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Watts, J.

Publications and source records attributed to Watts, J..

17 recordsLinked to original sources

A defined microbial community remodels host metabolism and pathogen resistance in Caenorhabditis elegans

The microbiome is an important regulator of metabolism and health, yet the mechanisms by which microbial communities influence host physiological state remain incompletely understood. Here we used a defined host-microbiota model consisting of Caenorhabditis elegans and an 11-member bacterial consortium representative of its natural microbiota (DefNatMta). We investigated how this native microbial community influences host metabolism and physiology relative to the standard laboratory diet, E. coli OP50. Transcriptomic analyses revealed remodelling of host pathways associated with lipid metabolism, immunity and xenobiotic detoxification. Comparison with fasting-responsive transcriptional programmes showed that the DefNatMta response is distinct from fasting or caloric restriction. DefNatMta enhanced resistance to Staphylococcus aureus infection, and this protective effect was consistent with roles for the conserved host defence regulators PMK-1/p38 MAPK and HLH-30/TFEB. Additionally, DefNatMta reduced lipid accumulation, modified expression of lipid metabolism genes, and altered fatty acid composition, including enrichment of monomethyl branched-chain fatty acids and polyunsaturated fatty acids. Together, these findings demonstrate that a defined microbial community can induce transcriptional, metabolic and physiological remodelling in the host. Our results are consistent with microbial communities shaping host metabolic state and immune competence.

physiology↗

Albumin-binding dendrimer-conjugated siRNA enables safe and effective gene silencing throughout the central nervous system

Improving siRNA delivery to the central nervous system (CNS) is a major focus for treating the numerous debilitating neurological conditions which have a genetic basis. Here, we present an albumin-binding siRNA based on an amphiphilic dendrimer conjugate (D-siRNA). We demonstrate that D-siRNA achieves effective and homogeneous delivery throughout the CNS following administration into the cerebrospinal fluid (CSF). In mice, a single CSF administration of D-siRNA resulted in potent and durable gene silencing across various brain regions, with effects lasting six months without detectable toxicity. We validate its utility in larger rodents (rats) using intrathecal administration--a clinically relevant route--showing effective and broad delivery and robust silencing. Benchmarking against other clinically relevant siRNA delivery scaffolds revealed that D-siRNA provides comparable delivery and efficacy, with more efficient conversion of gross uptake to functional uptake. These findings support the use of albumin-binding conjugates for brain delivery, and position D-siRNA as a safe, effective, and durable platform for gene silencing in the CNS.

pharmacology and toxicology↗

Population genomics of yellow-eyed penguins uncovers subspecies divergence and candidate genes linked to respiratory distress syndrome

Yellow-eyed penguins (hoiho/takaraka, Megadyptes antipodes) are among the worlds rarest penguins and are regarded as a taonga (treasured) species in Aotearoa New Zealand. Since 2019, chicks on the New Zealand mainland have been affected by a deadly neonatal disease called respiratory distress syndrome (RDS), contributing to a decline to fewer than 143 breeding pairs. To investigate the putative genetic basis of this disease, we generated high-quality whole-genome data from 249 individuals spanning the species range, including from the New Zealand mainland (Northern range) and subantarctic Enderby and Campbell Islands (Southern). Population genomic analyses unexpectedly revealed three deeply divergent lineages with negligible gene flow, consistent with recognition of three distinct subspecies. Phylogenetic divergence dating suggests that these splits predate human arrival by several millennia, with the Northern lineage diverging from the Southern populations 5-16 ka. Genome scans for local adaptation revealed regions of strong differentiation, and genome-wide association analyses identified candidate immune and respiratory genes linked to RDS. In partnership with Ng[a]i Tahu, who hold indigenous guardianship over yellow-eyed penguins, we recommend recognition of three subspecies, urgent conservation action for the critically small and rapidly declining Northern subspecies, and the need for immediate population size and trend assessments for Auckland and Campbell Island populations.

genomics↗

Bioelectronic Modulation of Glioblastoma via Wireless Carbon Nanotube Porin Interfaces

