Biology subjects

Lam, V.

Publications and source records attributed to Lam, V..

12 recordsLinked to original sources

bioRxiv2025

Targeting Ogt in ADPKD mitigates metabolic reprogramming and renal cystogenesis, extending survival

Aberrant cell metabolism drives autosomal dominant polycystic kidney disease (ADPKD). O-GlcNAcylation, a metabolically regulated post-translational modification, is elevated in ADPKD kidneys. Using rapidly and slowly progressive ADPKD mouse models, we demonstrate that deleting O-GlcNAc transferase (Ogt) reduces renal cystogenesis and extends survival in a rapidly progressive model from postnatal day 21 to over a year. Pharmacological OGT inhibition similarly reduced cyst formation of patient-derived renal epithelial cells in vitro. In Pkd1 conditional knockout kidneys, Ogt deletion maintained phosphorylated AMPK and mitochondrial respiratory chain complex levels, preserving cellular energy sensing and production. Further, metabolomic analysis revealed normalization of glycolysis and of the hexosamine and hyaluronic acid biosynthesis pathways. In contrast, dysregulation of these pathways in Pkd1 conditional knockout kidneys culminated in increased tricarboxylic acid cycle entry, increased O-GlcNAc, and increased hyaluronic acid in the extracellular matrix, respectively. These findings identify Ogt as a central metabolic regulator and therapeutic target, linking metabolism to intracellular and extracellular mechanisms of cyst formation.

cell biology↗

bioRxiv2025

Early impairment in dentate pattern separation in a rodent model of temporal lobe epilepsy.

The dentate gyrus of the hippocampal formation utilizes sparse neural coding to support memory formation. In temporal lobe epilepsy (TLE), the dentate undergoes extensive restructuring, including loss of local inhibition. It is unknown how circuit changes impact dentate network computations in awake behaving animals. Here we perform high-density tetrode recordings from the dentate in male rats treated with systemic kainic acid (KA) to induce TLE. In KA-treated rats, dentate spatial representations were less precise at the single neuron level, however the stability of the spatial code in representing repeated visits to the same location was retained at the population level. Despite spared spatial representation, the network computations for pattern separation were disrupted. The reorganized dentate network in KA-treated rats generated less distinct population activity patterns for different environments, specifically as a result of impaired rate-remapping. Changes in network computations paralleled impairments in a dentate-dependent memory task, potentially providing a link between altered pattern separation and behavioral discrimination. These deficits were present in animals with confirmed dentate circuit reorganization that had not yet developed spontaneous seizures - suggesting that the dentate network changes underlying altered rate-remapping and impaired dentate-dependent memory occur early in epileptogenesis.

neuroscience↗

bioRxiv2024

Effects of HA1 (a Probucol Analogue) and ApoC3 siRNA on Lipoprotein-Amyloid Metabolism, Neurovascular Integrity and Cognitive Function in db/db Mice

Background and aimsChronically elevated levels of circulating lipoprotein-amyloid-{beta} (A{beta}) are implicated in the disruption of the blood-brain barrier and the initiation of a neurodegenerative cascade leading to Alzheimers disease (AD). Type 2 diabetes is associated with BBB dysfunction, dyslipidaemia, and an increased risk of AD. However, alterations in triglyceride-rich lipoproteins (TRL)-A{beta} homeostasis and its downstream effects on the BBB in a diabetes context remain explored. This study aimed to 1) investigate, in a preclinical model of diabetes, the hypothesis that diabetes-induced impairments in TRL-A{beta} metabolism might compromise BBB integrity and exacerbate cognitive function and behavioural changes, and 2) assess the efficacy of interventions that improve TRL catabolism, including probucol, HA1, and ApoC3 siRNA, to prevent disease progression by lowering circulating TRL-A{beta} levels. MethodsFive-week-old db/db mice underwent a 9- or 23-weeks dietary interventions with probucol, a probucol prodrug HA1, or a standard diet with four-weekly injections of ApoC3 siRNA. Db/+ mice served as negative controls for each treatment duration. Blood levels of A{beta} and ApoB were measured using ELISA. Immunofluorescence imaging was used to quantify enterocytic levels of A{beta} and ApoB, and assess changes in neurovascular integrity (IgG, PDGFR{beta}, ZO1, occludin), neuroinflammation (GFAP, Iba1), and cerebral oxidative stress (8OHdG). ResultsOur results indicate that diabetes increased the abundance of plasma amyloid, specifically A{beta}42, which correlated with enterocytic abundance, suggesting exaggerated postprandial excretion. Disrupted plasma amyloid homeostasis was associated with BBB breakdown, including diminished barrier function, and the loss of pericytes and astrocytes. Provision of the probucol analogue, HA1, normalised plasma and enterocytic amyloidemia concomitant with the preservation of the neurovascular junction. Treatment with ApoC3 siRNA attenuated plasma A{beta}42 and modestly reduced neurovascular inflammation. ConclusionThe findings further support the hypothesis that aberrant peripheral metabolism of lipoprotein-A{beta} is associated with microvascular corruption and the development of anxiety-like behaviour. HA1 is more effective than probucol or ApoC3 siRNA in positively modulating lipoprotein-amyloid homeostasis in db/db mice and maintaining central capillary integrity. HighlightsO_LIEnterocytic and plasma lipoprotein-A{beta} levels are increased in diabetic db/db mice. C_LIO_LIElevated plasma lipoprotein-A{beta} levels correlate with BBB breakdown and anxiety-like behavior. C_LIO_LIHA1 lowers enterocytic and plasma A{beta} levels, protects BBB, alleviates oxidative stress and anxiety. C_LIO_LIApoC3 siRNA lowers plasma lipoprotein-A{beta}, mitigates neuroinflammation and anxiety. C_LI

