Biology subjects

Smith, G. A.

Publications and source records attributed to Smith, G. A..

13 recordsLinked to original sources

bioRxiv2026

Phosphoinositide turnover through PLCγ regulates Draper-dependent engulfment in glia

Glial engulfment of degenerating neuronal material is essential for nervous system development, maintenance and repair. Genome-wide association studies have identified protective variants in the phosphoinositide-metabolising enzyme PLCG2 that modify Alzheimers disease risk, but how PLCG2-dependent phosphoinositide signalling regulates glial engulfment remains unclear. Using Drosophila, we investigated the role of small wing (sl), the fly orthologue of human PLCG2, in glial responses to axonal injury and amyloid pathology. Glial knockdown of sl altered immune-associated transcriptional pathways and significantly delayed clearance of degenerating olfactory receptor neuron axons following axotomy. Loss of sl disrupted injury-induced phosphoinositide remodelling, resulting in elevated basal PIP2 levels and impaired post-injury accumulation of PIP3. Similar defects were observed following knockdown of the engulfment receptor Draper, placing phosphoinositide turnover downstream of Draper signalling. Simultaneous Pten knockdown restored phosphoinositide signalling and rescued delayed neuronal clearance in sl-deficient glia. Loss of sl also prevented injury-induced Draper upregulation and disrupted glial calcium signalling responses to axonal injury. In a model of A{beta}42 accumulation, sl knockdown altered brain PIP2/PIP3 balance and improved survival independently of amyloid burden. Together, these findings identify PLC{gamma}-dependent phosphoinositide turnover as a conserved regulator of Draper-mediated glial engulfment and provide mechanistic insight into how PLCG2 influences glial function and neurodegenerative disease risk. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/729572v1_ufig1.gif" ALT="Figure 1"> View larger version (49K): org.highwire.dtl.DTLVardef@5beb6org.highwire.dtl.DTLVardef@12bc7c5org.highwire.dtl.DTLVardef@1486ba0org.highwire.dtl.DTLVardef@1921395_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Murine osteosarcoma recapitulates the driver landscape and genomic complexity of osteosarcoma evolution in humans

Osteosarcoma (OS) genomes are characterized by complex genomic rearrangements (CGRs) that drive genomic instability and clonal diversification early in tumor evolution. As a result, OS tumors display high inter-patient variability, which has hindered molecular stratification and targeted therapeutic development. To study genomic complexity in OS and credential a genetically engineered mouse model of the disease (Sp7-Cre Trp53fl Rb1fl), we performed high-depth and multi-region whole genome sequencing (WGS) of 35 tumor samples from 24 mice. Similar to human OS, the murine OS tumors (mOS) had a high number of somatic structural variants (158 per tumor) with low tumor mutational burden of single nucleotide variants (0.87 mutations/MB). CGRs were identified in 63% (15/24) of mOS cases, most frequently affecting chromosome 15 (33%, 8/24 mice) and resulting in Myc amplification in 6 mice, ranging from 5 to 104 copies. Myc amplification was verified with DNA FISH, long-read sequencing and gene expression data, which revealed examples of Myc amplification in both extrachromosomal circular DNA (ecDNA) and in derivative chromosomes generated by CGRs. PTEN loss occurred frequently (59% 12/22 mice), and contributed to osteosarcomagenesis, as demonstrated by tumor initiation with in vivo CRISPR/Cas9-mediated deletion experiments (2 mice). Together, these results demonstrate that a preclinical model of osteosarcoma can generate the genomic heterogeneity and complexity of the human disease, thereby facilitating research into mechanisms of tumor initiation and drivers of progression and relapse.

