Biology subjects

Haney, M.

Publications and source records attributed to Haney, M..

8 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

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↗

bioRxiv2024

Exosomes are vehicles for the stress-regulated secretion of histones

Histones are conserved nuclear proteins that function as part of the nucleosome in the regulation of chromatin structure and gene expression. Interestingly, extracellular histones populate biofluids from healthy individuals and when elevated may contribute to various acute and chronic diseases. It is generally assumed that most extracellular histones exist as nucleosomes, as components of extracellular chromatin. We analysed cell culture models under normal and stressed conditions to identify pathways of histone secretion. We report that core and linker histones localize to extracellular vesicles (EVs) and are secreted via the multivesicular body/exosome pathway. Upregulation of histone EV secretion occurs in response to cellular stress, with enhanced vesicle secretion and a shift towards a population of smaller EVs. Most histones were membrane associated with the outer surface of EVs. Degradation of EV-DNA did not impact significantly on EV-histone association. Individual histones or histone octamers bound strongly to liposomes and EVs, but nucleosomes did not, showing histones do not require DNA for EV binding. EV histones colocalized most frequently with the tetraspanin CD63 but using genetic or pharmacological intervention, we found that all known pathways of exosome biogenesis acted positively on histone secretion. Inhibition of autophagy and lysosomal degradation had a strong positive effect on EV histone release. Unexpectedly, EV-associated histones lacked the extensive post-translational modification of their nuclear counterparts, suggesting loss of PTMs may be involved in their trafficking or secretion. Our data does not support a significant role for EV-histones existing as nucleosomes. We show for the first time that histones are secreted from cells as membrane proteins via EVs/exosomes. This fundamental discovery provides support for further investigation of the biological activity of exosome associated histones and their role in disease.

cell biology↗

bioRxiv2023

APOE4/4 is linked to damaging lipid droplets in Alzheimer's microglia

Several genetic risk factors for Alzheimers Disease (AD) implicate genes involved in lipid metabolism and many of these lipid genes are highly expressed in glial cells. However, the relationship between lipid metabolism in glia and AD pathology remains poorly understood. Through single-nucleus RNA-sequencing of AD brain tissue, we have identified a microglial state defined by the expression of the lipid droplet (LD) associated enzyme ACSL1 with ACSL1-positive microglia most abundant in AD patients with the APOE4/4 genotype. In human iPSC-derived microglia (iMG) fibrillar A{beta} (fA{beta}) induces ACSL1 expression, triglyceride synthesis, and LD accumulation in an APOE-dependent manner. Additionally, conditioned media from LD-containing microglia leads to Tau phosphorylation and neurotoxicity in an APOE-dependent manner. Our findings suggest a link between genetic risk factors for AD with microglial LD accumulation and neurotoxic microglial-derived factors, potentially providing novel therapeutic strategies for AD.

neuroscience↗

bioRxiv2022

Poly(2-oxazoline)-based polyplexes as a PEG-free plasmid DNA delivery platform

The present study expands the versatility of cationic poly(2-oxazoline) (POx) copolymers as a PEG-free platform for gene delivery to immune cells, such as monocytes and macrophages. Several block copolymers are developed by varying non-ionic hydrophilic blocks (poly(2-methyl-2-oxazoline) (pMeOx) or poly(2-ethyl-2-oxazoline) (pEtOx), cationic blocks, and an optional hydrophobic block (poly(2-isopropyl-2-oxazoline) (iPrOx). The cationic blocks are produced by side chain modification of 2-methoxy-carboxyethyl-2-oxazoline (MestOx) block precursor with diethylenetriamine (DET) or tris(2-aminoethyl)amine (TREN). For the attachment of a targeting ligand, mannose, we employed azide-alkyne cycloaddition click chemistry methods. Of the two cationic side chains, polyplexes made with DET-containing copolymers transfect macrophages significantly better than those made with TREN-based copolymer. Likewise, non-targeted pEtOx-based diblock copolymer is more active in cell transfection than pMeOx-based copolymer. The triblock copolymer with hydrophobic block iPrOx performs poorly compared to the diblock copolymer which lacks this additional block. Surprisingly, attachment of a mannose ligand to either of these copolymers is inhibitory for transfection. Despite similarities in size and design, mannosylated polyplexes result in lower cell internalization compared to non-mannosylated polyplexes. Thus, PEG-free, non-targeted DET- and pEtOx-based diblock copolymer outperforms other studied structures in the transfection of macrophages and displays transfection levels comparable to GeneJuice, a commercial non-lipid transfection reagent.

