Biology subjects

Ngo, S.

Publications and source records attributed to Ngo, S..

11 recordsLinked to original sources

bioRxiv2026

The ABC-F protein Uup, Rescues Stalled Ribosomal Termination Complexes to Modulate DNA Maintenance

The cytosolic ATP-binding cassette F (ABC-F) family modulates ribosomal activity in eukaryotes and prokaryotes. Although they all bind to the E site of the ribosome, some bacterial ABC-Fs confer resistance to ribosome-targeting antibiotics, while housekeeping members have poorly defined roles. Interestingly, in Escherichia coli, which possesses four ABC-F (EttA, Uup, YbiT and YheS), Uup has been rather implicated in DNA recombination. Using an unbiased approach, we reconcile this apparent discrepancy by showing that Uup's involvement in DNA recombination is indirect and is dictated by Uup-mediated regulation of the last steps of translation that rescues problematic translation of genes involved in DNA maintenance such as ssb and dnaX. Accordingly, the elongated cell phenotype observed in uup deletion background is reverted by expressing a ssb variant that no longer depends on Uup. Unlike its paralog EttA, which helps ribosomes in translating proteins with repeats of negatively charged residues in the N-terminal 30 amino acids, Uup instead facilitates the rescue of stalled translation termination events that, in its absence, are handled by the tmRNA pathway.

microbiology↗

bioRxiv2026

Schwann Cell-Specific TDP-43 Rescue Improves Peripheral Nerve Myelin Pathology Without Altering Motor Behaviour in a Mouse Model of ALS

Amyotrophic lateral sclerosis (ALS) is a terminal disease caused by motor neuron loss. Schwann cells, the myelinating cells of the peripheral nervous system, metabolically and structurally support neurons. ALS patients exhibit Schwann cell pathology, such as TDP-43 proteinopathy, therefore Schwann cell dysfunction may contribute to disease progression. Here, we have characterised myelinating Schwann cell pathology in a TDP-43Q331K (TDP-43) transgenic mouse model of ALS. We also crossed the floxxed TDP-43 mouse with a myelin protein zero (P0)-cre mouse to excise the transgene from Schwann cells alone (P0-cre/TDP-43) to assess rescue. Compared to wild-type (WT) littermates, 10 mo TDP-43 mice exhibited changes to myelin architecture, including loss of myelin binding proteins at the paranodes, decreased node of Ranvier length, and non-compact, degenerating myelin. In P0-cre/TDP-43 mice these myelin disruptions were rescued. However, this improved histology did not lead to a functional rescue, with both P0-cre/TDP-43 and TDP-43 mice exhibiting slowed sciatic nerve conduction and worsened motor behaviour. Further histological analyses revealed that Bungner Schwann cells, a subtype of Schwann cells triggered by neuronal injury, were activated in both TDP-43 and P0-cre/TDP-43 mice. Activation of Bungner Schwann cells can trigger damaging inflammation through the recruitment of macrophages, which can hinder motor and electrophysiological performance, potentially underpinning the lack of functional rescue in the P0-cre/TDP-43. We established that the rescue of Schwann cells indeed protects myelin in this ALS model, however understanding how Bungner Schwann cells exacerbate neuronal pathology is essential for developing effective therapeutics that can improve functional output. Significance StatementAmyotrophic lateral sclerosis (ALS) is a fatal neurodegenerative disease with no cure and limited treatments. Given that the average patient life expectancy is 3-5 years following diagnosis, finding novel treatment targets is of the utmost importance. Recent research has revealed that non-neuronal cells, such as Schwann cells, contribute to the disease, however the extent of their pathology remains elusive. Investigating Schwann cell and peripheral myelin pathology in ALS may lead to the identification of previously unrecognized disease mechanisms, opening novel avenues for therapeutic development. Identifying approaches through which to target glial and neuronal pathology concurrently would enable more holistic treatment of the various aspects of ALS pathobiology to improve patient outcomes.

