Biology subjects

Jackson, M. R.

Publications and source records attributed to Jackson, M. R..

12 recordsLinked to original sources

bioRxiv2026

High-Throughput Screening Identifies Small-Molecule Inhibitors of the Tau-LRP1 Interaction

The cellular uptake and propagation of tau are central features of tauopathies, including Alzheimers disease, and are mediated by the endocytic receptor low-density lipoprotein receptor-related protein 1 (LRP1). While prior studies have implicated LRP1 in tau binding and internalization, the biochemical features of this interaction and its suitability for therapeutic targeting remain incompletely defined. Here, we establish a quantitative and scalable framework to interrogate the tau-LRP1 interaction and identify small-molecule modulators. We engineered and purified the LRP1 ligand-binding domain 4 (BD4), a key region mediating tau interaction, and developed multiple orthogonal assays, including fluorescence polarization, split luciferase complementation, and time-resolved FRET, to measure LRP1-BD4 interactions with tau and a known peptide ligand. Across assay formats, we observe consistent binding affinities in the nanomolar range and demonstrate competitive displacement by tau, receptor-associated protein (RAP), and a peptide ligand, supporting overlapping binding interfaces. Leveraging these platforms, we performed small molecule high-throughput screening and identified a set of candidate inhibitors of the LRP1-BD4-tau interaction. Selected compounds reduced tau uptake in a cellular assay, phenocopying competitive inhibition by tau and a peptide ligand. Together, these studies define the LRP1-BD4-tau interaction as a biochemically tractable and druggable interface and establish an integrated discovery pipeline linking mechanistic characterization to functional cellular outcomes. This work provides a foundation for the development of therapeutic strategies targeting LRP1-mediated tau uptake.

biochemistry↗

bioRxiv2026

Utilizing a cell culture based novel cellular thermal shift assay to understand the isoform-dependent thermal stability of ApoE variants

Apolipoprotein E (ApoE) is the primary genetic risk modifier of late-onset Alzheimers disease, with the {varepsilon}4 allele increasing risk up to 15-fold relative to {varepsilon}3. The structural differences between isoforms are thought to underlie their distinct effects on lipid transport, receptor binding, and disease risk. ApoE4 exhibits reduced thermodynamic stability compared to ApoE3, but prior characterisation has relied on purified recombinant protein, leaving open whether these differences are preserved in native cellular environments and how they relate to rare disease-associated variants. Here, we employed the cellular thermal shift assay (CETSA) and a bioluminescence-based thermal stability assay (BiTSA) to systematically characterise ApoE thermal stability across isoforms and variants. Using CETSA on brain tissue from humanised APOE knock-in mice and post-mortem human brain, we confirm that ApoE4 exhibits significantly reduced thermal stability compared to ApoE3 in native tissue, with this difference conserved across species despite variation in absolute melting temperatures. We developed BiTSA, which leverages a split-luciferase HiBiT tag to quantify soluble ApoE across a thermal gradient in living cells, providing a higher-throughput platform that faithfully recapitulates isoform stability differences. Applying BiTSA to rare AD-associated variants, we found that L28P exerts divergent, isoform-dependent effects, destabilising ApoE3 while paradoxically stabilising ApoE4--a finding supported by AlphaFold modelling revealing isoform-specific differences in helix 1 architecture. These results establish BiTSA as a robust cellular tool for ApoE variant characterisation and demonstrate that isoform background critically modulates the structural consequences of rare mutations.

neuroscience↗

bioRxiv2026

ClonoScreen3D-CRISPRi Uncovers Genetic Modifiers of Radiation Response in Glioblastoma