neuroscience↗

bioRxiv2024

A Self-Supervised Learning Approach for High Throughput and High Content Cell Segmentation

In principle, AI-based algorithms should enable rapid and accurate cell segmentation in high-throughput settings. However, reliance on large datasets, human input, and computational expertise, along with issues of limited generalizability and the necessity for specialized training are notable drawbacks of nominally "automated" segmentation tools. To overcome this roadblock, we introduce an innovative, user-friendly self-supervised learning method (SSL) for pixel classification that requires no dataset-specific modifications or curated labelled data sets, thus providing a more streamlined cell segmentation approach for high-throughput and high-content research. We demonstrate that our algorithm meets the criteria of being fully automated with versatility across various magnifications, optical modalities and cell types. Moreover, our SSL algorithm is capable of identifying complex cellular structures and organelles which are otherwise easily missed, thereby broadening the machine learning applications to high-content imaging. Our SSL technique displayed consistent F1 scores across segmented images, with scores ranging from 0.831 to 0.876, outperforming the popular Cellpose algorithm, which showed greater variance in F1 scores from 0.645 to 0.8815, mainly due to errors in segmentation. On average, our SSL method achieved an F1 score of 0.852 {+/-}0.017, exceeding Cellposes average of 0.804 {+/-}0.08. This novel SSL method not only advances segmentation accuracy but also minimizes the need for extensive computational expertise and data security concerns, making it easier for biological researchers to incorporate automated segmentation into their studies.

bioengineering↗

bioRxiv2024

Structural basis for catalysis and selectivity of phospholipid synthesis by eukaryotic choline-phosphotransferase

Phospholipids are the most abundant component in lipid membranes and are essential for the structural and functional integrity of the cell. In eukaryotic cells, phospholipids are primarily synthesized de novo through the Kennedy pathway that involves multiple enzymatic processes. The terminal reaction is mediated by a group of cytidine-5-diphosphate (CDP)-choline /CDP-ethanolamine-phosphotransferases (CPT/EPT) that use 1,2-diacylglycerol (DAG) and CDP-choline or CDP-ethanolamine to produce phosphatidylcholine (PC) or phosphatidylethanolamine (PE) those are the main phospholipids in eukaryotic cells. Here we present the structure of the yeast CPT1 in multiple substrate-bound states. Structural and functional analysis of these binding-sites reveal the critical residues for the DAG acyl-chain preference and the choline/ethanolamine selectivity. Additionally, we present the structure in complex with a potent inhibitor characterized in this study. The ensemble of structures allows us to propose the reaction mechanism for phospholipid biosynthesis by the family of CDP-alcohol phosphatidyltransferases (CDP-APs).

biochemistry↗

bioRxiv2024

Oncogenic Mutant p53 Sensitizes Non-Small Cell Lung Cancer Cells to Proteasome Inhibition via Oxidative Stress-Dependent Induction of Mitochondrial Apoptosis