The membrane potential (Vmem) and faradaic charge transfer, resulting from altered charge distribution due to ion channels, play a crucial role in cellular bioelectricity. Disruption of Vmem can activate pathways associated with cancer proliferation. Manipulating ion channels may therefore present an effective strategy for treating cancers that fail to respond to conventional therapies. One approach to target these channels, is to manipulate the membrane charge which involves the use of wireless bipolar electrodes such as carbon nanotube porins (CNTPs), which could be inserted into cell membranes to mimic these channels. By utilizing membrane dyes, we observed alterations in Vmem induced by CNTPs and externally applied electric fields. Analyses of cellular behaviors and processes indicated that Vmem is more receptive to stimuli in invasive cancers, while it leads to increased metabolism in less invasive cancers, with notable changes in the cell cycle occurring at approximately 48 hours post-treatment in GBM cell lines. This work shows that CNTPs and electric fields can be used to modulate Vmem and alter cancer cell processes, supporting their potential therapeutic capability.

biophysics↗

BtuJ1, a novel surface-exposed B12-binding protein in Bacteroidetes, functions as an extracellular vitamin reservoir that enhances fitness.

The acquisition of vitamin B12 and related cobamides is a key determinant for the fitness of Bacteroidetes in the gut. Depending on the species, this uptake process relies on one to four transport systems centered on conserved core outer membrane (OM) complexes composed of the TonB-dependent transporter BtuB and the surface-exposed lipoprotein BtuG. Additionally, the surface-exposed lipoprotein BtuH, although not tightly associated with the BtuBG complex, contributes to cobamide uptake and provides a fitness advantage. Here, we report the functional and structural characterization of BtuJ1 from Bacteroides thetaiotaomicron (B. theta), a novel B12-binding lipoprotein. Under limiting B12 conditions, BtuJ1 is the most abundant component among the three B12-transport systems encoded by B. theta. BtuJ1 is surface exposed and binds vitamin B12 and cobinamide (an intermediate in B12 biosynthesis) with low nM affinity, conferring a fitness advantage in B12-limited environments. In vitro B12 transfer experiments suggest a role for BtuJ1 as an extracellular reservoir for B12, expanding the functionalities of the diverse group of accessory OM proteins employed by Bacteroides to scavenge this essential cofactor in the competitive environment of the human gut. IMPORTANCEUnderstanding how key molecules support bacterial colonization of the human GI tract is essential to rationalize the structure of the complex microbial community inhabiting the distal gut. The Bacteroidetes are one of the dominant phyla in this environment. Given that most Bacteroidetes cannot make vitamin B12 but depend on it for growth, the fitness of many species likely depends on the acquisition of vitamin B12. Unlike the classical model bacterium Escherichia coli, which encodes a single OM B12 transporter, the genomes of Bacteroidetes often encode multiple uptake systems comprising a heterogeneous repertoire of surface-exposed lipoproteins. These proteins may assist OM assemblies for vitamin B12 transport that provide fitness advantages in vivo.

microbiology↗

Swine reporter model for preclinical evaluation and characterization of gene delivery vectors

Delivery of gene therapy vectors targeted to any somatic cell remains a key barrier for the development of genetic medicines. While rodent models provide insights into vector biodistribution and cellular tropism, their anatomical and physiological differences from humans limit their translational potential and studies in large animal models are often required. In this study, we developed a swine reporter model (SRM-1) to evaluate both viral and nonviral vector delivery in a large animal system. The SRM-1 model harbors a Cre- and CRISPR-activated tdTomato reporter at the Rosa26 locus that allows for tracing of cell-specific delivery and expression of gene therapy vectors in vivo. To evaluate this model, we administered adeno-associated virus serotype 9 (AAV9) and lipid nanoparticles (LNPs) carrying mRNA systemically and found successful in vivo reporter activation across a variety of tissues. Intracerebroventricular (ICV) administration of LNP-Cre mRNA was also performed and demonstrated localized activation in cortical brain cells. In addition to biodistribution studies, this model has utility for testing safety and clinically relevant administration methods, surgical and non-surgical, of delivery vectors. Our findings support the SRM-1 model as a valuable tool for advancing gene therapies from preclinical testing to clinical application.

genetics↗

Generation of a Synthetic Single Domain Antibody Library for Radiopharmaceutical Ligand Discovery

