Biology subjects

Le, T.

Publications and source records attributed to Le, T..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Association between high-frequency hearing sensitivity and visual cross-modal plasticity in typical-hearing adults

Visual cross-modal plasticity after deafness describes when auditory cortical regions increase responsiveness to visual stimulation. Such neuroplasticity demonstrates that sensory cortex adapts to profound peripheral impairment by upregulating healthy sensory function. However, whether cross-modal plasticity occurs for mild, partial hearing loss is less clear. Here we investigated cross-modal plasticity in "normal" hearing adults who had varying high-frequency hearing sensitivity, and if cross-modal plasticity was linked to adaptive visual behaviours. Twenty-five participants (aged 18 to 78) were tested in a modified Sternberg task with text-based visual words. Participants viewed a five-word sentence presented word-by-word during an encoding period and were asked to hold those words in short-term memory during a retention period. After, they reported if a target word probe was present in the encoding period. Multichannel EEG recorded visual cortical activity throughout. Results showed separate effects of high-frequency hearing sensitivity and age on visual cortical responses. At scalp sensors, visual N1 amplitudes were larger with worse hearing sensitivity, and P2 latencies were longer. In contrast, age was associated with shorter P2 latencies. Source analysis found that N1 amplitude increased with worse hearing sensitivity in right auditory cortex, but no effects were found in visual cortex, or for age. Hearing sensitivity and visual encoding activity did not correlate with behavioural performance or neural oscillations during the retention period. Results suggest for the first time that even a slight hearing decline in the high-frequency range is associated with higher visual activation of right auditory cortex, consistent with cross-modal plasticity.

neuroscience↗

bioRxiv2024

Phosphatidylethanolamine is a phagocytic ligand implicated in the binding and removal of microbial extracellular vesicles

The efficient recognition and removal of apoptotic cells by phagocytes is critical to prevent secondary necrosis and maintain tissue homeostasis. Such detection involves receptors and bridging molecules that recognize lipids -normally restricted to the inner leaflet of healthy cells- which become exposed on the surface of dead cells and the vesicles they produce. A majority of studies focus on phosphatidylserine (PS) for which there are well-established receptors that either bind to the lipid directly or indirectly via intermediary proteins. Phosphatidylethanolamine (PE) is even more prevalent than PS in the inner leaflet of mammalian cells and also becomes exposed by the action of scramblases during cell death, though little is known about the effects of PE once scrambled. Here, we report that PE can itself serve as a phagocytic ligand for macrophages by engaging CD300 family receptors. CD300a and CD300b specifically modulated PE-mediated uptake, and this process involved ITAM-containing adaptors and the spleen tyrosine kinase (Syk). For bacteria, which contain PE but largely lack PS in their membranes, we report that PE engagement enabled the binding and uptake of spheroplasts and extracellular vesicles (EVs) that were unsheathed by the cell wall. The inflammatory responses of macrophages to PE particles containing LPS was also curtailed by CD300a expression. Based on these observations, we posit that the direct recognition of PE facilitates mechanisms of clearance that stand to have a broad impact on the immune response.

cell biology↗

bioRxiv2024

Mutations of schizophrenia risk gene SETD1A dysregulate synaptic function in human neurons

Schizophrenia (SCZ) is a complex neuropsychiatric disorder associated with both common risk variants of small effect sizes and rare risk variants of high penetrance. Rare protein truncating variants (PTVs) in SETD1A (SET Domain Containing 1A) show a strong association with SCZ; however, it remains largely unclear how rare PTVs in SETD1A contribute to the pathophysiology of SCZ. To understand the impact of SETD1A rare PTVs in human neurons, we CRISPR/Cas9-engineered five isogenic pairs of human induced pluripotent stem cells (iPSCs), with a recurrent heterozygous patient-specific PTV mutation c.4582-2delAG in two donor lines and a heterozygous frameshift mutation c.4596_4597insG (p. Leu1533fs) in three donor lines. These two mutations are predicted to cause a premature stop codon in exon 16 of SETD1A, leading to the loss of the conserved SET domain that is critical for its histone methyltransferase activity. We found that these presumably loss-of-function (LoF) mutations caused the SETD1A mRNAs to be degraded by nonsense-mediated decay (NMD), accompanied by a reduction of full-length SETD1A protein level in iPSCs. We then characterized the morphological, electrophysiological, and transcriptomic impacts of the SETD1A+/- LoF mutations in iPSC-derived human excitatory neurons induced by NGN2. We found that the SETD1A+/- exon-16 LoF mutations altered dendrite complexity, dysregulated synaptic transmission, and synaptic plasticity, likely by dysregulating genes involved in synaptic function. These results provide mechanistic insights into how SETD1A+/-exon-16 patient-specific LoF mutations affect neuron phenotypes that may be relevant to the pathophysiology of SCZ.

