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Le, S.

Publications and source records attributed to Le, S..

28 records · Page 2Linked to original sources

Early activation of cellular stress and death pathways caused by cytoplasmic TDP-43 in the rNLS8 mouse model of ALS/FTD

TAR DNA binding protein 43 (TDP-43) pathology is a key feature of over 95% of amyotrophic lateral sclerosis (ALS) and nearly half of frontotemporal dementia (FTD) cases. The pathogenic mechanisms of TDP-43 dysfunction are poorly understood, however activation of cell stress pathways may contribute to pathogenesis. We therefore sought to identify which cell stress components are critical for driving disease onset and neurodegeneration in ALS/FTD. We studied the rNLS8 transgenic mouse model, which expresses human TDP-43 with a genetically-ablated nuclear localisation sequence within neurons of the brain and spinal cord resulting in cytoplasmic TDP-43 pathology and progressive motor dysfunction. Amongst numerous cell stress-related biological pathways profiled using qPCR arrays, several critical ISR effectors, including CCAAT/enhancer-binding homologous protein (Chop/Ddit3) and activating transcription factor 4 (Atf4), were upregulated in the cortex of rNLS8 mice prior to disease onset. This was accompanied by early up-regulation of anti-apoptotic gene Bcl2 and diverse pro-apoptotic genes including BH3-interacting domain death agonist (Bid). However, pro-apoptotic signalling predominated after onset of motor phenotypes. Notably, pro-apoptotic caspase-3 protein was elevated in the cortex of rNLS8 mice at later disease stages, suggesting that downstream activation of apoptosis drives neurodegeneration following failure of early protective responses. Unexpectedly, suppression of Chop in the brain and spinal cord using antisense oligonucleotide-mediated silencing had no effect on overall TDP-43 pathology or disease phenotypes in rNLS8 mice. Cytoplasmic TDP-43 accumulation therefore causes very early activation of ISR and both anti-and pro-apoptotic signalling that switches to predominant pro-apoptotic activation later in disease. These findings suggest that precise temporal modulation of cell stress and death pathways may be beneficial to protect against neurodegeneration in ALS and FTD. Key pointsO_LIISR genes Atf4 and Chop, anti-apoptotic Bcl2 and pro-apoptotic gene Bid, Bim, Noxa were upregulated in the cortex of rNLS8 mice prior to disease onset C_LIO_LIKnockdown of Chop had limited effects on TDP-43 pathology and did not alter motor deficits in rNLS8 mice C_LIO_LIBoth anti-and pro-apoptotic genes are upregulated prior to disease onset, and switches to activation of pro-apoptotic signalling at later disease stages C_LIO_LICaspase-3 activation likely drives neurodegeneration in the cortex of rNLS8 mice C_LI

neuroscience↗

Tension Gauge Tethers as tension-dependent lifetime sensors

Mechanotransduction of cells relies on responding to tension transmitted along various supramolecular linkages. Tension gauge tethers (TGTs), short double-stranded DNA (dsDNA) fragments that undergo irreversible tension-dependent dissociation under shear-stretching mode, have been widely applied in live cell experiments to provide critical insights into the mechanotransduction activities of cells. However, the current physical understanding of the mechanical responses of TGTs remains limited, which restricts the range of information that can be extracted from experimental observations. In order to provide quantitative in-depth understanding and interpretation of experimental observations, in this work, we quantified the tension-dependent lifetime of TGTs from which the mechanical stability of TGTs under various physiologically relevant stretching conditions can be derived. Applications of the determined mechanical stability of TGTs to cell studies strongly suggest revisiting the previous interpretations of several reported experimental observations.

biophysics↗

Inferring cell-specific gene regulatory networks from single cell gene expression data