Single domain antibodies, often known as nanobodies, are versatile molecules with therapeutic and diagnostic applications, but they are primarily developed through immunization of camelids. This approach is not scalable by automation, not effective for non-immunogenic or toxic antigens, and prevents the use of modified scaffolds for altered pharmacokinetic properties. Synthetic libraries allow for pre-selection of a single domain framework tailored to its intended downstream use. One area of interest for these biologic vectors is radiopharmaceuticals. Ideal radiopharmaceutical pharmacokinetic properties differ from most traditional therapeutics, as short plasma circulation and rapid kidney clearance are necessary to avoid dose-limiting organ radiation. Although there are a growing number of nanobody radiopharmaceuticals in clinical trials, their frameworks and corresponding pharmacokinetic properties vary. One potential method for improving the development of novel single domain antibody radiopharmaceuticals is through synthetic libraries based on nanobodies with proven clinically acceptable pharmacokinetics. We developed a modular synthetic nanobody phage display vector based on the scaffold of the 2Rs15d nanobody that allows for manipulation of the binding and framework regions. Using this vector, we created a library of nanobodies with a randomized CDR2 containing over 1.7x106 unique sequences/{micro}L. As a proof-of-concept, we panned the library for nanobodies binding calreticulin (CALR), a protein critical in immunogenic cell death. One isolated clone, Cal3, has a measured affinity of 140 nM for CALR and is cross-reactive with mouse and human CALR. Using positron emission tomography (PET) imaging, the radiolabeled 64Cu-NOTA-Cal3 demonstrated CALR binding in vivo, representing the first reported synthetic nanobody characterized by PET imaging. This study demonstrates the feasibility of building and panning synthetic libraries for high-affinity radiopharmaceutical nanobodies as an alternative to immunized camelid libraries.

bioengineering↗

EMMAi: fast enzyme-allocation constraints in GEMs for improved biomass prediction across carbon sources

Genome-scale metabolic models (GEMs) predict emergent phenotypes by modeling the metabolic networks encoded in genomes. While GEMs have significantly advanced systems biology, metabolic engineering, biomedicine, and environmental science, they require extensive time and resources for manual curation, which can limit their utility in rapidly evolving research landscapes. Recent findings suggest that manually curated reactions can sometimes reduce prediction accuracy, indicating that integrating additional biologically grounded constraints may better capture emergent phenotypes. One promising approach is the incorporation of enzyme allocation constraints, which has been shown to enhance the predictive accuracy in metabolic models. Enzymatically constrained GEMs (ecGEMs) rely on enzyme turnover rates (kcat) and protein molecular weights (MWs) to account for intracellular resource limitations by introducing an enzyme pool variable and assigning costs to reactions, thereby simulating enzymatic resource constraints. Tools such as GECKO, AutoPACMEN, and ECMpy provide computational pipelines for ecGEM generation. However, these pipelines are often limited by their reliance on experimentally measured kcat values or deep learning-predicted values, such as those generated by DLKcat, which face challenges in predicting kinetics for enzymes dissimilar to their training data. Additionally, these methods frequently require extensive manual curation of kcat values based on empirical data, a time-intensive process that hampers scalability and applicability to non-model organisms. To address these limitations, we introduce EMMAi (Enzyme-constrained Metabolic Models with AI), a pipeline that fully automates the incorporation of enzyme constraints into GEMs. Unlike existing pipelines, EMMAi exclusively utilizes kcat values predicted by UniKP, an AI framework with improved accuracy over DLKcat, particularly for enzymes not present in training datasets. UniKP achieves a 13% improvement in correlation for unseen enzymes, enabling EMMAi to deliver ecGEMs with enhanced prediction accuracy without manual curation requirements. We evaluated EMMAi by applying it to three GEMs: two manually curated models, iJO1366 (Escherichia coli str. K-12 substr. MG1655) and iMO1056 (Pseudomonas aeruginosa PAO1), and one draft GEM constructed and gap-filled using CarveMe. EMMAi-generated ecGEMs showed an average Pearson Correlation Coefficient (PCC) improvement of 0.27 for manually curated GEMs when compared to predicted and experimentally measured growth rates and Biolog readings. Notably, for the draft GEM of Pseudomonas aeruginosa PAO1, the PCC improved dramatically from -0.3 to 0.6. EMMAi demonstrates that automating the integration of enzyme allocation constraints using AI-predicted kinetic parameters significantly enhances the prediction accuracy of GEMs, even in the absence of manual curation. These results underscore EMMAis potential as a scalable, efficient, and accurate tool for advancing GEM-based research in systems biology, metabolic engineering, and beyond.

systems biology↗

Influence of past climate changes and human-mediated introduction on patterns of genetic diversity distribution of the Papuan nutmeg (Myristica argentea) Warb.

