bioRxiv Science⌕ Search

Biology subjects

Sim, J.

Publications and source records attributed to Sim, J..

16 recordsLinked to original sources

Sotagliflozin Reprograms Hepatic Lipid Metabolism and Attenuates Atherosclerosis Beyond Empagliflozin in CKM Mice

Background: Sodium-glucose cotransporter-2 (SGLT2) inhibitors reduce cardiovascular mortality and chronic kidney disease (CKD) progression in cardiovascular-kidney-metabolic (CKM) syndrome, but this benefit derives primarily from reductions in heart failure and cardiovascular mortality rather than in atherothrombotic events. Sotagliflozin, which inhibits both intestinal SGLT1 and renal SGLT2, is the only drug in this class shown to lower rates of myocardial infarction and stroke in CKD. However, its mechanism remains unclear, and its effectiveness in non-diabetic CKD has not been studied. We hypothesized that dual SGLT1/2 inhibition reprograms systemic substrate utilization toward fatty acid oxidation, which may partially account for this protective effect. Methods: CKD was induced in male low-density lipoprotein receptor-deficient mice by 5/6 nephrectomy. Sham and CKD mice received a high-fat diet and drinking water containing sotagliflozin, empagliflozin, or vehicle for 16 weeks, at doses that produced equivalent fractional excretion of glucose. We quantified atherosclerosis en face and in the aortic sinus. Indirect calorimetry, echocardiography, hepatic RNA sequencing, plasma acylcarnitine profiling, and in vivo deuterium labeling of palmitate were performed. Results: At matched levels of glucosuria and plasma total cholesterol, sotagliflozin decreased body mass, atherosclerosis burden, triglycerides, and TNF- more than empagliflozin, and raised postprandial total GLP-1 approximately 3-fold, while both drugs similarly improved albuminuria and diastolic function. Sotagliflozin increased energy expenditure independent of body mass and lowered respiratory exchange ratio despite compensatory hyperphagia. Sotagliflozin reduced hepatic lipogenic genes and de novo lipogenic flux, while increasing {beta}-oxidation and ketogenesis; empagliflozin only activated the oxidative pathway. Conclusions: In experimental CKM syndrome, dual SGLT1/2 inhibition reduces atherosclerosis and metabolic syndrome more effectively than selective SGLT2 inhibition and is associated with reprogramming of hepatic lipid metabolism. These results suggest that sotagliflozin could be an attractive candidate for mitigating atherosclerotic risk in non-diabetic CKD.

pharmacology and toxicology↗

TRPV1-expressing neurons are dispensable for photophobia: evidence from a novel mouse light sensitivity assay

Background: Light hypersensitivity, or photophobia, affects nearly 80% of people with migraine and is the most prevalent symptom after headache. Despite its high prevalence, the neural pathways underlying migraine-associated light hypersensitivity remain poorly understood, in part due to the lack of behavioral assays that directly assess light sensitivity in mice. Consequently, whether nociceptors contribute to the development of photophobia remains unclear. Methods: We established a novel light sensitivity assay (LSA) to quantify the response to light in mice by measuring facial grimacing. The assay was applied to evaluate light hypersensitivity elicited by three established migraine triggers: calcitonin gene-related peptide (CGRP), nitric oxide donor (sodium nitroprusside), and repeated stress. To determine the contribution of TRPV1 nociceptors, mice were treated with resiniferatoxin (RTX) to ablate these neurons. Results: The LSA detected light hypersensitivity following administration of CGRP, sodium nitroprusside, and repeated stress in wild-type (WT) mice. Sex differences were not observed in CGRP- or stress-induced light hypersensitivity. Furthermore, ablation of TRPV1 nociceptors did not reduce light hypersensitivity induced by migraine triggers. Conclusions: These findings present the LSA as a robust, reproducible, and easy to implement behavioral assay for measuring light sensitivity in preclinical migraine models. Our results further demonstrate that TRPV1 nociceptors are dispensable for the development of migraine-associated light hypersensitivity. This assay provides a useful method for investigating the mechanisms underlying light sensitivity and for evaluating potential therapeutic strategies.

neuroscience↗

LEN-Seek: Fast and scalable ligand binding-site similarity search in the latent space of an SE(3)-invariant graph VAE