neuroscience↗

bioRxiv2024

Dissecting autonomous enzyme variability in single cells

Metabolic enzymes perform life-sustaining functions in various cellular compartments. Anecdotally, metabolic activity is observed to vary between genetically identical cells, which impacts drug resistance, differentiation, and immune cell activation. However, no large-scale resource systematically reporting metabolic cellular heterogeneity exists. Here, we leverage imaging-based single-cell spatial proteomics to reveal the extent of non-genetic variability of the human enzymatic proteome, as a proxy for metabolic states. Nearly two fifths of enzymes exhibit cell-to-cell variable expression, and half localize to multiple cellular compartments. Metabolic heterogeneity arises largely autonomously of cell cycling, and individual cells reestablish these myriad metabolic phenotypes over several cell divisions. Multiplexed imaging revealed that metabolic states are continuous and that the correlation between metabolic pathways is metabolic state dependent. These results establish cell-to-cell enzymatic heterogeneity as an organizing principle of cell biology that may rewire our understanding of drug resistance, treatment design, and other aspects of medicine.

cell biology↗

bioRxiv2024

An orbitocortical-thalamic circuit suppresses binge alcohol-drinking.

Alcohol consumption remains a significant global health challenge, causing millions of direct and indirect deaths annually. Intriguingly, recent work has highlighted the prefrontal cortex, a major brain area that regulates inhibitory control of behaviors, whose activity becomes dysregulated upon alcohol abuse. However, whether an endogenous mechanism exists within this brain area that limits alcohol consumption is unknown. Here we identify a discrete GABAergic neuronal ensemble in the medial orbitofrontal cortex (mOFC) that is selectively recruited during binge alcohol-drinking and intoxication. Upon alcohol intoxication, this neuronal ensemble suppresses binge drinking behavior. Optogenetically silencing of this population, or its ablation, results in uncontrolled binge alcohol consumption. We find that this neuronal ensemble is specific to alcohol and is not recruited by other rewarding substances. We further show, using brain-wide analysis, that this neuronal ensemble projects widely, and that its projections specifically to the mediodorsal thalamus are responsible for regulating binge alcohol drinking. Together, these results identify a brain circuit in the mOFC that serves to protect against binge drinking by halting alcohol intake. These results provide valuable insights into the complex nature of alcohol abuse and offers potential avenues for the development of mOFC neuronal ensemble-targeted interventions.

neuroscience↗

bioRxiv2024

High-Resolution In Silico Painting with Generative Models

Label-free organelle prediction presents a longstanding challenge in cellular imaging, given the promise to to circumvent the numerous drawbacks associated with fluorescent microscopy, including its high costs, cytotoxicity, and time-consuming nature. Recent advancements in deep learning have introduced numerous effective algorithms, primarily deterministic, for predicting fluorescent patterns from transmitted light microscopy images. However, existing models frequently suffer from poor performance or are limited to specific datasets, image modalities, and magnifications, thus lacking a universal solution. In this paper, we present a simplified VQGAN training scheme that is easily adapted with different input/output channels for image-to-image translation tasks. We applied the algorithm to generate multi-channel organelle staining outputs from bright field inputs, equivalent to the popular Cell Painting assay. The same algorithm also participated and placed first in the ISBI 2024 Light My Cell challenge.

bioengineering↗

bioRxiv2024

SCAPE-APA: a package for estimating alternative polyadenylation events from scRNA-seq data

