar reagents 2) minimize excipient concentration and 3) achieve a working concentration of 5 mg/mL Remdesivir to achieve a deliverable dose which is 5-10% of the IV dose. In this work, we discovered that Poly(2-oxazoline) block copolymers can stabilize drug nanocrystal suspensions and provide suitable formulation characteristics for aerosol delivery while maintaining anti-viral efficacy. We believe POx block copolymers can be used as a semi-ubiquitous stabilizer for the rapid development of nanocrystal formulations for new and existing diseases.

bioengineering↗

bioRxiv2021

Bioequivalence Assessment of High-Capacity Polymeric Micelle Nanoformulation of Paclitaxel and Abraxane(R) in Rodent and Non-Human Primate Models Using a Stable Isotope Tracer Assay

The in vivo fate of nanoformulated drugs is governed by the physicochemical properties of the drug and the functionality of nanocarriers. Nanoformulations such as polymeric micelles, which physically encapsulate poorly soluble drugs, release their payload into the bloodstream during systemic circulation. This results in three distinct fractions of the drug-nanomedicine: encapsulated, protein-bound, and free drug. Having a thorough understanding of the pharmacokinetic (PK) profiles of each fraction is essential to elucidate mechanisms of nanomedicine-driven changes in drug exposure and PK/PD relationships pharmacodynamic activity. Here, we present a comprehensive preclinical assessment of the poly(2-oxazoline)-based polymeric micelle of paclitaxel (PTX) (POXOL hl-PM), including bioequivalence comparison to the clinically approved paclitaxel nanomedicine, Abraxane(R). Physicochemical characterization and toxicity analysis of POXOL hl-PM was conducted using standardized protocols by the Nanotechnology Characterization Laboratory (NCL). The bioequivalence of POXOL hl-PM to Abraxane(R) was evaluated in rats and rhesus macaques using the NCLs established stable isotope tracer ultrafiltration assay (SITUA) to delineate the plasma PK of each PTX fraction. The SITUA study revealed that POXOL hl-PM and Abraxane(R) had comparable PK profiles not only for total PTX but also for the distinct drug fractions, suggesting bioequivalence in given animal models. The comprehensive preclinical evaluation of POXOL hl-PM in this study showcases a series of widely-applicable standardized studies by NCL for assessing nanoformulations prior to clinical investigation. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/457164v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@a505a1org.highwire.dtl.DTLVardef@149eccorg.highwire.dtl.DTLVardef@1c5631eorg.highwire.dtl.DTLVardef@1ee6c68_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2021

Drug-dependent morphological transitions in spherical and worm-like polymeric micelles define stability and pharmacological performance of micellar drugs

Significant advances in physicochemical properties of polymeric micelles enable optimization of therapeutic drug efficacy, supporting nanomedicine manufacturing and clinical translation. Yet, the effect of micelle morphology on pharmacological efficacy has not been adequately addressed. We addressed this gap by assessing pharmacological efficacy of polymeric micelles with spherical and worm-like morphologies. We observed that poly(2-oxazoline)-based polymeric micelles can be elongated over time from a spherical structure to worm-like structure, with elongation influenced by several conditions, including the amount and type of drug loaded into the micelles. We further evaluated the role of different morphologies of olaparib micelles on pharmacological performance against a triple-negative breast cancer tumor (TNBC) model. Spherical micelles accumulated rapidly in the tumor tissue while retaining large amounts of drug; worm-like micelles accumulated more slowly and only upon releasing significant amounts of drug. These findings suggest that the dynamic character of the drug-micelle structure and the micelle morphology play a critical role in pharmacological performance, and that spherical micelles are better suited for systemic delivery of anticancer drugs to tumors when drugs are loosely associated with the polymeric micelles.

pharmacology and toxicology↗

bioRxiv2021

Nanoparticle-delivered palbociclib enable CDK4/6 inhibitor therapy while combination with mTORC1 inhibitor sapanisertib induces long term benefits in SHH medulloblastoma.