MotivationLigand binding-site similarity search is a crucial step in drug discovery that reduces the conformational search space for docking and other downstream tasks by comparing a target protein against experimentally identified binding sites. Existing methods rely on either direct structural alignment or lossy compression of structural information, producing a trade-off between scalability and precision. ResultsWe propose LEN-Seek, a ligand binding-site search method based on a graph neural network (GNN)-driven variational autoencoder (VAE) that encodes the 3D structural and physicochemical context of a binding site into a probabilistic latent space, enabling similarity search within a low-dimensional vector space. A binding site is modeled as a graph of amino acid residues, with node features adopted from the protein language model, Ankh, and edges encoded as SE(3)-invariant (roto-translational invariant) geometric relationships, thereby avoiding expensive data augmentation or SE(3)-equivariant models. Compared to ProBiS, the purely geometric graph-clique based method, LEN-Seek successfully retrieves a substantial portion of similar binding sites with a roughly 3,400-fold lower per-comparison cost, demonstrating its potential as a scalable approach to template-based ligand binding-site search in large-scale protein structure databases. Supplementary informationSupplementary data are available at Bioinformatics online.

bioinformatics↗

MitoAtlas: a Domain-Resolved Spatial Map of the HumanMitochondrial Proteome

Mitochondrial function depends on the precise sub-organellar localization and topological orientation of its proteome. However, mapping this architecture with domain-level precision across the double-membrane system has remained challenging. Here, we present MitoAtlas, a spatial systems biology resource built on SR-PL (super-resolution proximity labeling) that resolves the sub-mitochondrial architecture of 861 proteins at domain-level resolution. By deploying 42 spatially restricted APEX2 and BioID/BioID2 baits across mitochondrial compartments and cytosol in HEK293T-REx cells, we mapped 13,440 unique proximity-labeled sites. Integrating high-density spatial data with a machine-learning classification pipeline and AlphaFold structural modeling, we resolved membrane topologies for 196 transmembrane proteins and assigned sub-mitochondrial localizations to 160 previously unannotated mitochondrial proteins absent from MitoCarta3.0, including MINPP1 as an intermembrane space resident. Coupling bait-specific proximity labeling signatures with AlphaFold structure prediction and metabolite docking identified 47 protein-protein interactions, including the LETM1-Citrate Synthase complex, and 155 protein-metabolite interactions. MitoAtlas is available at mitoatlas.org as a domain-resolution spatial map of mitochondrial architecture and metabolism.

cell biology↗

Mast cell-derived chymases are essential for the resolution of inflammatory pain in mice

Immune cells play a critical role in the transition from acute to chronic pain. However, the role of mast cells in pain remains under-investigated. Here, we demonstrated that the resolution of inflammatory pain is markedly delayed in mast-cell-deficient mice. In response to Complete Freund Adjuvant (CFA), mast-cell-deficient mice showed greater levels of nitric oxide and altered cytokine/chemokine profile in inflamed skin in both sexes. In Wild-Type (WT) mice, the number of mast cell and mast cell-derived chymases; chymase 1 (CMA1) and mast cell protease 4 (MCPT4) increased in the inflamed skin. Inhibiting chymase enzymatic activity delayed the resolution of inflammatory pain. Consistently, local pharmacological administration of recombinant CMA1 and MCPT4 promoted the resolution of pain hypersensitivity and attenuated the upregulation of cytokines and chemokines under inflammation. We identified CCL9 as a target of MCPT4. Inhibition of CCL9 promoted recruitment of CD206+ myeloid cells and alleviated inflammatory pain. Our work reveals a new role of mast cell-derived chymases in preventing the transition from acute to chronic pain and suggests new therapeutic avenues for the treatment of inflammatory pain. SummaryMast cell-derived chymases play an unexpected role in the resolution of inflammatory pain and regulate the immune response. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=154 SRC="FIGDIR/small/606617v1_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@ba757dorg.highwire.dtl.DTLVardef@17783c4org.highwire.dtl.DTLVardef@16be9d3org.highwire.dtl.DTLVardef@1c42bc2_HPS_FORMAT_FIGEXP M_FIG Mast cells derived chymase MCPT4 degrades CCL9 to promote acute inflammatory pain resolution and prevent chronic pain. CFA-induced inflammation increases mast cells that degranulate and release chymases, like MCPT4 and CMA1, which in turn cleaves cytokines and chemokines such as CCL9. CCL9 cleavage induces the recruitment of CD206+ myeloid cells to promote the resolution of pain and prevent the transition from acute to chronic pain. C_FIG

immunology↗

Interleukin-10-producing monocytes contribute to sex differences in pain resolution in mice and humans.