neuroscience↗

bioRxiv2026

Systematic benchmarking of multi-modal approaches for tumor-naive ctDNA detection and quantification

Longitudinal monitoring of circulating tumor DNA (ctDNA) has emerged as a promising framework for characterizing treatment response dynamics in cancer. Scalable tumor-naive approaches for quantifying ctDNA often involve whole-genome sequencing (WGS) or DNA methylation profiling, but their comparative performance and capacity for complementary integration remain poorly understood. Here we systematically benchmarked tumor-naive WGS- and methylation-based ctDNA quantification methods using plasma from 150 patients with colorectal, lung and breast cancer. Using paired high-depth WGS and EM-seq data, we generated 40,000 in silico samples and evaluated detection accuracy, limits of detection (LoD) and quantification (LoQ) across cancer types and sequencing depths (0.1x-30x). We further assessed single- and multimodal method combinations, identifying conditions under which integrated approaches enhance analytical performance for detection and quantification relative to single modalities. This benchmark delineates key performance trade-offs and provides a practical framework to support method development and guide future research applications in ctDNA-based biomarker studies.

bioinformatics↗

bioRxiv2024

Base composition at the start of the coding sequence controls the balance between translation initiation and mRNA degradation in E. coli .

Protein synthesis efficiency is highly dependent on the mRNA coding sequence. Furthermore, there is extensive evidence of a correlation between mRNA stability and protein expression level, though the mechanistic determinants remain unclear. Using yellow fluorescent protein (YFP) as a reporter gene, we herein demonstrate that adenosine (A) abundance in the first six codons is a critical determinant for achieving high protein synthesis in E. coli. Increasing A and/or decreasing guanosine (G) content in this region with synonymous codons results in substantial increases in protein expression level both in vivo and in vitro that are correlated with steady-state mRNA concentration in vivo. The change in mRNA concentration is attributable to changes in the stability of the mRNA that are directly coupled to its translation efficiency. Increasing A content promotes mRNA incorporation into the functional 70S ribosomal initiation complex without altering its affinity for the 30S ribosomal subunit. These results support a model in which base composition in the first six codons modulates local mRNA folding energy and single-strandedness to control the balance between productive translation initiation versus degradation of mRNAs bound to the 30S ribosomal subunit. Based on these findings, we developed a short N-terminal coding sequence that optimizes translation initiation efficiency for protein production in E. coli.

microbiology↗

bioRxiv2023

Global regulation via modulation of ribosome pausing by EttA

Having multiple rounds of translation of the same mRNA creates dynamic complexities along with opportunities for regulation related to ribosome pausing and stalling at specific sequences. Yet, mechanisms controlling these critical processes and the principles guiding their evolution remain poorly understood. Through genetic, genomic, physiological, and biochemical approaches, we demonstrate that regulating ribosome pausing at specific amino acid sequences can produce [~]2-fold changes in protein expression levels which strongly influence cell growth and therefore evolutionary fitness. We demonstrate, both in vivo and in vitro, that the ABC-F protein EttA directly controls the translation of mRNAs coding for a subset of enzymes in the tricarboxylic acid (TCA) cycle and its glyoxylate shunt, which modulates growth in some chemical environments. EttA also modulates expression of specific proteins involved in metabolically related physiological and stress-response pathways. These regulatory activities are mediated by EttA rescuing ribosomes paused at specific patterns of negatively charged residues within the first 30 amino acids of nascent proteins. We thus establish a unique global regulatory paradigm based on sequence-specific modulation of translational pausing.

microbiology↗

bioRxiv2023

Arylamine N-acetyltransferase-1 reveals a subpopulation of ALS patients with altered metabolic capacity