SummarySCAPE is a package we previously developed to estimate alternative polyadenylation events from single cell RNA-seq (scRNA-seq) data, which is composed of ad-hoc python scripts and has speed issues when handling large scRNA-seq data. To suit the needs of analyzing large scRNA-seq datasets, we present SCAPE-APA, which is a re-implementation of SCAPE with substantial changes. We made the following updates to the package (1) we binned similar reads together to accelerate the estimation (2) we re-derived the mixture model to tailor it for binned reads (3) we implemented the inference algorithm using Taichi language for acceleration (4) we re-implemented the untranslated region (UTR) annotation extraction script using the professional package gffutils for better maintenance (5) we wrote a script to detect spurious alternative polyadenylation sites generated due to junction reads and (6) we made a formal python package and uploaded it to the Python Package Index website (Pypi). Availability and ImplementationScape-apa is freely available at https://github.com/chengl7-lab/scape and can be easily installed using pip. Contactlu.cheng.ac@gmail.com

bioinformatics↗

bioRxiv2023

Identifying cooperative genes causing cancer progression with dynamic causal inference

Cancer progression is driven by complex gene interactions, which are not fully understood due to the dynamic and multifaceted nature of the disease. Traditional methods for identifying genes driving cancer typically focus on detecting mutational events, often neglecting other genetic alterations and the temporal dynamics of the cancer development. This study introduces a novel approach that expands our understanding of cancer by identifying cooperative networks of cancer drivers through dynamic causal inference, complementing classical mutation-based methods. We developed a data-driven causal inference method that integrates a temporal dimension to gene expression data through pseudotime analysis. By modelling cancer progression as a dynamic system, the method evaluates gene interactions and their causal relationships using causal kinetic models (CKMs). This approach enables detecting cancer driver genes regardless of their mutational status. The approach was applied to both single cell and bulk sequencing datasets of breast cancer to identify and rank cancer driver genes based on their stability on the causal model. The proposed method effectively identifies and ranks cancer driver genes by considering their dynamic interactions during cancer progression. It systematically identified cancer driver genes in both categories: those with single nucleotide variants (SNVs) and those with other alterations. The method demonstrated a significant overlap with known cancer driver genes from the Cancer Gene Census, validating its effectiveness. Additionally, the method uncovered novel driver genes that act cooperatively to influence cancer development, offering a more comprehensive view of the genetic mechanisms underlying cancer. Our approach, along with the scripts for the experiments and datasets used, can be found at https://github.com/AndresMCB/DynamicCancerDriverKM

bioinformatics↗

bioRxiv2023

A single-cell atlas of pig gastrulation as a resource for comparative embryology

Early mammalian gastrulations cell-fate decisions are poorly understood due to difficulties obtaining non-rodent embryos. The bilaminar disc of pig embryos mirrors humans, making them a useful proxy for studying gastrulation. Here we present a single-cell transcriptomic atlas of pig gastrulation, revealing cell-fate emergence dynamics, as well as conserved and divergent gene programs governing early porcine, primate, and murine development. We highlight heterochronicity in extraembryonic cell-type development, despite the broad conservation of cell-type-specific transcriptional programs. We apply these findings in combination with functional investigations, to outline conserved spatial, molecular, and temporal events during definitive endoderm (DE). We find early FOXA2+/TBXT-embryonic disc cells directly from DE, contrasting later-emerging FOXA2/TBXT+ node/notochord progenitors. Unlike mesoderm, none of these progenitors undergo epithelial-to-mesenchymal transition. DE/Node fate hinges on balanced WNT and hypoblast-derived NODAL, which is extinguished upon DE differentiation. These findings emphasise the interplay between temporal and topological signalling in early fate decisions during gastrulation.

developmental biology↗

bioRxiv2023

Regulation of Oocyte Meiotic Maturation: Unraveling the Interplay between PKA Inhibition and Cdk1 Activation