CDK4/6 inhibitors hold promise for brain tumor treatment, but efficacy has been limited by recurrence in both preclinical models and clinical trials. To address recurrence, we tested a nanoparticle formulation of the CDK4/6 inhibitor palbociclib (POx-palbo) in mice genetically-engineered to develop SHH-driven medulloblastoma. We then analyzed medulloblastomas in mice receiving palbociclib treatment, and compared the efficacy of combining palbociclib with specific inhibitors suggested by our analysis. POx-Palbo showed reduced toxicity compared to conventional palbociclib, was tolerable in parenteral administration, improved CNS pharmacokinetics, and extended survival of mice with medulloblastoma. Recurrence, however, remained problematic as fractions of tumor cells proliferated during therapy. ScRNA-seq identified a gene expression pattern unique to proliferating medulloblastoma cells in POx-Palbo-treated mice, marked by up-regulation of the glutamate transporter Slc1a2 and down-regulation of diverse ribosomal genes. Reduced mTORC1 signaling, suggested by ribosomal suppression in POx-Palbo-treated tumors was confirmed by decreased 4EBP1 phosphorylation (p4EBP1). Further reducing mTORC1 activity by combining POx-Palbo with the mTORC1 inhibitor sapanisertib produced mutually enhancing effects, with increased suppression of both pRB and p4EBP1, and prolonged mouse survival compared to either agent alone. In contrast, targeting cell cycle progression by combining POx-Palbo with the SHH-pathway inhibitor vismodegib, or with the replication-targeting agents gemcitabine or etoposide, failed to enhance efficacy. Our data show the potential of nanoparticle formulation and scRNA-seq analysis of resistance to improve brain tumor treatment, and identify POx-palbo plus sapanisertib as effective combinatorial therapy for SHH medulloblastoma. This combination may be appropriate for testing in patients with recurrence, who need new options.

cancer biology↗

bioRxiv2018

Causal Discovery of Feedback Networks with Functional Magnetic Resonance Imaging

We test the adequacies of several proposed and two new statistical methods for recovering the causal structure of systems with feedback that generate noisy time series closely matching real BOLD time series. We compare: an adaptation for time series of the first correct method for recovering the structure of cyclic linear systems; multivariate Granger causal regression; the GIMME algorithm; the Ramsey et al. non-Gaussian methods; two non-Gaussian methods proposed by Hyv{diaeresis}arinen and Smith; a method due to Patel, et al.; and the GlobalMIT algorithm. We introduce and also compare two new methods, the Fast Adjacency Skewness (FASK) and Two-Step, which exploit non-Gaussian features of the BOLD signal in different ways. We give theoretical justifications for the latter two algorithms. Our test models include feedback structures with and without direct feedback (2-cycles), excitatory and inhibitory feedback, models using experimentally determined structural connectivities of macaques, and empirical resting state and task data. We find that averaged over all of our simulations, including those with 2-cycles, several of these methods have a better than 80% orientation precision (i.e., the probability a directed edge is in the true generating structure given that a procedure estimates it to be so) and the two new methods also have better than 80% recall (probability of recovering an orientation in the data generating model). Recovering inhibitory direct feedback loops between two regions is especially challenging.

neuroscience↗

bioRxiv2017

Identification of Mechanisms of Functional Signaling Between Human Hippocampus Regions

BackgroundStandard BOLD connectivity analyses depend on aggregating the signals of individual voxels within regions of interest (ROIs). In certain cases, this spatial aggregation implies a loss of valuable functional and anatomical information about subsets of voxels that drive the ROI level connectivity.\n\nNew MethodWe use the FGES algorithm, a data-driven score-based graphical search method, to identify subsets of voxels that are chiefly responsible for exchanging signals between ROIs. We apply the method to high-resolution resting state functional magnetic resonance imaging (rs-fMRI) data from medial temporal lobe regions of interest of a single healthy individual measured repeated times over a year and a half.\n\nResultsThe FGES algorithm recovered subsets of voxels within larger medial temporal lobe ROIs of entorhinal cortex and hippocampus subfields that show spatially consistency across different scanning sessions, and are statistically significant under tests that validate the role of these subsets as main drivers of effective connectivity between hippocampal regions of interest.\n\nComparison with Existing MethodsIn contrast to standard functional connectivity methods, the FGES algorithm is robust against false positive connections produced by transitive closures of adjacencies (correlation methods) and common effect conditioning (Markov random field methods).\n\nConclusionsThe FGES algorithm allows for identification of communication subsets of voxels driving the connectivity between regions of interest, recovering valuable anatomical and functional information that is lost when ROIs are aggregated. The FGES algorithm is specially suited for voxelwise connectivity research, given its short running time and scalability to big data problems.

neuroscience↗