cancer biology↗

bioRxiv2025

Zyxin Restricts Viral Fusion and Entry across Multiple Virus Families

The entry of enveloped viruses into host cells requires fusion of the viral envelope with a host cell membrane. The composition and dynamics of cellular membranes are impacted by the underlying cytoskeleton. Zyxin, a cytosolic protein that bridges the actin cytoskeleton with adhesion receptor proteins, was recently identified as an antiviral factor that antagonizes HSV-1 entry. To determine if zyxin specifically interferes with membrane fusion, we examined its impact in a quantitative cell-cell fusion assay. HSV-1 entry proteins exhibited enhanced fusion activity with retinal pigment epithelial (RPE) cells when the cells were knocked out (KO) for zyxin. Zyxin-KO cells also showed enhanced fusion activity with pseudorabies virus (PRV), paramyxovirus and rhabdovirus fusion proteins. Additionally, the size of plaques formed following infection with members of each viral family were increased in the absence of zyxin. Bulk RNA sequencing of wild-type (WT) and zyxin-KO RPE cells identified 18 genes that enrich into several ontology groups of interest, including regulation of membrane potential, herpes simplex virus 1 infection (CCL2 and ZNF14), NABA core matrisome (CCL2 and ZNF14), extracellular matrix organization (CTSK, SERPINE1 and TGFB2), cell-cell adhesion (RAC2 and TGFB2), anchoring fibril formation, and regulation of the MAPK cascade (ACKR3 and TGFB2). These results highlight zyxin as a broadly active antiviral factor and suggest potential therapeutic implications for viral infections. IMPORTANCEEnveloped viruses enter host cells by fusing their envelope with a cellular membrane. This process is triggered when a viral glycoprotein(s) engages with a cellular membrane receptor. Less well understood are the cytoplasmic factors that indirectly govern viral fusion and entry. We report that zyxin, a cellular protein that bridges cell-adhesion receptors with the underlying actin cytoskeleton, antagonizes the fusion and entry of several enveloped viruses.

microbiology↗

bioRxiv2025

Alzheimer's disease risk gene Wwox protects against amyloid pathology through metabolic reprogramming

Genome wide association studies have identified multiple loci that mediate the risk of developing late-onset Alzheimers Disease (LOAD). The gene WW-domain containing oxidoreductase (WWOX) has been identified in recent LOAD risk meta-analyses, yet its function in the brain is poorly understood. Using Drosophila, we discovered that knockdown of the highly conserved Wwox gene impacts longevity and sleep, having roles in both neuronal and glial subtypes. In an amyloid beta 42 (A{beta}42) transgenic model of AD, RNAi-mediated knockdown of Wwox significantly decreased both lifespan and locomotion whilst elevating soluble A{beta}42. Transcriptomic and metabolomic analyses revealed that these effects were accompanied by elevated lactate dehydrogenase (Ldh) mRNA and lactate levels, downstream of an increase in the key unfolded protein response protein Atf4. Strikingly, we found that upregulation of Wwox in the A{beta}42 model through CRISPR activation significantly reduced amyloid load, improved longevity and locomotion. Multi-omics analysis revealed Wwox upregulation partially reversed several key A{beta}42-induced transcriptional pathways in the brain and reduced levels of L-methionine and associated enzymes. These findings support a role for reduced WWOX levels in the genetic risk of developing LOAD via pyruvate metabolism and point towards WWOX activation as a protective therapeutic strategy.

neuroscience↗

bioRxiv2024

New insights into the functions of ACBD4/5-like proteins using a combined phylogenetic and experimental approach across model organisms

Acyl-CoA binding domain-containing proteins (ACBDs) perform diverse but often uncharacterised functions linked to cellular lipid metabolism. Human ACBD4 and ACBD5 are closely related peroxisomal membrane proteins, involved in tethering of peroxisomes to the ER and capturing fatty acids for peroxisomal {beta}-oxidation. ACBD5 deficiency causes neurological abnormalities including ataxia and white matter disease. Peroxisome-ER contacts depend on an ACBD4/5-FFAT motif, which interacts with ER-resident VAP proteins. As ACBD4/5-like proteins are present in most fungi and all animals, we combined phylogenetic analyses with experimental approaches to improve understanding of their evolution and functions. Notably, all vertebrates exhibit gene sequences for both ACBD4 and ACBD5, while invertebrates and fungi possess only a single ACBD4/5-like protein. Our analyses revealed alterations in domain structure and FFAT sequences, which help understanding functional diversification of ACBD4/5-like proteins. We show that the Drosophila melanogaster ACBD4/5-like protein possesses a functional FFAT motif to tether peroxisomes to the ER via Dm_Vap33. Depletion of Dm_Acbd4/5 caused peroxisome redistribution in wing neurons and reduced life expectancy. In contrast, the ACBD4/5-like protein of the filamentous fungus Ustilago maydis lacks a FFAT motif and does not interact with Um_Vap33. Loss of Um_Acbd4/5 resulted in an accumulation of peroxisomes and early endosomes at the hyphal tip. Moreover, lipid droplet numbers increased and mitochondrial membrane potential declined, implying altered lipid homeostasis. Our findings reveal differences between tethering and metabolic functions of ACBD4/5-like proteins across evolution, improving our understanding of ACBD4/5 function in health and disease. The need for a unifying nomenclature for ACBD proteins is discussed.