Oocyte meiosis is arrested at the first prophase stage, until hormonal stimulation triggers progression into the meiotic divisions. This process, called meiotic maturation, depends on extensive post-transcriptional events. In all vertebrates, two bottleneck events orchestrate meiosis resumption: first, the inhibition of PKA and, second, the activation of Cdk1, the master regulator of eukaryotic cell division. However, the molecular events occurring between these two steps are almost unknown. To address this issue, we took advantage of a Cdk1 inhibitor to identify the early events that depend on PKA downregulation and occur independently of Cdk1 activity. Unexpectedly, we show that accumulation of Cyclin B1 and Mos, the kinase responsible for MAPK activation in oocytes, are regulated in an opposing manner by a two-step mechanism. PKA downregulation induces first the accumulation of Cyclin B1 without any increase of its translation, independently of Cdk1 activation. Subsequently, the rate of Cyclin B1 translation increases in response to Cdk1 activation. In contrast, Mos translation begins downstream PKA inhibition, but the protein does not accumulate until Cdk1 is activated. These intertwined regulations create the positive feedback loops required for the full activation of Cdk1. Additionally, we show that two consecutive waves of translation occur during the G2-M transition, the first induced by PKA inhibition and the second by Cdk1 activation. Finally, we demonstrate that Arpp19, the only known early substrate of PKA in Xenopus oocytes, is not involved in the control of these early events. This study reveals that PKA downregulation promotes multiple molecular pathways that converge on the activation of Cdk1 to induce the G2/M transition in vertebrate oocytes.

cell biology↗

bioRxiv2023

Endothelial TMEM16F lipid scramblase regulates angiogenesis

Dynamic loss of lipid asymmetry through the activation of TMEM16 Ca2+-activated lipid scramblases (CaPLSases) has been increasingly recognized as an essential membrane event in a wide range of physiological and pathological processes, including blood coagulation, microparticle release, bone development, pain sensation, cell-cell fusion, and viral infection. Despite the recent implications of TMEM16F CaPLSase in vascular development and endothelial cell-mediated coagulation, its signaling role in endothelial biology remains to be established. Here, we show that endothelial TMEM16F regulates in vitro and in vivo angiogenesis through intracellular signaling. Developmental retinal angiogenesis is significantly impaired in TMEM16F deficient mice, as evidenced by fewer vascular loops and larger loop areas. Consistent with our in vivo observation, TMEM16F siRNA knockdown in human umbilical vein endothelial cells compromises angiogenesis in vitro. We further discovered that TMEM16F knockdown enhances VE-cadherin phosphorylation and reduces its expression. Moreover, TMEM16F knockdown also promotes Src kinase phosphorylation at tyrosine 416, which may be responsible for downregulating VE-cadherin expression. Our study thus uncovers a new biological function of TMEM16F in angiogenesis and provides a potential mechanism for how the CaPLSase regulates angiogenesis through intracellular signaling.

physiology↗

bioRxiv2023

Cross-species analysis of ARPP19 phosphorylation during oocyte meiotic maturation charts the emergence of a new cAMP-dependent role in vertebrates

In many animal species, elevated cAMP-PKA signaling initiates oocyte meiotic maturation upon hormonal stimulation, whereas in vertebrates, it acts as a negative regulator of this process. To address this "cAMP paradox", we have focused on ARPP19 proteins. Dephosphorylation of Xenopus ARPP19 on a specific PKA site has been identified as a key step in initiating oocyte maturation. We first tracked evolution of the ARPP19 PKA phosphorylation site, revealing that it appeared early during the emergence of metazoans. This contrasts with strong conservation across eukaryotes of a phosphorylation site for the kinase Gwl in ARPP19 proteins, able to transform them into potent PP2A-B55 inhibitors and thus promote M-phase entry. We then compared the phosphorylation and function of Xenopus ARPP19 with its orthologue from the jellyfish Clytia, a model species showing cAMP-induced oocyte maturation. We confirmed that Clytia ARPP19 is phosphorylated on the conserved Gwl site in vitro as well as in maturing Xenopus and Clytia oocytes, behaving as a PP2A inhibitor and contributing to Cdk1 activation. However, Gwl-phosphorylated ARPP19 was unable to initiate oocyte maturation in Clytia, suggesting the presence of additional locks released by hormonal stimulation. Clytia ARPP19 was in vitro phosphorylated by PKA uniquely on the predicted site, but it was a much poorer substrate of PKA and of its antagonizing phosphatase, PP2A-B55{delta}, than the Xenopus protein. Correspondingly, PKA-phosphomimetic Clytia ARPP19 had a much weaker inhibitory activity on meiosis resumption in Xenopus oocytes than its Xenopus counterpart. Hence, poor recognition of Clytia ARPP19 by PKA and the absence of its targets in Clytia oocytes account for the cAMP paradox. This cross-species study of ARPP19 illustrates how initiation of oocyte maturation has complexified during animal evolution, and provides further insight into its biochemical regulation.