Single cell profiling techniques including multi-omics and spatial-omics technologies allow researchers to study cell-cell variation within a cell population. These variations extend to biological networks within cells, in particular, the gene regulatory networks (GRNs). GRNs rewire as the cells evolve, and different cells can have different governing GRNs. However, existing GRN inference methods usually infer a single GRN for a population of cells, without exploring the cell-cell variation in terms of their regulatory mechanisms. Recently, jointly profiled single cell transcriptomics and chromatin accessibility data have been used to infer GRNs. Although methods based on such multi-omics data were shown to improve over the accuracy of methods using only single cell RNA-seq (scRNA-seq) data, they do not take full advantage of the single cell resolution chromatin accessibility data. We propose CeSpGRN (Cell Specific Gene Regulatory Network inference), which infers cell-specific GRNs from scRNA-seq, single cell multi-omics, or single cell spatial-omics data. CeSpGRN uses a Gaussian weighted kernel that allows the GRN of a given cell to be learned from the sequencing profile of itself and its neighboring cells in the developmental process. The kernel is constructed from the similarity of gene expressions or spatial locations between cells. When the chromatin accessibility data is available, CeSpGRN constructs cell-specific prior networks which are used to further improve the inference accuracy. We applied CeSpGRN to various types of real-world datasets and inferred various regulation changes that were shown to be important in cell development. We also quantitatively measured the performance of CeSpGRN on simulated datasets and compared with baseline methods. The results show that CeSpGRN has a superior performance in reconstructing the GRN for each cell, as well as in detecting the regulatory interactions that differ between cells. CeSpGRN is available at https://github.com/PeterZZQ/CeSpGRN.

bioinformatics↗

Identifying a novel role for the master regulator Tal1 in the Endothelial to Hematopoietic Transition

Recent progress in the generation of bona-fide Hematopoietic Stem and Progenitor Cells (HSPCs) in vitro and ex vivo has been built on the knowledge of developmental hematopoiesis, underscoring the importance of understanding in detail this developmental process. Here, we sought to elucidate the function of the hematopoietic regulators Tal1, Lmo2 and Lyl1 in the Endothelial to Hematopoietic Transition (EHT), the process through which HSPCs are generated from endothelial precursors during embryogenesis. We used a mouse embryonic-stem cell (mESC)-based differentiation system to model hematopoietic development, and combined gain-of-function experiments in sorted vascular smooth muscle cells (VSM) with multi-omics to obtain mechanistic insights into the mode of action of Tal1, Lmo2 and Lyl1. We found that these factors promote the silencing of the VSM transcriptional program and the activation of the hematopoietic one. Through this approach and the use of a Tet-on system to control the expression of Tal1 during hematopoietic specification from mESCs, we discovered that its expression in endothelial cells is crucial for the EHT to occur.

developmental biology↗

Mechano-Biochemical Regulation of the C. elegans HMP1-HMP2 protein complex

The HMP1-HMP2 protein complex, a counterpart of -catenin-{beta}-catenin complex in C. elegans, mediates the tension transmission between HMR1 (cadherin) and actin cytoskeleton and serves as a critical mechanosensor at the cell-cell adherens junction. The complex has been shown to play critical roles in embryonic development and tissue integrity in C. elegans. The complex is subject to tension due to internal actomyosin contractility and external mechanical micro-environmental perturbations. However, how tension regulates the stability and interaction of HMP1-HMP2 complex has yet to be investigated. Here, we directly quantify the mechanical stability of the full-length HMP1 and its force-bearing modulation domains (M1-M3), and show that they unfold within physiological level of tension (pico-newton scale). The inter-domain interactions within the modulation domain leads to strong mechanical stabilization of M1 in HMP1, resulting in a significantly stronger force threshold to expose the buried vinculin binding site compared to the M1 domain in -catenins. Moreover, we also quantify the mechanical stability of the inter-molecular HMP1-HMP2 interface and show that it is mechanically stable enough to support the tension-transmission and tension-sensing of the HMP1 modulation domains. Further, we show that single-residue phosphomimetic mutation (Y69E) on HMP2 weakens the mechanical stability of the HMP1-HMP2 interface and thus weakens the force-transmission molecular linkage and the associated mechanosensing functions. Together, these results provide a mechano-biochemical understanding of C. elegans HMP1-HMP2 protein complexs roles in mechanotransduction.