Understanding the distribution of genetic diversity of endemic food tree species holds significant importance for conservation planning and the formulation of effective management strategies. Natural and anthropogenic factors can influence species geographic range and distribution of genetic diversity. Here, we tested the relative influence of barriers to gene flow (rivers, mountains and past climate change) and recent human activities on the evolutionary history of an endemic species from Fakfak district, Papua Island, Myristica argentea Warb (Myristicaceae), better known as Papuan nutmeg. Myristica argentea is a spice tree species used by local populations since centuries/millennia. The species has been introduced in other locations from the region. Fourteen microsatellite markers (nSSRs), whole chloroplast (cp) genome, and nuclear-targeted sequence genes (nrDNA sequence) were used to characterize the genetic diversity, population structure, and demographic history of the species across its distribution range (native and introduced populations). We found that native populations of the species in Fakfak present higher levels of genetic diversity than introduced populations. We further detected the presence of a moderate genetic structure (FST = 0.143), and the presence of three intraspecific genetic clusters. Additionally, our findings indicate that population fragmentation within the native range of the species in Fakfak, may have been influenced by the presence of riparian networks, mountain ranges and by Pleistocene climatic fluctuations. Our results suggest that all introduced populations were sourced mainly from the native population of Raduria, in the South of Fakfak region. Given the population genetic variation across the ranges of Papuan nutmeg, management plans should not treat them as single populations, but rather consider the broader genetic diversity within its range.

evolutionary biology↗

Antisense oligonucleotide targeting pathogenic sense repeat RNA in C9ORF72 suppresses production of antisense-dependent dipeptide repeat proteins implicated in ALS/FTD

A six nucleotide repeat expansion in intron-1 of the C9ORF72 gene is the most common genetic mutation affecting individuals with Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Bi-directional transcription of the repeat expansion generates sense and antisense repeat RNAs that can then be translated in all reading frames to produce six distinct dipeptide repeat (DPR) proteins with unique termini. The precise site of translation initiation of these proteins within the C9ORF72 repeat expansion remains elusive. We used CRISPR-Cas9 genome editing and steric-blocking antisense oligonucleotides (ASOs) to investigate the contribution of different AUG codons in the antisense repeat RNA to the production of DPR proteins, poly(GP) and poly(PR) in C9ORF72 expansion carrier motor neurons and lymphoblast cells. We then utilized ASOs targeting C9ORF72 sense repeat RNA to examine whether sense or antisense RNA is the major source of the poly(GP) protein - a question for which conflicting evidence exists. We found that these ASOs reduced the intended sense RNA target, but also the antisense RNA, thus preventing the production of poly(PR). Our data highlights the importance of the sequences preceding the antisense CCCCGG repeat expansion for the synthesis of antisense DPR proteins and supports the use of sense C9ORF72 ASOs to prevent the accumulation of both sense- and antisense-dependent DPR proteins in C9ORF72 ALS/FTD.

neuroscience↗

Next generation APOBEC3 inhibitors: Optimally designed for potency and nuclease stability

APOBEC3 (or A3) enzymes have emerged as potential therapeutic targets due to their role in introducing heterogeneity in viruses and cancer, often leading to drug resistance. Inhibiting these enzymes has remained elusive as initial phosphodiester (PO) linked DNA based inhibitors lack stability and potency. We have enhanced both potency and nuclease stability, of 2'-deoxy-zebularine (dZ), substrate-based oligonucleotide inhibitors for two critical A3s: A3A and A3G. While replacing the phosphate backbone with phosphorothioate (PS) linkages increased nuclease stability, fully PS-modified inhibitors lost potency (1.4-3.7 fold) due to the structural constraints of the active site. For both enzymes, mixed PO/PS backbones enhanced potency (2.3-9.2 fold), while also vastly improving nuclease resistance. We also strategically introduced 2'-fluoro sugar modifications, creating the first nanomolar inhibitor of A3G-CTD2. With hairpin-structured inhibitors containing optimized PS patterns and LNA sugar modifications, we characterize the first single-digit nanomolar inhibitor targeting A3A. These extremely potent A3A inhibitors, were highly resistant to nuclease degradation in serum stability assays. Overall, our optimally designed A3 oligonucleotide inhibitors show improved potency and stability, compared to previous attempts to inhibit these critical enzymes, opening the door to realize the therapeutic potential of A3 inhibition.