evolutionary biology↗

bioRxiv2023

Impact of pathogen genetics on clinical phenotypes in a population of Talaromyces marneffei from Vietnam

Talaromycosis, a severe and invasive fungal infection caused by Talaromyces marneffei, is difficult to treat and impacts those living in endemic regions of southeast Asia, India, and China. While 30% of infections result in mortality, our understanding of the genetic basis of pathogenesis for this fungus is limited. To address this, we apply population genomics and genome wide association study approaches to a cohort of 336 T. marneffei isolates collected from patients who enrolled in the Itraconazole versus Amphotericin B for Talaromycosis (IVAP) trial in Vietnam. We find that isolates from northern and southern Vietnam form two distinct geographical clades, with isolates from southern Vietnam associated with increased disease severity. Leveraging longitudinal isolates, we identify multiple instances of disease relapse linked to unrelated strains, highlighting the potential for multi-strain infections. In more frequent cases of persistent talaromycosis caused by the same strain, we identify variants arising over the course of patient infections that impact genes predicted to function in the regulation of gene expression and secondary metabolite production. By combining genetic variant data with patient metadata for all 336 isolates, we identify pathogen variants significantly associated with multiple clinical phenotypes. In addition, we identify genes and genomic regions under selection across both clades, highlighting loci undergoing rapid evolution, potentially in response to external pressures. With this combination of approaches, we identify links between pathogen genetics and patient outcomes and identify genomic regions that are altered during T. marneffei infection, providing an initial view of how pathogen genetics affects disease outcomes.

genomics↗

bioRxiv2023

Segmenting functional tissue units across human organs using community-driven development of generalizable machine learning algorithms

The development of a reference atlas of the healthy human body requires automated image segmentation of major anatomical structures across multiple organs based on spatial bioimages generated from various sources with differences in sample preparation. We present the setup and results of the "Hacking the Human Body" machine learning algorithm development competition hosted by the Human Biomolecular Atlas (HuBMAP) and the Human Protein Atlas (HPA) teams on the Kaggle platform. We showcase how 1,175 teams from 78 countries engaged in community- driven, open-science code development that resulted in machine learning models which successfully segment anatomical structures across five organs using histology images from two consortia and that will be productized in the HuBMAP data portal to process large datasets at scale in support of Human Reference Atlas construction. We discuss the benchmark data created for the competition, major challenges faced by the participants, and the winning models and strategies.

bioinformatics↗

bioRxiv2022

Sequence Controlled Secondary Structure Determines Site-selectivity of Lanthipeptides

Lanthipeptides are ribosomally synthesized and post-translationally modified peptides that are generated from precursor peptides through a dehydration and cyclization process in the biosynthetic pathways. In contrast to most other lanthipeptide synthetases, ProcM, a class II lanthipeptide synthetase, demonstrates high substrate tolerance. It is enigmatic that a single enzyme can catalyze the cyclization process of a diverse range of substrates with high fidelity. Previous studies suggested that the site-selectivity of lanthionine formation is determined by substrate sequence rather than by the enzyme. However, exactly how substrate sequence contributes to site-selective lanthipeptide biosynthesis is not clear. In this study, we performed molecular dynamic simulations for ProcA3.3 core peptide variants to explore how the predicted solution structure of the substrate without enzyme correlates to final product formation. Our simulation results support a model in which the secondary structure of the core peptide controls the ring pattern of the final product. We also demonstrate that the dehydration step in the biosynthesis pathway does not influence the site-selectivity of ring formation. In addition, we performed simulation for the core peptides of ProcA1.1 and 2.8, which are well-suited candidates to investigate the connection between order of ring formation and solution structure. Simulation results indicate that in both cases, C-terminal ring formation is more likely which was supported by experimental results. Our findings indicate that the substrate sequence and its solution structure can be used to predict the site-selectivity and order of ring formation, and that secondary structure is a crucial factor influencing the site-selectivity. Taken together, these findings will facilitate our understanding of the lanthipeptide biosynthetic mechanism and accelerate bioengineering efforts for lanthipeptide-derived products.

biophysics↗

bioRxiv2022

Association Between Polygenic Risk Score And Gut Microbiome Of Multiple Sclerosis