cell biology↗

bioRxiv2022

Acyl ghrelin attenuates neurochemical and motor deficits in the 6OHDA model of Parkinsons disease

The feeding-related hormone, acyl-ghrelin, protects dopamine neurons in murine 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-based models of experimental Parkinsons disease (PD). However, the potential protective effect of acyl-ghrelin on substantia nigra pars compacta (SNpc) dopaminergic neurones and consequent behavioural correlates in the more widely used 6-hydroxydopamine (6-OHDA) rat medial forebrain bundle (MFB) lesion model of PD are unknown. To address this question, acyl-ghrelin levels were raised directly by mini-pump infusion for 7-days prior to unilateral injection of 6-OHDA into the MFB with assessment of amphetamine-induced rotations on days 27 and 35, and immunohistochemical analysis of dopaminergic neurone survival. While acyl-ghrelin treatment was insufficient to elevate food intake or body weight, it attenuated amphetamine-induced circling behaviour and SNpc dopamine neurone loss induced by 6-OHDA. These data support the notion that elevating circulating acyl-ghrelin may be a valuable approach to slow or impair progression of neurone loss in PD. HighlightsO_LIAcyl-ghrelin attenuates SNpc dopamine cell loss in rat 6-OHDA-lesion model of PD C_LIO_LIAcyl-ghrelin attenuates motor deficits in rat 6-OHDA-lesion model of PD C_LI

neuroscience↗

bioRxiv2021

Oncogenic RAS commandeers amino acid sensing machinery to aberrantly activate mTORC1 in multiple myeloma

Oncogenic mutations within the RAS pathway are common in multiple myeloma (MM), an incurable malignancy of plasma cells. However, the mechanisms of pathogenic RAS signaling in this disease remain enigmatic and difficult to inhibit therapeutically. We employed an unbiased proteogenomic approach to dissect RAS signaling in MM by combining genome-wide CRISPR-Cas9 screening with quantitative mass spectrometry focused on RAS biology. We discovered that mutant isoforms of RAS organized a signaling complex with the amino acid transporter, SLC3A2, and MTOR on endolysosomes, which directly activated mTORC1 by co-opting amino acid sensing pathways. MM tumors with high expression of mTORC1-dependent genes were more aggressive and enriched in RAS mutations, and we detected interactions between RAS and MTOR in MM patient tumors harboring mutant RAS isoforms. Inhibition of RAS-dependent mTORC1 activity synergized with MEK and ERK inhibitors to quench pathogenic RAS signaling in MM cells. This study redefines the RAS pathway in MM and provides a mechanistic and rational basis to target this novel mode of RAS signaling.

cancer biology↗

bioRxiv2021

Circuit organization of the excitatory sensorimotor loop through hand/forelimb S1 and M1

Sensory-guided limb control relies on communication across sensorimotor loops. For active touch with the hand, the longest loop is the transcortical continuation of ascending pathways, particularly the lemnisco-cortical and corticocortical pathways carrying tactile signals via the cuneate nucleus, ventral posterior lateral (VPL) thalamus, and primary somatosensory (S1) and motor (M1) cortices to reach corticospinal neurons and influence descending activity. We characterized excitatory connectivity along this pathway in the mouse. In the lemnisco-cortical leg, disynaptic cuneate[->]VPL[->]S1 connections excited mainly layer (L) 4 neurons. In the corticocortical leg, S1[->]M1 connections from L2/3 and L5A neurons mainly excited downstream L2/3 neurons, which excite corticospinal neurons. The findings provide a detailed new wiring diagram for the hand/forelimb-related transcortical circuit, delineating a basic but complex set of cell-type-specific feedforward excitatory connections that selectively and extensively engage diverse intratelencephalic projection neurons, thereby polysynaptically linking subcortical somatosensory input to cortical motor output to spinal cord.