BackgroundGlioblastoma (GBM) is the most aggressive primary brain tumor in adults. Radioresistance, partly mediated by glioma stem-like cells, represents a major clinical challenge which could be overcome by the identification of the modulators of radioresistance. Existing CRISPR screens in human GBM models have largely used two-dimensional cultures with short-term viability readouts, failing to capture the long-term clonogenic behaviour underlying tumour recurrence after radiotherapy. MethodWe developed ClonoScreen3D-CRISPRi, combining CRISPRi-mediated gene knockdown with three-dimensional clonogenic survival assays. Two GBM cell lines (G7 and GBML20), differing in MGMT promoter methylation status, were engineered to express the KRAB-dCas9 editor. Nine candidate radiosensitivity modifiers, selected through transcriptomic analysis, pharmacological studies, and literature review, were examined in both lines. Target validation was performed using full radiation dose-response assays and a pharmacological inhibitor. ResultsThe majority of candidate genes significantly altered survival fraction following irradiation in both cell lines. Knockdown of NFKB2, RELB, and CDK9 produced the most potent radiosensitization, with sensitizer enhancement ratios of 1.39-1.70 in validation studies -- exceeding those of established radiosensitizers including PARP and ATM inhibitors. Notably, knockdown of these genes induced no significant cytotoxicity in the absence of radiation. Pharmacological validation using an IKK inhibitor confirmed these findings, implicating non-canonical NF-{kappa}B signalling and CDK9-dependent transcriptional elongation as critical adaptive mechanisms in GBM radioresistance. ConclusionsClonoScreen3D-CRISPRi is a scalable, physiologically relevant platform for identifying genetic modifiers of radioresistance. The non-canonical NF-{kappa}B pathway and CDK9 represent promising radiosensitizing targets, and larger screens could enable systematic prioritisation of candidates for clinical translation. Key PointsO_LIClonoScreen3D-CRISPRi combines gene knockdown with 3D clonogenic survival assays C_LIO_LIWe identified NFKB2, RELB, and CDK9 as modifiers of radioresistance in two GBM cell lines C_LIO_LIValidation experiments show ClonoScreen3D-CRISPRi reliably identifies radiosensitizers in GBM C_LI Importance of the studyGlioblastoma (GBM) remains one of the most lethal human cancers, with radioresistance representing a central barrier to improved patient outcomes. While CRISPR-based screens have begun to illuminate genetic drivers of GBM biology, prior approaches using human models have largely relied on two-dimensional culture systems and short-term viability readouts that inadequately model the disease. This study introduces ClonoScreen3D-CRISPRi, a novel platform that integrates CRISPRi-mediated gene knockdown with three-dimensional clonogenic survival assays in patient-derived GBM cells -- more faithfully recapitulating the long-term clonogenic potential that underlies post-radiotherapy recurrence. Using this platform, we identified NFKB2, RELB, and CDK9 as potent genetic modifiers of radioresistance, with sensitizer enhancement ratios exceeding those of established clinical radiosensitizers such as PARP and ATM inhibitors. Pharmacological validation of the non-canonical NF-{kappa}B pathway demonstrates direct translational relevance, providing a rationale for targeting this axis in combination with radiotherapy to improve GBM treatment.

cancer biology↗

bioRxiv2025

LARP6 regulates the mRNA translation of fibrogenic genes in liver fibrosis

Metabolic syndrome and excessive alcohol consumption result in liver injury and fibrosis, which is characterized by increased collagen production by activated Hepatic Stellate Cells (HSCs). LARP6, an RNA-binding protein, was shown to facilitate collagen production. However, LARP6 expression and functionality as a regulator of fibrosis development in a disease relevant model remains elusive. By using snRNA-sequencing, we show that LARP6 is upregulated mainly in HSCs of liver fibrosis patients. Moreover, LARP6 knockdown in human HSCs suppresses fibrogenic gene expression. By integrating eCLIP analysis and ribosome profiling in HSCs, we show that LARP6 interacts with mature mRNAs comprising over 300 genes, including RNA structural elements within COL1A1, COL1A2, and COL3A1 to regulate mRNA expression and translation. Furthermore, LARP6 knockdown in HSC attenuates fibrosis development in human liver spheroids. Altogether, our results suggest that targeting LARP6 in human HSCs may provide new strategies for anti-fibrotic therapy. HighlightsO_LILARP6 is upregulated in liver fibrosis, mainly in HSCs. C_LIO_LILARP6 knockdown in human HSCs reduces liver fibrosis development. C_LIO_LIOf the hundreds of gene targets, LARP6 interacts most with collagen mRNAs. C_LIO_LILARP6 regulates mRNA translation via interaction with 5UTRs. C_LI