Non-small cell lung cancer (NSCLC) cells with oncogenic mutant p53 alleles (Onc-p53) exhibit significantly higher levels of proteasome activity, indicating that Onc-p53 induces proteotoxic stress which may be leveraged as a therapeutic vulnerability. Proteasome inhibitors (PIs), such as bortezomib (BTZ), can induce toxic levels of oxidative stress in cancer cells and thus we investigated whether PIs exhibit preferential cytotoxicity in Onc-p53 NSCLC cells. Indeed, BTZ and other PIs exhibited the IC50 6-7-fold lower in Onc-p53 cells vs. wild-type (WT) p53 cells. BTZ cytotoxic effects in Onc-p53 cells were nearly completely rescued by antioxidants such as N-acetyl cysteine, indicating that oxidative stress is the critical driver of BTZ-dependent cytotoxic effects in Onc-p53 cells. Importantly, we observed oxidative stress-dependent transcriptional induction of the pro-apoptotic NOXA with downstream cleaved caspase-3, consistent with apoptotic cell death in Onc-p53 but not in WT p53 cells treated with BTZ, and BTZ-generated oxidative stress was linked to nuclear translocation of NRF2 and transcriptional activation of ATF3, which in turn was required for NOXA induction. Validating BTZs translational potential in Onc-p53 NSCLC, BTZ and carboplatin or the BH3-mimetic navitoclax were synergistically cytotoxic in Onc-p53 but not WT p53 cells in vitro, and BTZ effectively limited growth of Onc-p53 NSCLC xenografts when combined with either carboplatin or navitoclax in vivo. Our data therefore support further investigation of the therapeutic utility of PIs combined with carboplatin or BH3-mimetics in Onc-p53 human NSCLC as novel therapeutic strategies. SignificanceNon-small cell lung cancer (NSCLC) is the leading cause of cancer death due, in part, to a lack of active therapies in advanced disease. We demonstrate that proteasome inhibitor/BH3-mimetic combination therapy is an active precision therapy in NSCLC cells and tumors expressing oncogenic mutant p53 alleles (Onc-p53).

cancer biology↗

bioRxiv2022

Plasma amyloid-beta homeostasis is associated with Body Mass Index and weight-loss in people with overweight and obesity

BACKGROUNDObesity is linked to a higher incidence of Alzheimers disease (AD). Studies show that plasma amyloid-{beta} (A{beta}) dyshomeostasis, particularly low 42/40 ratio indicates a heightened risk for developing AD. However, the relationship between body mass index (BMI) and circulating plasma A{beta} has not been extensively studied. OBJECTIVEWe hypothesised that people with a high BMI have altered plasma A{beta} homeostasis compared with people with a lower BMI. We also tested whether reducing BMI by calorie-restriction could normalise plasma concentrations of A{beta}. METHODSPlasma concentrations of A{beta}40, A{beta}42 and A{beta}42/40 ratio were measured in 106 participants with BMIs classified as lean, overweight, or obese. From this cohort, twelve participants with overweight or obese BMIs entered a 12-week calorie-restriction weight loss program. We then tested whether decreasing BMI affected plasma A{beta} concentrations. RESULTSPlasma A{beta}42/40 ratio was 17.54% lower in participants with an obese BMI compared to lean participants (p<0.0001), and 11.76% lower compared to participants with an overweight BMI (p<0.0001). The weight loss regimen decreased BMI by an average of 4.02% (p=0.0005) and was associated with a 6.5% decrease in plasma A{beta}40 (p=0.0425). However, weight loss showed negligible correlations with plasma A{beta}40, A{beta}42 and A{beta}42/40 ratio. CONCLUSIONObesity is associated with aberrant plasma A{beta} homeostasis which may be associated with an increased risk for AD. Weight loss appears to lower A{beta}40, but large-scale longitudinal studies in addition to molecular studies are required to elucidate the underlying mechanisms of how obesity and weight loss influence plasma A{beta} homeostasis.

physiology↗

bioRxiv2022

A highly sensitive LC-MS/MS method for quantitative determination of 7 vitamin D metabolites in mouse brain tissue

Despite its critical role in neurodevelopment and brain function, vitamin-D (vit-D) homeostasis, metabolism and kinetics within the central nervous system remain largely undetermined. Thus, it is of critical importance to establish an accurate, highly sensitive and reproducible method to quantitate vit-D in brain tissue. Here, we present a novel liquid chromatography tandem mass spectrometry (LC-MS/MS) method and for the first time, demonstrate detection of seven major vit-D metabolites in brain tissues of C57BL/6J wild-type mice, namely: 1,25(OH)2D3, 3-epi-1,25(OH)2D3, 1,25(OH)2D2, 25(OH)D3, 25(OH)D2, 24,25(OH)2D3, and 24,25(OH)2D2. Chromatographic separation was achieved on a pentaflurophenyol column 3 mM ammonium formate with water/methanol [A] and methanol/isopropanol [B] phases. Detection was by positive-ion electrospray tandem mass spectrometry. We used calibration standards of each metabolite prepared in brain matrices to validate the detection range, precision, accuracy and recovery. Isotopically labelled analogues, 1,25(OH)2D3-d3, 25(OH)D3-C5 and 24,25(OH)2D3-d6, served as the internal standards for the closest molecular related metabolite in all measurements. The calibration range was between 1 fg/mL to 10 ng/mL with an LLOD and LLOQ of 10 fg/mL and 3 fg/mL, respectively. The intra-/inter-day precision and accuracy for measuring brain vit-D metabolites ranged between 0.12-11.53% and 0.28-9.11%, respectively. Recovery ranged between 99.06% and 106.9% for all metabolites. Collectively, the sensitivity and efficiency of our method supersedes previously reported protocols used to measure vit-D and to our knowledge, the first protocol to reveal the abundance of 25(OH)D2, 1,25(OH)D2 and 24,25(OH)2D2, in brain tissue of any species. This technique may be important in supporting the future advancement of pre-clinical research into the function of vit-D in neurophysiological, neuropsychiatric, and neurodegeneration.