biochemistry↗

Anti-prion drugs do not improve survival in knock-in models of inherited prion disease

Prion diseases uniquely manifest in three distinct forms: inherited, sporadic, and infectious. Wild-type prions are responsible for the sporadic and infectious versions, while mutant prions cause inherited variants like fatal familial insomnia (FFI) and familial Creutzfeldt-Jakob disease (fCJD). Although some drugs can prolong prion incubation times up to four-fold in rodent models of infectious prion diseases, no effective treatments for FFI and fCJD have been found. In this study, we evaluated the efficacy of various anti-prion drugs on newly-developed knock-in mouse models for FFI and fCJD. These models express bank vole prion protein (PrP) with the pathogenic D178N and E200K mutations. We applied various drug regimens known to be highly effective against wild-type prions in vivo as well as a brain-penetrant compound that inhibits mutant PrPSc propagation in vitro. None of the regimens tested (Anle138b, IND24, Anle138b + IND24, cellulose ether, and PSCMA) significantly extended disease-free survival or prevented mutant PrPSc accumulation in either knock-in mouse model, despite their ability to induce strain adaptation of mutant prions. Paradoxically, the combination of Anle138b and IND24 appeared to accelerate disease by 16% and 26% in kiBVIE200K and kiBVID178N mice, respectively, and accelerated the aggregation of mutant PrP molecules in vitro. Our results show that anti-prion drugs originally developed to treat infectious prion diseases do not necessarily work for inherited prion diseases, and that the recombinant sPMCA is not a reliable platform for identifying compounds that target mutant prions. This work underscores the need to develop therapies and validate screening assays specifically for mutant prions.

pharmacology and toxicology↗

Upregulated pexophagy limits the capacity of selective autophagy

Selective autophagy is an essential mechanism to maintain organelle integrity and cellular homeostasis through the constant recycling of damaged or superfluous components. While distinct selective autophagy pathways mediate the degradation of diverse cellular substrates including organelles and pathogens, whether these distinct pathways can influence one another remains unknown. We address this question here using pexophagy, the autophagic degradation of peroxisomes, as a model. We demonstrate in cells that upregulated pexophagy exhausts selective autophagy and limits the degradation of both mitochondria and protein aggregates. We confirmed this finding in the pexophagy-mediated form of Zellweger Spectrum Disorder, a rare disease characterized by peroxisome dysfunction. Further, we extend the generalizability of limited selective autophagy by determining that increased aggrephagy reduces pexophagy using a model of Huntingtons Disease. Our findings suggest that the degradative capacity of selective autophagy can become limited by an increased substrate load.

cell biology↗

Nuclear receptor signaling via NHR-49/MDT-15 regulates stress resilience and proteostasis in response to reproductive and metabolic cues

The ability to sense and respond to proteotoxic insults declines with age, leaving cells vulnerable to chronic and acute stressors. Reproductive cues modulate this decline in cellular proteostasis to influence organismal stress resilience in C. elegans. We previously uncovered a pathway that links the integrity of developing embryos to somatic health in reproductive adults. Here, we show that the nuclear receptor NHR-49, a functional homolog of mammalian peroxisome proliferator-activated receptor alpha (PPAR), regulates stress resilience and proteostasis downstream of embryo integrity and other pathways that influence lipid homeostasis, and upstream of HSF-1. Disruption of the vitelline layer of the embryo envelope, which activates a proteostasis-enhancing inter-tissue pathway in somatic tissues, also triggers changes in lipid catabolism gene expression that are accompanied by an increase in fat stores. NHR-49 together with its co-activator MDT-15 contributes to this remodeling of lipid metabolism and is also important for the elevated stress resilience mediated by inhibition of the embryonic vitelline layer as well as by other pathways known to change lipid homeostasis, including reduced insulin-like signaling and fasting. Further, we show that increased NHR-49 activity is sufficient to suppress polyglutamine aggregation and improve stress resilience in an HSF-1-dependent manner. Together, our results establish NHR-49 as a key regulator that links lipid homeostasis and cellular resilience to proteotoxic stress.