cell biology↗

bioRxiv2024

Design of allosteric modulators that change GPCR G protein subtype selectivity

G protein-coupled receptors (GPCRs), the largest family of drug targets, can signal through 16 subtypes of G proteins. Biased compounds that selectively activate therapy-relevant pathways promise to be safer, more effective medications. The determinants of bias are poorly understood, however, and rationally-designed, G protein-subtype-selective compounds are lacking. Here, using the prototypical class A GPCR neurotensin receptor 1 (NTSR1), we find that small molecules binding the intracellular GPCR-transducer interface change G protein coupling by subtype-specific and predictable mechanisms, enabling rational drug design. We demonstrate that the compound SBI-553 switches NTSR1 G protein preference by acting both as a molecular bumper and a molecular glue. Structurally, SBI-553 occludes G protein binding determinants on NTSR1, promoting association with select G protein subtypes for which an alternative, shallow-binding conformation is energetically favorable. Minor modifications to the SBI-553 scaffold produce allosteric modulators with distinct G protein subtype selectivity profiles. Selectivity profiles are probe-independent, conserved across species, and translate to differences in in vivo activity. These studies demonstrate that G protein selectivity can be tailored with small changes to a single chemical scaffold targeting the receptor-transducer interface and, as this pocket is broadly conserved, present a strategy for pathway-selective drug discovery applicable to the diverse GPCR superfamily.

pharmacology and toxicology↗

bioRxiv2024

Circular RNAs correlate with DNA damage in ageing human placental tissue and in stillbirth