Pain is closely associated with the immune system, which exhibits sexual dimorphism. For these reasons, neuro-immune interactions are suggested to drive sex differences in pain pathophysiology. However, our understanding of peripheral neuro-immune interactions on sex differences in pain resolution remains limited. Here, we have shown, in both a mouse model of inflammatory pain and in humans following traumatic pain, that males had higher levels of interleukin (IL)-10 than females, which were correlated with faster pain resolution. Following injury, we identified monocytes (CD11b+ Ly6C+ Ly6G-F4/80mid) as the primary source of IL-10, with IL-10-producing monocytes being more abundant in males than females. In a mouse model, neutralizing IL-10 signaling through antibodies, genetically ablating IL-10R1 in sensory neurons, or depleting monocytes with clodronate all impaired the resolution of pain hypersensitivity in both sexes. Furthermore, manipulating androgen levels in mice reversed the sexual dimorphism of pain resolution and the levels of IL-10-producing monocytes. These results highlight a novel role for androgen-driven peripheral IL-10-producing monocytes in the sexual dimorphism of pain resolution. These findings add to the growing concept that immune cells play a critical role in resolving pain and preventing the transition into chronic pain. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/565129v1_ufig1.gif" ALT="Figure 1"> View larger version (46K): org.highwire.dtl.DTLVardef@6e158corg.highwire.dtl.DTLVardef@148c8b5org.highwire.dtl.DTLVardef@1711d2dorg.highwire.dtl.DTLVardef@132a755_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Tonic Meningeal Interleukin-10 Upregulates Delta Opioid Receptor to Prevent Relapse to Pain

Chronic pain often alternates between transient remission and relapse of severe pain. While most research on chronic pain has focused on mechanisms maintaining pain, there is a critical unmet need to understand what prevents pain from re-emerging in those who recover from acute pain. We found that interleukin (IL)-10, a pain resolving cytokine, is persistently produced by resident macrophages in the spinal meninges during remission from pain. IL-10 upregulated expression and analgesic activity of {delta}-opioid receptor ({delta}OR) in the dorsal root ganglion. Genetic or pharmacological inhibition of IL-10 signaling or {delta}OR triggered relapse to pain in both sexes. These data challenge the widespread assumption that remission of pain is simply a return to the naive state before pain was induced. Instead, our findings strongly suggest a novel concept that: remission is a state of lasting pain vulnerability that results from a long-lasting neuroimmune interactions in the nociceptive system.

neuroscience↗

β-carotene accelerates resolution of atherosclerosis by promoting regulatory T cell expansion in the atherosclerotic lesion

{beta}-carotene oxygenase 1 (BCO1) catalyzes the cleavage of {beta}-carotene to form vitamin A. Besides its role in vision, vitamin A regulates the expression of genes involved in lipid metabolism and immune cell differentiation. BCO1 activity is associated with the reduction of plasma cholesterol in humans and mice, while dietary {beta}-carotene reduces hepatic lipid secretion and delays atherosclerosis progression in various experimental models. Here we show that {beta}-carotene also accelerates atherosclerosis resolution in two independent murine models, independently of changes in body weight gain or plasma lipid profile. Experiments in Bco1-/- mice implicate vitamin A production in the effects of {beta}-carotene on atherosclerosis resolution. To explore the direct implication of dietary {beta}-carotene on regulatory T cells (Tregs) differentiation, we utilized anti-CD25 monoclonal antibody infusions. Our data show that {beta}-carotene favors Treg expansion in the plaque, and that the partial inhibition of Tregs mitigates the effect of {beta}-carotene on atherosclerosis resolution. Our data highlight the potential of {beta}-carotene and BCO1 activity in the resolution of atherosclerotic cardiovascular disease.

immunology↗

Statistically unbiased prediction enables accurate denoising of voltage imaging data

Here we report SUPPORT (Statistically Unbiased Prediction utilizing sPatiOtempoRal information in imaging daTa), a self-supervised learning method for removing Poisson-Gaussian noise in voltage imaging data. SUPPORT is based on the insight that a pixel value in voltage imaging data is highly dependent on its spatially neighboring pixels in the same time frame, even when its temporally adjacent frames do not provide useful information for statistical prediction. Such spatiotemporal dependency is captured and utilized to accurately denoise voltage imaging data in which the existence of the action potential in a time frame cannot be inferred by the information in other frames. Through simulation and experiments, we show that SUPPORT enables precise denoising of voltage imaging data while preserving the underlying dynamics in the scene.