bioengineering↗

bioRxiv2021

Nanopore sequencing methods detect cell-free DNA associated with minimal residual disease and central nervous system infiltration in pediatric Acute Lymphoblastic Leukemia

Acute Lymphoblastic Leukemia (ALL) patients that are positive for minimal residual disease (MRD) after therapy or have leukemic infiltration into the central nervous system (CNS) are considered high risk and receive intensive chemotherapy regimens. Current methods to diagnose MRD and CNS infiltration rely on detecting leukemic cells in patient samples using pathology, flow cytometry, or next-generation sequencing. However, leukemic blasts may persist in the patient but not be physically present in bone marrow biopsy or biofluid sample, leading to inaccurate or delayed patient diagnosis. We have developed a nanopore sequencing workflow to detect B-ALL-associated cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) samples. Quantitation of B-cell specific VDJ recombination events in cfDNA samples defined B-ALL clonal heterogeneity. This workflow allowed us to track the response of individual B-ALL clones throughout treatment. Detection of cfDNA also predicted the clinical diagnosis of MRD and CNS disease. Importantly, we identified patients diagnosed as CNS negative who had low B-cell derived cell-free DNA levels in their CSF sample that correlated with B-cell clones present in the bone marrow. These data suggest that cfDNA assays may be useful in detecting the presence of ALL in the patient even when blasts are not in the biofluid sample. Nanopore analysis of cell-free DNA is a simple, rapid, and inexpensive assay that can serve as a valuable complement to traditional clinical diagnostic approaches for ALL. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=50 SRC="FIGDIR/small/462067v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@1373bd3org.highwire.dtl.DTLVardef@138b2e3org.highwire.dtl.DTLVardef@168661forg.highwire.dtl.DTLVardef@1088626_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2019

Lipid droplet accumulating microglia represent a dysfunctional and pro-inflammatory state in the aging brain

Microglia become progressively activated and seemingly dysfunctional with age, and genetic studies have linked these cells to the pathogenesis of a growing number of neurodegenerative diseases. Here we report a striking buildup of lipid droplets in microglia with aging in mouse and human brains. These cells, which we call lipid droplet-accumulating microglia (LAM), are defective in phagocytosis, produce high levels of reactive oxygen species, and secrete pro-inflammatory cytokines. RNA sequencing analysis of LAM revealed a transcriptional profile driven by innate inflammation distinct from previously reported microglial states. An unbiased CRISPR-Cas9 screen identified genetic modifiers of lipid droplet formation; surprisingly, variants of several of these genes, including progranulin, are causes of autosomal dominant forms of human neurodegenerative diseases. We thus propose that LAM contribute to age-related and genetic forms of neurodegeneration.

neuroscience↗

bioRxiv2017

Local and global chromatin interactions are altered by large genomic deletions associated with human brain development

BackgroundLarge copy number variants (CNVs) in the human genome are strongly associated with common neurodevelopmental, neuropsychiatric disorders such as schizophrenia and autism. Using Hi-C analysis of long-range chromosome interactions and ChIP-Seq analysis of regulatory histone marks we studied the epigenomic effects of the prominent large deletion CNV on chromosome 22q11.2 and also replicated a subset of the findings for the large deletion CNV on chromosome 1q21.1.\n\nResultsWe found that, in addition to local and global gene expression changes, there are pronounced and multilayered effects on chromatin states, chromosome folding and topological domains of the chromatin, that emanate from the large CNV locus. Regulatory histone marks are altered in the deletion proximal regions, and in opposing directions for activating and repressing marks. There are also significant changes of histone marks elsewhere along chromosome 22q and genome wide. Chromosome interaction patterns are weakened within the deletion boundaries and strengthened between the deletion proximal regions. We detected a change in the manner in which chromosome 22q folds onto itself, namely by increasing the long-range contacts between the telomeric end and the deletion proximal region. Further, the large CNV affects the topological domain that is spanning its genomic region. Finally, there is a widespread and complex effect on chromosome interactions genome-wide, i.e. involving all other autosomes, with some of the effect directly tied to the deletion region on 22q11.2.\n\nConclusionsThese findings suggest novel principles of how such large genomic deletions can alter nuclear organization and affect genomic molecular activity.

genetics↗