Amyotrophic lateral sclerosis (ALS) is a heterogeneous disease characterised by metabolic changes at onset and throughout disease progression. Here, we investigate the role of arylamine N-acetyltransferase 1 (NAT1), a cytosolic protein associated with mitochondrial function, in ALS. We demonstrate that expression of the murine homolog (mNat2) increases in skeletal muscle of SODG93A mice, but not control animals, at onset of symptoms and remains elevated until end stage of the disease. Measurement of mitochondrial respiration in peripheral blood mononuclear cells of patients with ALS identified patient sub-populations with low and high metabolic potential, which was strongly associated with NAT1 activity. Those patients with high NAT1 activity had elevated basal respiration, ATP production, mitochondrial reserve, and aerobic glycolysis. NAT1 predicted increased whole body metabolic index, which may be clinically significant as these patients show increased functional decline and shorter survival. NAT1 may be a novel target in those patients with elevated activity.

biochemistry↗

bioRxiv2022

IL-33-induced neutrophilic inflammation and NETosis underlie rhinovirus-triggered exacerbations of asthma

Rhinovirus-induced neutrophil extracellular traps (NETs) contribute to acute asthma exacerbations, however the molecular factors that trigger NETosis in this context remain ill-defined. Here, we sought to implicate a role for IL-33, an epithelial cell-derived alarmin rapidly released in response to infection. In mice with chronic experimental asthma (CEA), but not naive controls, rhinovirus inoculation induced an early (1 day post infection; dpi) inflammatory response dominated by neutrophils, neutrophil-associated cytokines (IL-1, IL-1{beta}, CXCL1) and NETosis, followed by a later, type-2 inflammatory phase (3-7 dpi), characterized by eosinophils, elevated IL-4 levels, and goblet cell hyperplasia. Notably, both phases were ablated by HpARI (Heligmosomoides polygyrus Alarmin Release Inhibitor), which blocks IL-33 release and signalling. Instillation of exogenous IL-33 recapitulated the rhinovirus-induced early phase, including the increased presence of NETs in the airway mucosa, in a PAD4-dependent manner. Ex vivo IL-33-stimulated neutrophils from mice with CEA, but not naive mice, underwent NETosis, and produced greater amounts of IL-1/{beta}, IL-4, and IL-5. In nasal samples from rhinovirus-infected people with asthma, but not healthy controls, IL-33 levels correlated with neutrophil elastase and dsDNA. Our findings suggest that IL-33 blockade ameliorates the severity of an asthma exacerbation by attenuating neutrophil recruitment and the downstream generation of NETs.

immunology↗

bioRxiv2022

Profound lipid dysregulation in mutant TDP-43 mice is ameliorated by the glucocerebrosidase 2 inhibitor ambroxol

The importance of dyslipidemia in amyotrophic lateral sclerosis (ALS) patients is increasingly recognised as a potential key mechanism driving disease onset, progression and survival. Evidence in familial ALS models suggests that lipid composition is significantly affected, however clinically relevant models have yet to be investigated. Using a powerful lipidomic approach, we uncover significant dysregulation of glycosphingolipid (GSL) metabolism in both the spinal cord and skeletal muscles of transgenic TDP-43Q331K mice. Treatment with the selective glucocerebrosidase 2 (GBA2) inhibitor ambroxol at symptom onset significantly improved motor and gait functions in TDP-43Q331K mice. Ambroxol treatment preserved motor neurons and neuromuscular junctions which was associated with modulation of GSL metabolism. Our study establishes significant lipid dysregulation in a clinically relevant model of ALS. Importantly, we show positive therapeutic outcomes in a mouse model of TDP-43 proteinopathy, suggesting that ambroxol may be a promising candidate to treat underlying dyslipidemia and symptoms of ALS.

neuroscience↗

bioRxiv2021

Regulation and mechanistic basis of macrolide resistance by the ABC-F ATPase MsrD