neuroscience↗

A conserved HOTAIRM1-HOXA1 regulatory axis coordinates early neuronal differentiation

HOTAIRM1 is unlike most long non-coding RNAs in that its sequence is highly conserved across mammals. Such evolutionary conservation points to it having a role in key cellular processes. We previously reported that HOTAIRM1 is required to curb premature activation of downstream HOXA genes in a cell model recapitulating their sequential induction during development. We found that it regulates 3 HOXA gene expression by a mechanism involving epigenetic and three-dimensional chromatin changes. Here we show that HOTAIRM1 is required for proper progression through the early stages of neuronal differentiation. We found that it associates with the HOXA1 transcription factor and participates in its downstream transcriptional program. Particularly, HOTAIRM1 affects the NANOG/POU5F1/SOX2 core pluripotency network maintaining an undifferentiated cell state. HOXA1 depletion similarly perturbed expression of these pluripotent factors, suggesting that HOTAIRM1 is a modulator of this transcription factor pathway. Also, given that binding of HOTAIRM1 to HOXA1 was observed in different cell types and species, our results point to this ribonucleoprotein complex as an integral part of a conserved HOTAIRM1-HOXA1 regulatory axis controlling the transition from a pluripotent to a differentiated neuronal state.

molecular biology↗

Lymphatic dysfunction in lupus contributes to cutaneous photosensitivity and lymph node B cell responses

Patients with systemic lupus erythematosus (SLE) are photosensitive, developing skin inflammation with even ambient ultraviolet radiation (UVR), and this cutaneous photosensitivity can be associated with UVR-induced flares of systemic disease, which can involve increased autoantibodies and further end organ injury. Mechanistic insight into the link between the skin responses and autoimmunity is limited. Signals from skin are transmitted directly to the immune system via lymphatic vessels, and here we show evidence for potentiation of UVR-induced lymphatic flow dysfunction in SLE patients and murine models. Improving lymphatic flow by manual lymphatic drainage (MLD) or with a transgenic model with increased lymphatic vessels reduces both cutaneous inflammation and lymph node B and T cell responses, and long term MLD reduces splenomegaly and titers of a number of autoantibodies. Mechanistically, improved flow restrains B cell responsesS in part by stimulating a lymph node fibroblastic reticular cell-monocyte axis. Our results point to lymphatic modulation of lymph node stromal function as a link between photosensitive skin responses and autoimmunity and as a therapeutic target in lupus, provide insight into mechanisms by which the skin state regulates draining lymph node function, and suggest the possibility of MLD as an accessible and cost-effective adjunct to add to ongoing medical therapies for lupus and related diseases.

immunology↗

ECPAS/Ecm29-Mediated 26S Proteasome Disassembly Is an Adaptive Response to Glucose Starvation

The 26S proteasome consists of loosely associated 20S catalytic and 19S regulatory complexes. Approximately half of the proteasomes in eukaryotic cells exist as free 20S complexes; however, our mechanistic and physiological understanding of what determines the ratio of 26S to 20S species remains incomplete. Here, we show that glucose starvation in mammalian cells results in the uncoupling of 26S holoenzymes into intact 20S and 19S subcomplexes. Subcomplex affinity-purification and quantitative mass spectrometry revealed that Ecm29 proteasome adaptor and scaffold (ECPAS) is a crucial mediator of this structural remodeling. The loss of ECPAS abrogated 26S dissociation, leading to decreased degradation of 20S proteasome substrates such as puromycylated polypeptides and lysine-less cyclin B. In silico modeling analysis suggested that the conformational changes of ECPAS may commence the disassembly process. ECPAS was also essential for proper endoplasmic reticulum stress response and cell survival during glucose starvation. In addition, we evaluated the role of ECPAS in vivo using the mouse xenograft model and observed that glucose-deprived tumor tissues had significantly elevated 20S proteasome levels. Collectively, our results indicate that the 20S-19S disassembly mediated by ECPAS is a novel mechanism adapting global proteolysis to physiological needs and an effective cellular strategy against proteotoxic stress.