physiology↗

bioRxiv2021

The effects of chronic consumption of lipid-rich and delipidated bovine dairy milk on brown adipose tissue volume in wild-type mice

Brown adipose tissue (BAT) activation is associated with increased energy expenditure by inducing non-shivering thermogenesis. Ingestion of a milk fat globule membrane (MFGM) supplement and a high calorie diet are reported gateways into BAT activation. However, little is known about the effect of MFGM and high calorie diets on BAT volume. To gain insight into this, mice were maintained on a high fat (HF) or low-fat (LF) diet in conjunction with either full-cream (FC) or skim bovine dairy milk (BDM). After being maintained on their respective diets for 13 weeks, body composition, including BAT volume, was measured using X-ray microtomography. A high calorie diet resulted in an increase in BAT volume and mice consuming a HF diet in conjunction with FC BDM had significantly greater BAT volume than all other groups. Conversely, mice consuming a HF diet in addition to skim milk had lower BAT volume compared to the HF control. The data presented suggests that consumption of a high calorie diet in conjunction with FC BDM increases BAT volume in wild-type mice. This study may provide valuable insight into future studies investigating BAT volume and BAT activity in relation to environmental factors including diet.

physiology↗

bioRxiv2021

Targeted, collaborative biodiversity conservation in the global ocean can benefit fisheries economies

Marine protected areas (MPAs) are key to averting continued loss of species and ecosystem services in our oceans, but concerns around economic trade-offs hamper progress. Here we provide optimized planning scenarios for global MPA networks that secure species habitat while minimizing impacts on fisheries revenues. We found that MPA coverage requirements differ vastly among nations, and that two-thirds of nations benefit economically from a collaborative approach. Immediate global protection of marine biodiversity habitat comes with losses of ~19% of total fisheries revenues, but international cooperation in concert with high seas protection improves economic losses for most countries, safeguards all species, and could save ~5B USD annually worldwide. Nations and fishery economies both share benefits from a coordinated approach to conserving marine biodiversity, with direct relevance to current international policies.

ecology↗

bioRxiv2021

A modular platform for engineering function ofnatural and synthetic biomolecular condensates

Phase separation is emerging as a universal principle for how cells use dynamic subcompartmentalization to organize biochemical reactions in time and space1,2. Yet, whether the emergent physical properties of these biomolecular condensates are important for their biological function remains unclear. The intrinsically disordered protein PopZ forms membraneless condensates at the poles of the bacterium Caulobacter crescentus and selectively sequesters kinase-signaling cascades to regulate asymmetric cell division3-5. By dissecting the molecular grammar underlying PopZ phase separation, we find that unlike many eukaryotic examples, where unstructured regions drive condensation6,7, a structured domain of PopZ drives condensation, while conserved repulsive features of the disordered region modulate material properties. By generating rationally designed PopZ mutants, we find that the exact material properties of PopZ condensates directly determine cellular fitness, providing direct evidence for the physiological importance of the emergent properties of biomolecular condensates. Our work codifies a clear set of design principles illuminating how sequence variation in a disordered domain alters the function of a widely conserved bacterial condensate. We used these insights to repurpose PopZ as a modular platform for generating synthetic condensates of tunable function in human cells.

cell biology↗

bioRxiv2020

Keratin 19 maintains E-cadherin localization at the cell surface and stabilizes cell-cell adhesion of MCF7 cells

A cytoskeletal protein keratin 19 (K19) is highly expressed in breast cancer but its effects on breast cancer cell mechanics are unclear. Using KRT19 knockout (KO) cells and cells where K19 expression was rescued, we found that K19 is required to maintain rounded epithelial-like shape and tight cell-cell adhesion of MCF7 cells. A loss of K19 resulted in a lower level of plakoglobin and internalization of E-cadherin in early and recycling endosomes. Inhibiting internalization restored cell-cell adhesion of KRT19 KO cells, suggesting E-cadherin internalization contributes to defective adhesion. Ultimately, while K19 inhibited cell migration, it was required for cells to form colonies in suspension. Our results suggest that K19 stabilizes E-cadherin complexes at the cell membrane to maintain cell-cell adhesion which inhibits cell migration but provides growth and survival advantages for circulating tumor cells. These findings provide context-dependent roles of K19 during metastasis.

cell biology↗