Structured AbstractO_ST_ABSBackgroundC_ST_ABSUnexplained stillbirth may occur due to premature placental ageing, with unexpected deterioration of placental function for gestational age. Circular RNAs (circRNAs) are enzyme-resistant RNA molecules that accumulate in ageing tissues. Furthermore, circRNAs bind gDNA directly, forming circRNA:DNA complexes which can induce DNA breaks and genomic instability. ObjectivesThis study investigated tissue ageing and circRNA accumulation with gestational age in healthy and stillbirth placentae, and determined whether circRNAs directly interact with placental DNA causing DNA damage and cellular senescence. Study designPlacenta samples (n=60 term uncomplicated; n=4 unexplained stillbirth, 23, 26, 31, 34 weeks gestation) were assessed. Abundance of 7 candidate circRNAs (circ_0009000, circ_0024157, circ_0061017, circ_0036877, circ_0054624, circ_0111277 and circ_0000284), and their linear transcripts, was quantified using qPCR. Total RNA, in the presence and absence of RNase R and RNase H1, was determined using the Qubit fluorimeter. Physical interaction of candidate circRNAs with DNA was confirmed by DNA:RNA ImmunoPrecipitation (DRIP)-qPCR. Telomere length was assessed using real-time PCR. Relative abundance of senescence-associated genes was quantified using qPCR. DNA damage was assessed using an alkaline Comet Assay. Patient-derived trophoblast stem cells (TSCs) differentiation into syncytiotrophoblasts or extravillous trophoblasts was confirmed using immunofluorescence microscopy. The effect of circ_0000284 knockdown was assessed following transfection with either a siRNA (designed to knockdown circ_0000284) or a scrambled siRNA control, at 5, 10 and 20 nM final concentrations using Lipofectamine RNAiMax. Abundance of circRNAs in maternal blood sampled between 15-16 weeks gestation (n=12 control, n=6 women who went on to have a stillbirth) was determined using qPCR. Appropriate statistical analyses were undertaken (SPSS). ResultsPlacental DNA damage, senescence and expression of 7 candidate circRNAs, but not their linear transcripts, were increased in 40 and 41+ weeks gestation samples, and in stillbirth, compared with earlier gestations (37-39 weeks). DRIP-qPCR signal size was significantly larger in term placentae than in enzyme-treated controls, confirming that all candidate circRNA loci bind to placental DNA. Abundance of circRNA was significantly decreased with the addition of RNase H1, compared with all healthy gestation samples, indicating that stillbirth placentae may lack RNase H1. Telomere length is shorter in placentae from stillbirths compared with healthy 37 weeks placentae. Depletion of circ_0000284 by specific siRNA in primary cells significantly reduced DNA damage and increased expression of senescence-associated genes compared to control. Abundance of candidate circRNAs are increased in maternal blood at 16 weeks gestation for women who went on to have a stillbirth compared with women who had live births. ConclusionsStillbirth placentae show accelerated ageing with shortened telomeres, premature DNA breaks, increased cellular senescence and accumulation of candidate circRNAs, at levels consistent with older gestation tissue. These circRNAs bind to DNA in the placenta, and circ_0000284 knockdown reduces DNA breaks and senescence in primary placental cells. Therefore, circRNAs play a role in placental ageing and associate with stillbirth, likely via decreased RNase H1 abundance, preventing circRNA degradation and facilitating circRNA accumulation, and subsequent circR-loop formation. circRNAs present a viable method of stillbirth risk screening. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=159 SRC="FIGDIR/small/610398v4_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@4a5a15org.highwire.dtl.DTLVardef@160231borg.highwire.dtl.DTLVardef@a0d0aeorg.highwire.dtl.DTLVardef@1e4590f_HPS_FORMAT_FIGEXP M_FIG C_FIG AJOG at a GlanceO_LIThis study was conducted to confirm premature placental ageing in cases of unexplained stillbirth, and to investigate the role of circular RNAs in the process of placental ageing. C_LIO_LICircular RNAs accumulate in ageing healthy placenta and accumulate prematurely in stillbirth placentae. Circular RNAs bind directly to placental DNA, inducing DNA breaks and cellular senescence, thereby contributing to overall functional decline of the placenta, reducing its ability to support the fetus. Circular RNAs in maternal blood represents a novel screening tool for detection of stillbirth risk. C_LIO_LIPremature placental ageing has previously been associated with stillbirth, however circular RNAs have never before been implicated in this process. Circular RNA accumulation in ageing tissues has been shown in model species (i.e. C. elegans, Drosophila Melanogaster, mice) but this is the first evidence in human tissues and in the placenta. C_LI

molecular biology↗

bioRxiv2024

β-arrestin-biased Allosteric Modulator of Neurotensin Receptor 1 Reduces Ethanol Drinking and Responses to Ethanol Administration in Rodents

Alcohol use disorders (AUDs) impose an enormous societal and financial burden, and world-wide, alcohol misuse is the 7th leading cause of premature death1. Despite this, there are currently only 3 FDA approved pharmacological treatments for the treatment of AUDs in the United States. The neurotensin (Nts) system has long been implicated in modulating behaviors associated with alcohol misuse. Recently, a novel compound, SBI-553, that biases the action of Nts receptor 1 (NTSR1) activation, has shown promise in preclinical models of psychostimulant misuse. Here we investigate the efficacy of this compound to alter ethanol-mediated behaviors in a comprehensive battery of experiments assessing ethanol consumption, behavioral responses to ethanol, sensitivity to ethanol, and ethanol metabolism. Additionally, we investigated behavior in avoidance and cognitive assays to monitor potential side effects of SBI-553. We find that SBI-553 reduces binge-like ethanol consumption in mice without altering avoidance behavior or novel object recognition. We also observe sex-dependent differences in physiological responses to sequential ethanol injections in mice. In rats, we show that SBI-553 attenuates sensitivity to the interoceptive effects of ethanol (using a Pavlovian drug discrimination task). Our data suggest that targeting NTSR1 signaling may be promising to attenuate alcohol misuse, and adds to a body of literature that suggests NTSR1 may be a common downstream target involved in the psychoactive effects of multiple reinforcing substances.