BackgroundMultiple sclerosis (MS) is a complex autoimmune disease in which both the roles of genetic susceptibility and environmental/microbial factors have been investigated. More than 200 genetic susceptibility variants have been identified along with the dysbiosis of gut microbiota, both independently have been shown to be associated with MS. We hypothesize that MS patients harboring genetic susceptibility variants along with gut microbiome dysbiosis are at a greater risk of exhibiting the disease. We investigated the polygenic risk score for MS in conjunction with gut microbiota in the same cohort of 117 relapsing remitting MS (RRMS) and 26 healthy controls. DNA samples were genotyped using Illuminas Infinium Immuno array-24 v2 chip followed by calculating polygenic risk score and the microbiota was determined by sequencing the V4 hypervariable region of the 16S rRNA gene. ResultsWe identified two clusters of MS patients, Cluster A and B both having a higher polygenic risk score than the control group. The Cluster B with the higher polygenic risk score had a distinct gut microbiota, different than the Cluster A. MS group whose microbiome was similar to that of the control group despite a higher genetic risk score than the control group. This could be due to i) the non-active state of the disease in that group of MS patients at the time of fecal sample collection and/or ii) the restoration of the gut microbiome post disease modifying therapy to treat the MS. ConclusionOur study showed that there seems to be association between polygenic risk score and gut microbiome dysbiosis in triggering the disease in a small cohort of MS patients. The MS Cluster A who have a higher polygenic risk score but microbiome profile similar to that of healthy controls could be due to the remitting phase of the disease or due to the effect of disease modifying therapies.

genetics↗

bioRxiv2022

Binge alcohol drinking alters the differential control of cholinergic interneurons over nucleus accumbens D1 and D2 medium spiny neurons

BackgroundVentral striatal cholinergic interneurons (ChIs) play a central role in basal ganglia function by regulating associative learning and reward processing. In the nucleus accumbens (NAc), ChIs regulate glutamatergic, dopaminergic, and GABAergic neurotransmission. However, it is unclear how ChIs orchestrate the control of these neurotransmitters to determine the excitability of medium spiny neurons (MSNs) expressing either dopamine D1 or D2 receptors. Additionally, the effects of binge alcohol drinking on ChIs-mediated modulation of glutamatergic synaptic transmission in NAc MSNs are also undefined. MethodsWe optogenetically stimulated ChIs while recording evoked and spontaneous excitatory postsynaptic currents (sEPSCs) in D1- and D2-MSN of ChAT.ChR2.eYFPxDrd1.tdtomato mice. To determine the effect of ChIs on mouse behavior and alcohol consumption, we implanted ChAT.ChR2.eYFP mice with fiber optic cannulas and stimulated ChIs while mice were allowed to drink 20% alcohol using the binge alcohol drinking- in-the-dark (DID) paradigm. ResultsWe demonstrated that NAc ChIs decrease the frequency of spontaneous excitatory postsynaptic currents (sEPSCs) in both D1- and D2-MSNs. While inhibition of D1-MSNs glutamate release by ChIs depends on dopamine release, that of D2-MSNs results from a direct interactions between ChIs and glutamatergic terminals. Interestingly, after two weeks of binge alcohol drinking, the effect of ChIs stimulation on glutamate release was reversed in D1-MSNs, while its effect on D2-MSNs remained unchanged. Finally, in vivo optogenetic stimulation of NAc ChIs significantly increased alcohol consumption. ConclusionsThese results identify ChIs as a key target for the regulation of NAc circuitry and as a potential treatment of alcohol addiction.

neuroscience↗

bioRxiv2022

Liquid droplet aging and fibril formation of the stress granule protein TIA1 low complexity domain

Protein domains biased toward a few amino acid types are vital for the formation of biomolecular condensates in living cells. These membraneless compartments are formed by molecules exhibiting a range of molecular motions and structural order. Missense mutations increase condensate persistence lifetimes or structural order, properties that are thought to underlie pathological protein aggregation. We examined seeded fibrils of the T-cell restricted intracellular antigen-1 low complexity domain and determined residues 338-357 compose the rigid fibril core. Aging of wild-type and P362L mutant low complexity domain liquid droplets resulted in fibril assemblies that are structurally distinct from the seeded fibril preparation. The results show that most disease mutations lie outside the region that forms homogeneous fibril structure, the droplets age into conformationally heterogenous fibrils, and the P362L disease mutation does not favor a specific fibril conformation.

biophysics↗