neuroscience↗

bioRxiv2020

Genome-Wide Screening Reveals CSDE1 as a Novel Regulator of the LDL Receptor

The low-density lipoprotein receptor (LDLR) controls cellular delivery of cholesterol and clears LDL from the bloodstream, protecting against atherosclerotic heart disease, the leading cause of death in the United States. We therefore sought to identify regulators of the LDLR beyond the targets of current clinical therapies and known causes of familial hypercholesterolemia. We show that Cold Shock Domain-Containing Protein E1 (CSDE1) enhances hepatic LDLR mRNA decay via its 3 untranslated region to regulate atherogenic lipoproteins in vivo. Using parallel phenotypic genome-wide CRISPR interference screens, we found 40 specific regulators of the LDLR left unidentified by observational human genetics. Among these, we show that CSDE1 regulates the LDLR at least as strongly as the mechanistically distinct pathways exploited by the best available clinical therapies: statins and PCSK9 inhibitors. Additionally, we show that hepatic gene silencing of Csde1 treats diet-induced dyslipidemia in mice better than that of Pcsk9. Our results reveal the therapeutic potential of manipulating a newly identified key factor in the post-transcriptional regulation of the LDLR mRNA for the prevention of cardiovascular disease. We anticipate that our approach of modelling a clinically relevant phenotype in a forward genetic screen, followed by mechanistic pharmacologic dissection and in vivo validation, will serve as a generalizable template for the identification of therapeutic targets in other human disease states. One Sentence SummaryA genome-wide CRISPR screen identifies CSDE1 as a key regulator of hepatic LDLR mRNA decay in vivo, making it a promising target for heart disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=137 HEIGHT=200 SRC="FIGDIR/small/235028v2_ufig1.gif" ALT="Figure 1"> View larger version (53K): org.highwire.dtl.DTLVardef@d53b79org.highwire.dtl.DTLVardef@133b48corg.highwire.dtl.DTLVardef@1926d97org.highwire.dtl.DTLVardef@58d863_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2019

The herpes simplex virus type I deamidase enhances propagation but is dispensable for retrograde axonal transport into the nervous system

Upon replication in mucosal epithelia and transmission to nerve endings, capsids of herpes simplex virus type I (HSV-1) travel retrograde within axons to peripheral ganglia where life-long latent infections are established. A capsid-bound tegument protein, pUL37, is an essential effector of retrograde axonal transport and also houses a deamidase activity that antagonizes innate immune signaling. In this report, we examined whether the deamidase of HSV-1 pUL37 contributes to the neuroinvasive retrograde axonal transport mechanism. We conclude that neuroinvasion is enhanced by the deamidase, but the critical contribution of pUL37 to retrograde axonal transport functions independently of this activity.\n\nIMPORTANCEHerpes simplex virus type 1 invades the nervous system by entering nerve endings and sustaining long-distance retrograde axonal transport to reach neuronal nuclei in ganglia of the peripheral nervous system. The incoming viral particle carries a deamidase activity on its surface that antagonizes antiviral responses. We examined the contribution of the deamidase to the hallmark neuroinvasive property of this virus.

microbiology↗

bioRxiv2018

The apical region of the herpes simplex virus major capsid protein promotes capsid maturation

The herpesvirus capsid assembles in the nucleus as an immature procapsid precursor built around viral scaffold proteins. The event that initiates procapsid maturation is unknown, but it is dependent upon activation of the VP24 internal protease. Scaffold cleavage triggers angularization of the shell and its decoration with the VP26 and pUL25 capsid-surface proteins. In both the procapsid and mature angularized capsid, the apical region of the major capsid protein (VP5) is surface exposed. We investigated whether the VP5 apical region contributes to intracellular transport dynamics following entry into primary sensory neurons and also tested the hypothesis that conserved negatively-charged amino acids in the apical region contribute to VP26 acquisition. To our surprise neither hypothesis proved true. Instead, mutation of glutamic acid residues in the apical region delayed viral propagation and induced focal capsid accumulations in nuclei. Examination of capsid morphogenesis based on epitope unmasking, capsid composition, and ultrastructural analysis indicated that these clusters consisted of procapsids. The results demonstrate that, in addition to established events that occur inside the capsid, the exterior capsid shell promotes capsid morphogenesis and maturation.