neuroscience↗

bioRxiv2023

ClonoScreen3D: a novel three-dimensional clonogenic screening platform for identification of radiosensitizers for glioblastoma

PurposeGlioblastoma (GBM) is a lethal brain tumour. Standard of care treatment comprising surgery, radiation and chemotherapy results in median survival rates of 12-15 months. Molecular targeted agents identified using conventional two-dimensional (2D) in vitro models of GBM have failed to improve outcome in patients, rendering such models inadequate for therapeutic target identification. We developed a 3D GBM in vitro model that recapitulates key GBM clinical features and responses to molecular therapies and investigated its utility for screening novel radiation-drug combinations using gold-standard clonogenic survival as readout. ResultsPatient-derived GBM cell lines were optimized for inclusion in a 96-well plate 3D clonogenic screening platform, ClonoScreen3D. Radiation responses of GBM cells in this system were highly reproducible and comparable to those observed in low-throughout 3D assays. The screen methodology provided quantification of candidate drug single agent activity (EC50) and the interaction between drug and radiation (radiation interaction ratio, RIR). The PARP inhibitors talazoparib, rucaparib and olaparib, each showed a significant interaction with radiation by ClonoScreen3D and were subsequently confirmed as true radiosensitizers by full clonogenic assay. Screening a panel of DNA damage response inhibitors revealed the expected propensity of these compounds to interact significantly with radiation (13/15 compounds). A second screen assessed a panel of compounds targeting pathways identified by transcriptomic analysis and demonstrated single agent activity and a previously unreported interaction with radiation of dinaciclib and cytarabine (RIR 1.28 and 1.90, respectively). These compounds were validated as radiosensitizers in full clonogenic assays (sensitizer enhancement ratio 1.47 and 1.35, respectively). ConclusionsThe ClonoScreen3D platform was demonstrated to be a robust method to screen for single agent and radiation-drug combination activity. Using gold-standard clonogenicity, this assay is a tool for identification of novel radiosensitizers. We anticipate this technology will accelerate identification of novel radiation-drug combinations with genuine translational value.

cancer biology↗

bioRxiv2022

Enhanced survival and low proliferation marks multifunctional virus specific memory CD4 T cells

Cytokine production by memory T cells is a key mechanism of T cell mediated protection. However, we have a limited understanding of the survival and secondary responses of memory T cells with cytokine producing capacities. We interrogate antigen-specific CD4 T cells using a mouse influenza A virus infection model. CD4 T cells with the capacity to produce cytokines survive better than non-cytokine+ cells, displaying a low fold contraction and expressing high levels of pro-survival molecules, CD127 and Bcl2. Transcriptomic analysis reveals a heterogenous population of memory CD4 T cells with three clusters of cytokine+ cells. These clusters match flow cytometry data revealing an enhanced survival signature in cells capable of producing multiple cytokines. These multifunctional cells are, however, less likely to proliferate during and following primary and secondary infections. Despite this, multifunctional memory T cells form a substantial fraction of the secondary memory pool, indicating that survival rather than proliferation may dictate which populations survive within the memory pool. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/520219v3_ufig1.gif" ALT="Figure 1"> View larger version (22K): org.highwire.dtl.DTLVardef@93e62forg.highwire.dtl.DTLVardef@1ed2444org.highwire.dtl.DTLVardef@1e7f79borg.highwire.dtl.DTLVardef@30e31d_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOGraphical AbstractC_FLOATNO C_FIG

immunology↗

bioRxiv2022

Loss of cytoskeletal proteostasis links dysregulation of cell size and mechanotransduction in mesenchymal stem cell senescence