biophysics↗

Force-dependent interactions between talin and full-length vinculin

Talin and vinculin are part of a multi-component system involved in mechanosensing in cell-matrix adhesions. Both exist in auto-inhibited forms, and activation of vinculin requires binding to mechanically activated talin, yet how forces affect talins interaction with vinculin has not been investigated. Here by quantifying the force-dependent talin-vinculin interactions and kinetics using single-molecule analysis, we show that mechanical exposure of a single vinculin binding site (VBS) in talin is sufficient to relieve the autoinhibition of vinculin resulting in high-affinity binding. We provide evidence that the vinculin undergoes dynamic fluctuations between an auto-inhibited closed conformation and an open conformation that is stabilized upon binding to the VBS. Furthermore, we discover an additional level of regulation in which the mechanically exposed VBS binds vinculin significantly more tightly than the isolated VBS alone. Molecular dynamics simulations reveal the basis of this new regulatory mechanism, identifying a sensitive force-dependent change in the conformation of an exposed VBS that modulates binding. Together, these results provide a comprehensive understanding of how the interplay between force and autoinhibition provides exquisite complexity within this major mechanosensing axis.

biophysics↗

Talin mechanosensitivity is modulated by a direct interaction with cyclin-dependent kinase-1

Talin is a mechanosensitive component of adhesion complexes that directly couples integrins to the actin cytoskeleton. In response to force, talin undergoes switch-like behaviour of its multiple rod domains that modulate interactions with its binding partners. Cyclin-dependent kinase-1 (CDK1) is a key regulator of the cell cycle, exerting its effects through synchronised phosphorylation of a large number of protein targets. CDK1 activity also maintains adhesion during interphase, and its inhibition is a prerequisite for the tightly choreographed changes in cell shape and adhesiveness that are required for successful completion of mitosis. Using a combination of biochemical, structural and cell biological approaches, we demonstrate a direct interaction between talin and CDK1 that occurs at sites of integrin-mediated adhesion. Mutagenesis demonstrated that CDK1 contains a functional talin-binding LD motif, and the binding site within talin was pinpointed to helical bundle R8 through the use of recombinant fragments. Talin also contains a consensus CDK1 phosphorylation motif centred on S1589; a site that was phosphorylated by CDK1 in vitro. A phosphomimetic mutant of this site within talin lowered the binding affinity of KANK and weakened the mechanical response of the region, potentially altering downstream mechanotransduction pathways. The direct binding of the master cell cycle regulator, CDK1, to the primary integrin effector, talin, therefore provides a primordial solution for coupling the cell proliferation and cell adhesion machineries, and thereby enables microenvironmental control of cell division in multicellular organisms. SummaryThe direct binding of the master cell cycle regulator, CDK1, to the primary integrin effector, talin, provides a primordial solution for coupling the cell proliferation and cell adhesion machineries, and thereby enables microenvironmental control of cell division.

cell biology↗

Elevated SARS-CoV-2 Antibodies Distinguish Severe Disease in Early COVID-19 Infection

BackgroundSARS-CoV-2 has caused over 36,000,000 cases and 1,000,000 deaths globally. Comprehensive assessment of the multifaceted anti-viral antibody response is critical for diagnosis, differentiation of severe disease, and characterization of long-term immunity. Initial observations suggest that severe disease is associated with higher antibody levels and greater B cell/plasmablast responses. A multi-antigen immunoassay to define the complex serological landscape and clinical associations is essential. MethodsWe developed a multiplex immunoassay and evaluated serum/plasma from adults with RT-PCR-confirmed SARS-CoV-2 infections during acute illness (N=52) and convalescence (N=69); and pre-pandemic (N=106) and post-pandemic (N=137) healthy adults. We measured IgA, IgG, and/or IgM against SARS-CoV-2 Nucleocapsid (N), Spike domain 1 (S1), receptor binding domain (S1-RBD) and S1-N-terminal domain (S1-NTD). ResultsTo diagnose infection, the combined [IgA+IgG+IgM] or IgG for N, S1, and S1-RBD yielded AUC values -0.90 by ROC curves. From days 6-30 post-symptom onset, the levels of antigen-specific IgG, IgA or [IgA+IgG+IgM] were higher in patients with severe/critical compared to mild/moderate infections. Consistent with excessive concentrations of antibodies, a strong prozone effect was observed in sera from severe/critical patients. Notably, mild/moderate patients displayed a slower rise and lower peak in anti-N and anti-S1 IgG levels compared to severe/critical patients, but anti-RBD IgG and neutralization responses reached similar levels at 2-4 months. ConclusionThis SARS-CoV-2 multiplex immunoassay measures the magnitude, complexity and kinetics of the antibody response against multiple viral antigens. The IgG and combined-isotype SARS-CoV-2 multiplex assay is highly diagnostic of acute and convalescent disease and may prognosticate severity early in illness. One Sentence SummaryIn contrast to patients with moderate infections, those with severe COVID-19 develop prominent, early antibody responses to S1 and N proteins.