Antibiotic resistance ABC-Fs (ARE ABC-Fs) are translation factors currently proliferating among human pathogens that provide resistance against clinically important ribosome-targeting antibiotics. Here, we combine genetic and structural approaches to determine the regulation of streptococcal ARE ABC-F gene msrD in response to macrolide exposure and also demonstrate that MsrD twin-ATPase sites work asymmetrically to mediate the dynamic of MsrD interaction with the ribosome. We show that cladinose-containing macrolides lead to insertion of MsrDL leader peptide into an undocumented conserved crevice of the ribosomal exit tunnel concomitantly with 23S rRNA rearrangements that prevent peptide bond formation and preclude accommodation of release factors. The stalled ribosome obstructs formation of a Rho-independent terminator which prevents msrD transcriptional attenuation. This stalled ribosome is rescued by MsrD, but not by MsrD mutants which do not provide antibiotic resistance, showing evidence of equivalence between MsrD function in antibiotic resistance and its action on this complex.

microbiology↗

bioRxiv2019

Tumor establishment requires tumor autonomous and non autonomous decoupling of EGF signaling from apoptosis

SummaryIn healthy adult organs, robust feedback mechanisms control cell turnover to enforce homeostatic equilibrium between cell division and death [1, 2]. Nascent tumors must subvert these mechanisms to achieve cancerous overgrowth [3-7]. Elucidating the nature of this subversion can reveal how cancers become established and may suggest strategies to prevent tumor progression. In adult Drosophila intestine, a well-studied model of homeostatic cell turnover, the linchpin of cell equilibrium is feedback control of the EGF protease Rhomboid (Rho). Expression of Rho in apoptotic cells enables them to secrete EGFs, which stimulate nearby stem cells to undergo replacement divisions [8]. As in mammals, loss of adenomatous polyposis coli (APC) causes Drosophila intestinal stem cells to form adenomas [9]. Here we demonstrate that Drosophila APC-/- tumors trigger widespread Rho expression in non-apoptotic cells, resulting in chronic EGF signaling. Initially, nascent APC-/- tumors induce rho in neighbor wild-type cells via acute, non-autonomous activation of JNK. During later growth and multilayering, APC-/- tumors induce rho in tumor cells by autonomous downregulation of E-cadherin (E-cad) and consequent activity of p120-catenin. This sequential dysregulation of tumor non-autonomous and -autonomous EGF signaling converts tissue-level feedback into feed-forward activation that drives cancerous overgrowth. Since Rho, EGFR, and E-cad are associated with colorectal cancer in humans [10-17], our findings may shed light on how human colorectal tumors progress.

developmental biology↗

bioRxiv2017

Feedback regulation of steady-state epithelial turnover and organ size

Epithelial organs undergo steady-state turnover throughout adult life, with old cells being continually replaced by the progeny of stem cell divisions1. To avoid hyperplasia or atrophy, organ turnover demands strict equilibration of cell production and loss2-4. However, the mechanistic basis of this equilibrium is unknown. Using the adult Drosophila intestine5, we find that robustly precise turnover arises through a coupling mechanism in which enterocyte apoptosis breaks feedback inhibition of stem cell divisions. Healthy enterocytes inhibit stem cell division through E-cadherin, which prevents secretion of mitogenic EGFs by repressing transcription of the EGF maturation factor rhomboid. Individual apoptotic enterocytes promote divisions by loss of E-cadherin, which releases cadherin-associated {beta}-catenin/Armadillo and p120-catenin to induce rhomboid. Induction of rhomboid in the dying enterocyte triggers EGFR activation in stem cells within a discrete radius. When we block apoptosis, E-cadherin-controlled feedback suppresses divisions, and the organ retains the same number of cells. When we disrupt feedback, apoptosis and divisions are uncoupled, and the organ develops either hyperplasia or atrophy. Altogether, our work demonstrates that robust cellular balance hinges on the obligate coupling of divisions to apoptosis, which limits the proliferative potential of a stem cell to the precise time and place that a replacement cell is needed. In this manner, localized cell-cell communication gives rise to tissue-level homeostatic equilibrium and constant organ size.

developmental biology↗