Tissues are maintained by homeostatic feedback mechanisms where cells respond to, but also modify, the chemical and mechanical properties of the surrounding extracellular matrix. Mesenchymal stem cells (MSCs) resident in the marrow niche experience a diverse mechanical environment, but ageing can affect the composition and quality of bone and marrow tissues. Here we quantified the effect of replication-induced senescence on MSC morphology and their ability to correctly respond to different substrate stiffnesses. The matrix proteome was found to be sensitive to substrate stiffness, but pharmacological inhibition of cellular contractility perturbed this response, decreasing levels of tenascin-C, fibulins and fibronectin. Similar decreases in these mechanosensitive proteins were observed in senescent cells, suggested a decoupling of mechanotransduction pathways. Intracellular proteomic and transcriptomic analyses confirmed a decrease in components of the cytoskeletal chaperone complex CCT/TRiC in senescent MSCs. Finally, pharmacological inhibition of CCT/TRiC was able to partially recapitulate senescence-associated morphological changes in non-senescent MSCs. These results demonstrate a senescence-mediated perturbation to cytoskeletal homeostasis, pathways of mechanotransduction and the secretion of matrix proteins required for tissue maintenance.

cell biology↗

bioRxiv2021

Low-dose lung radiotherapy for COVID-19 lung disease: a pre-clinical efficacy study in a bleomycin model of pneumonitis.

PurposeLow-dose whole lung radiotherapy (LDLR) has been proposed as a treatment for patients with acute respiratory distress syndrome associated with SARS-CoV-2 infection and clinical trials are underway. There is an urgent need for preclinical evidence to justify this approach and inform dose, scheduling and mechanisms of action. Materials and methodsFemale C57BL/6 mice were treated with intranasal bleomycin sulphate (7.5 or 11.25 units/kg, day 0), then exposed to whole lung radiation therapy (0.5, 1.0, 1.5 Gy or sham, day 3). Bodyweight was measured daily and lung tissue harvested for histology and flow cytometry on day 10. Computed tomography (CT) lung imaging was performed pre-radiation (day 3) and pre-endpoint (day 10). ResultsBleomycin caused pneumonitis of variable severity which correlated with weight loss. LDLR at 1.0 Gy was associated with a significant increase in the proportion of mice recovering to 98% of initial bodyweight and a proportion of these mice exhibited less severe histopathological lung changes. Mice experiencing moderate initial weight loss were more likely to respond to LDLR than those experiencing severe initial weight loss. Additionally, LDLR (1.0 Gy) significantly reduced bleomycin-induced increases in interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids. Overall,bleomycin-treated mice exhibited significantly higher percentages of non-aerated lung in left than right lungs and LDLR (1.0 Gy) prevented further reductions in aerated lung volume in right but not left lungs. LDLR at 0.5 and 1.5 Gy did not modulate bodyweight or flow cytometric readouts of bleomycin-induced pneumonitis. ConclusionsOur data support the concept that LDLR can ameliorate acute inflammatory lung injury, identify 1.0 Gy as the most effective dose and provide preliminary evidence that it is more effective in the context of moderate than severe pneumonitis. Mechanistically, LDLR at 1.0 Gy significantly suppressed bleomycin-induced accumulation of pulmonary interstitial macrophages, CD103+ dendritic cells and neutrophil-DC hybrids.

immunology↗

bioRxiv2018

Nuclear decoupling is part of a rapid protein-level cellular response to high-intensity mechanical loading

Our current understanding of cellular mechano-signalling is based on static models, which do not replicate the dynamics of living tissues. Here, we examined the time-dependent response of primary human mesenchymal stem cells (hMSCs) to cyclic tensile strain (CTS). At low-intensity strain (1 hour, 4% CTS at 1 Hz) morphological changes mimicked responses to increased substrate stiffness. As the strain regime was intensified (frequency increased to 5 Hz), we characterised rapid establishment of a broad, structured and reversible protein-level response, even as transcription was apparently downregulated. Protein abundance was quantified coincident with changes to protein conformation and post transcriptional modification. Furthermore, we characterised changes within the linker of nucleo- and cytoskeleton (LINC) complex of proteins that bridges the nuclear envelope, and specifically to levels of SUN domain-containing protein 2 (SUN2). The result of this regulation was to decouple mechano-transmission between the cytoskeleton and the nucleus, thus conferring protection to chromatin.

biophysics↗