immunology↗

Riluzole does not ameliorate disease caused by cytoplasmic TDP-43 in a mouse model of amyotrophic lateral sclerosis

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease commonly treated with riluzole, a small molecule that may act via modulation of glutamatergic neurotransmission. However, riluzole only modestly extends lifespan for people living with ALS and its precise mechanisms of action remain unclear. Most ALS cases are characterised by accumulation of cytoplasmic TAR DNA binding protein of 43 kDa (TDP-43), and understanding the effects of riluzole in models that closely recapitulate TDP-43 pathology may provide insights for development of improved therapeutics. We therefore investigated the effects of riluzole in transgenic mice that inducibly express nuclear localisation sequence (NLS)-deficient human TDP-43 in neurons (NEFH-tTA/tetO-hTDP-43{Delta}NLS, rNLS, mice). Riluzole treatment from the first day of hTDP-43{Delta}NLS expression did not alter disease onset, weight loss or performance on multiple motor behavioural tasks. Riluzole treatment also did not alter TDP-43 protein levels, solubility or phosphorylation. Although we identified a significant decrease in GluA2 and GluA3 proteins in the cortex of rNLS mice, riluzole did not ameliorate this disease-associated molecular phenotype. Likewise, riluzole did not alter the disease-associated atrophy of hindlimb muscle in rNLS mice. Finally, riluzole treatment beginning after disease onset in rNLS mice similarly had no effect on progression of late-stage disease or animal survival. Together, we demonstrate specific glutamatergic receptor alterations and muscle fibre-type changes reminiscent of ALS in rNLS mice, but riluzole had no effect on these or any other disease phenotypes. Future targeting of pathways directly related to accumulation of TDP-43 pathology may be needed to develop better treatments for ALS. Significance StatementAccumulation of cytoplasmic TDP-43 protein is the hallmark pathology of ALS. Riluzole is the most widely used drug for ALS treatment, but provides only a short extension of lifespan. We demonstrate here in the rNLS mouse model, which mimics TDP-43 pathology, that riluzole does not ameliorate progressive alterations in motor strength and coordination, muscle atrophy, glutamate receptor levels, or TDP-43 protein levels and solubility, and does not prolong animal survival. Riluzole similarly did not affect decreased levels of glutamate receptor subunits GluA2/GluA3 in rNLS mice. The inability of riluzole to rescue pathological or phenotypic changes in this TDP-43 model provides further impetus for the discovery of improved therapies targeting the key drivers of ALS pathogenesis.

neuroscience↗

Tension-dependent stretching and folding of ZO-1 controls the localization of its interactors

Tensile forces regulate epithelial homeostasis, but the molecular mechanisms behind this regulation are poorly understood. Using structured illumination microscopy and proximity ligation assays we show that the tight junction protein ZO-1 undergoes actomyosin tension-dependent stretching and folding in vivo. Magnetic tweezers experiments using purified ZO-1 indicate that pN-scale tensions (~2-4 pN) are sufficient to maintain the stretched conformation of ZO-1, while keeping its structured domains intact. Actomyosin tension and substrate stiffness regulate the localization and expression of the transcription factor DbpA and the tight junction membrane protein occludin in a ZO-1/ZO-2-dependent manner, resulting in modulation of gene expression, cell proliferation, barrier function and cyst morphogenesis. Interactions between the N-terminal (ZPSG) and C-terminal domains of ZO-1 prevent binding of DbpA to the ZPSG, and folding is antagonized by heterodimerization with ZO-2. We propose that tensile forces regulate epithelial homeostasis by activating ZO proteins through stretching, to modulate their protein interactions and downstream signaling.

cell biology↗