microbiology↗

bioRxiv2018

Dissecting the herpesvirus architecture by targeted proteolysis

Herpesvirus particles have a complex architecture consisting of an icosahedral capsid that is surrounded by a lipid envelope. Connecting these two components is a layer of tegument that consists of varying amounts of twenty or more proteins. The arrangement of proteins within the tegument cannot easily be assessed and instead is inferred from tegument interactions identified in reductionist models. To better understand the tegument architecture, we have developed an approach to probe capsid-tegument interactions within extracellular viral particles by encoding tobacco etch virus (TEV) protease sites in viral structural proteins, along with distinct fluorescent tags in capsid and tegument components. In this study, TEV sites were engineered within the pUL36 large tegument protein: a critical structural element that is anchored directly on the capsid surface. Purified pseudorabies virus extracellular particles were permeabilized and TEV protease was added to selectively cleave the exposed pUL36 backbone. Interactions with the capsid were assessed in situ by monitoring the fate of the fluorescent signals following cleavage. Although several regions of pUL36 are proposed to bind capsids, pUL36 was found stably anchored to the capsid exclusively at its carboxyl terminus. Two additional tegument proteins, pUL37 and pUS3, were tethered to the capsid via pUL36 whereas the pUL16, pUL47, pUL48, and pUL49 tegument proteins were not stably bound to the capsid.\n\nIMPORTANCENeuroinvasive alphaherpesviruses produce diseases of clinical and economic significance in humans and veterinary animals, but are predominantly associated with less serious recurrent disease. Like all viruses, herpesviruses assemble a metastable particle that selectively dismantles during initial infection. This process is made more complex by the presence of a tegument layer that resides between the capsid surface and envelope. Components of the tegument are essential for particle assembly and also serve as critical effectors that promote infection upon entry into cells. How this dynamic network of protein interactions is arranged within virions is largely unknown. We present a molecular approach to dissect the tegument and with it, begin to tease apart the protein interactions that underlie this complex layer of the virion architecture.

microbiology↗

bioRxiv2017

Repurposing Tofacitinib As An Anti-Myeloma Therapeutic To Reverse Growth-Promoting Effects Of The Bone Marrow Microenvironment

The myeloma bone marrow microenvironment promotes proliferation of malignant plasma cells and resistance to therapy. Interleukin-6 (IL-6) and downstream JAK/STAT signaling are thought to be central components of these microenvironment-induced phenotypes. In a prior drug repurposing screen, we identified tofacitinib, a pan-JAK inhibitor FDA-approved for rheumatoid arthritis, as an agent that may reverse the tumor-stimulating effects of bone marrow mesenchymal stromal cells. Here, we validated both in vitro, in stromal-responsive human myeloma cell lines, and in vivo, in orthotopic disseminated murine xenograft models of myeloma, that tofacitinib showed both single-agent and combination therapeutic efficacy in myeloma models. Surprisingly, we found that ruxolitinib, an FDA-approved agent targeting JAK1 and JAK2, did not lead to the same anti-myeloma effects. Combination with a novel irreversible JAK3-selective inhibitor also did not enhance ruxolitinib effects. RNA-seq and unbiased phosphoproteomics revealed that marrow stromal cells stimulate a JAK/STAT-mediated proliferative program in myeloma plasma cells, and tofacitinib reversed the large majority of these pro-growth signals. Taken together, our results suggest that tofacitinib specifically reverses the growth-promoting effects of the tumor microenvironment through blocking an IL-6-mediated signaling axis. As tofacitinib is already FDA-approved, these results can be rapidly translated into potential clinical benefits for myeloma patients.

cancer biology↗