genetics↗

Formamide significantly enhances the efficiency of chemical adenylation of RNA sequencing ligation adaptors

Pre-adenylated single-stranded DNA ligation adaptors are essential reagents in many next generation RNA sequencing library preparation protocols. These oligonucleotides can be adenylated enzymatically or chemically. Enzymatic adenylation reactions have high yield but are not amendable to scale up. In chemical adenylation, Adenosine 5{square}-phosphorimidazolide (ImpA) reacts with 5' phosphorylated DNA. It is easily scalable but gives poor yields, requiring labor-intensive cleanup steps. Here, we describe an improved chemical adenylation method using 95% formamide as the solvent, which results in the adenylation of oligonucleotides with >90% yield. In standard conditions, with water as the solvent, hydrolysis of the starting material to adenosine monophosphate limits the yields. To our surprise, we find that rather than increasing adenylation yields by decreasing the rate of ImpA hydrolysis, formamide does so by increasing the reaction rate between ImpA and 5'-phosphorylated DNA by [~]10 fold. The method described here enables straightforward preparation of chemically adenylated adapters with higher than 90% yield, simplifying reagent preparation for NGS.

molecular biology↗

Structure of the catalytically active APOBEC3G bound to a DNA oligonucleotide inhibitor reveals tetrahedral geometry of the transition state

APOBEC3 proteins (A3s) are enzymes that catalyze deamination of cytidine to uridine in single-stranded DNA (ssDNA) substrates, thus playing a key role in innate antiviral immunity. However, APOBEC3 family has also been linked to many mutational signatures in cancer cells, which has led to intense interest to develop inhibitors of A3s catalytic activity as therapeutics as well as tools to study A3s biochemistry, structure and cellular function. Recent studies have shown that ssDNA containing 2'-deoxy-zebularine (dZ-ssDNA) is an inhibitor of A3s such as A3A, A3B and A3G, although atomic determinants of this activity remained unknown. To fill this knowledge gap, we determined a 1.5 [A] resolution structure of a dZ-ssDNA inhibitor bound to active A3G. The crystal structure revealed that the activated dZ/H2O mimics the transition state by coordinating the active site Zn2+ and engaging in additional stabilizing interactions, such as the one with the catalytic residues E259. Therefore, this structure allowed us to capture the first snapshot of the A3s transition state, and suggests that developing transition-state mimicking inhibitors may provide a new opportunity to design more targeted molecules for A3s in the future.

biochemistry↗

Chemotherapy Signatures Map Evolution of Therapy-Related Myeloid Neoplasms

Patients treated with cytotoxic therapies, including autologous stem cell transplantation, are at risk for developing therapy-related myeloid neoplasms1, 2. Pre-leukemic clones (i.e., clonal hematopoiesis) are detectable years before the development of these aggressive malignancies3-5, though the genomic events leading to transformation and expansion are not well-defined. Here, leveraging distinctive chemotherapy-associated mutational signatures6-12 from whole-genome sequencing data and targeted sequencing of pre-chemotherapy samples, we reconstruct the evolutionary life-history of 39 therapy-related myeloid malignancies. A dichotomy is revealed, in which neoplasms with evidence of chemotherapy-induced mutagenesis from platinum and melphalan are relatively hypermutated and enriched for complex structural variants (i.e., chromothripsis), while neoplasms with alternative exposures bear a similar profile to de novo acute myeloid leukemia. Using chemotherapy-associated mutational signatures as a temporal barcode in each patients life, we estimate that several complex events and genomic drivers are acquired after chemotherapy exposure. In the case of treatment with high-dose melphalan and autologous stem cell transplantation, we demonstrate that the procedure allows clonal hematopoiesis to escape chemotherapy exposure entirely, and to be reinfused to expand to malignancy. This information reveals a novel mode of malignant progression for therapy-related malignancies that is not reliant on direct mutagenesis or even exposure to chemotherapy, itself, and prompts further investigation into leukemia-permissive effects of cytotoxic drugs.

cancer biology↗