biochemistry↗

Kre28-Spc105 interaction is essential for their recruitment at the kinetochore

Kinetochores are macromolecular protein assemblies that attach sister chromatids to spindle microtubules and mediate accurate chromosome segregation during mitosis. The outer kinetochore consists of the KMN network, a protein super-complex comprising Knl1 (yeast Spc105), Mis12 (yeast Mtw1), and Ndc80 (yeast Ndc80), which harbors sites for microtubule binding. Within the KMN network, Spc105 acts as an interaction hub of components involved in spindle assembly checkpoint (SAC) signaling. It is known that Spc105 forms a complex with kinetochore component Kre28. However, where Kre28 physically localizes in the budding yeast kinetochore is not clear. The exact function of Kre28 at the kinetochore is also unknown. Here, we investigate how Spc105 and Kre28 interact and how they are organized within bioriented yeast kinetochores using genetics and cell biological experiments. Our microscopy data show that Spc105 and Kre28 localize at the kinetochore with a 1:1 stoichiometry. We also show that the Kre28-Spc105 interaction is important for Spc105 protein turn-over and essential for their mutual recruitment at the kinetochores. We created several truncation mutants of kre28 that affect Spc105 loading at the kinetochores. When over-expressed, these mutants sustain the cell viability, but SAC signaling and kinetochore biorientation are impaired. Therefore, we conclude that Kre28 contributes to chromosome biorientation and high-fidelity segregation at least indirectly by regulating Spc105 localization at the kinetochores.

cell biology↗

Whole-ExM: Expansion microscopy imaging of all anatomical structures of whole larval zebrafish

Nanoscale resolution imaging of whole vertebrates is required for a systematic understanding of human diseases, but this has yet to be realized. Expansion microscopy (ExM) is an attractive option for achieving this goal, but the expansion of whole vertebrates has not been demonstrated due to the difficulty of expanding hard body components. Here, we demonstrate whole-body ExM, which enables nanoscale resolution imaging of anatomical structures, proteins, and endogenous fluorescent proteins (FPs) of whole zebrafish larvae and mouse embryos by expanding them fourfold. We first show that post-digestion decalcification and digestion kinetics matching are critical steps in the expansion of whole vertebrates. Then, whole-body ExM is combined with the improved pan-protein labeling approach to demonstrate the three-dimensional super-resolution imaging of antibody- or FP-labeled structures and all major anatomical structures surrounding them. We also show that whole-body ExM enables visualization of the nanoscale details of neuronal structures across the entire body.

developmental biology↗

Minimization of cross-talk between Spindle Assembly Checkpoint silencing and error correction

Accurate chromosome segregation during cell division requires that the pair of sister kinetochores on each chromosome attach to microtubules originating from opposite spindle poles. This is ensured by the combined action of the Spindle Assembly Checkpoint (SAC), which detects unattached kinetochores, and an error correction mechanism that destabilizes incorrect attachment of both sister kinetochores to the same spindle pole. These processes are downregulated by Protein Phosphatase 1 (PP1), which both silences the SAC and stabilizes kinetochore-microtubule attachments. We find that this dual PP1 role can be problematic: if PP1 is recruited to the kinetochore for SAC silencing prior to chromosome biorientation, it interferes with error correction. We show that to mitigate this cross-talk, the yeast kinetochore uses independent PP1 sources to stabilize correct attachments and to silence the SAC, and also delays the recruitment of PP1 for SAC silencing. Consequently, chromosome biorientation precedes SAC silencing ensuring accurate chromosome segregation.

cell biology↗

Drosophila BEACH domain autophagic adaptor blue cheese shuttles between vesicle populations and is required for an early step in autophagy

Drosophila melanogaster blue cheese (bchs) encodes a large BEACH (Beige and Chediak-Higashi) family protein that is postulated to function as an adaptor protein with roles in vesicle trafficking. Mutation in bchs leads to the accumulation of ubiquitinated aggregates in aged brains, presumably because of a conserved function with its human homologue Autophagy-Linked FYVE (ALFY), which interacts with Atg5 and p62 to promote the clearance of aggregate-prone proteins. In this study, we present pharmacological and genetic evidence using a well-defined larval motorneuron paradigm that in Drosophila bchs mutants, autophagic deficit contributes to neurodegeneration. Specifically, we show that motorneuron death in larvae is accompanied by the accumulation of prominent ubiquitinated aggregates in synaptic termini, and that these are sensitive to autophagy modulating drugs. In primary bchs neurons, early autophagic compartments increase in number and intensity based on Atg5 expression, but fail to progress to Atg8-labelled compartments, indicating non-clearance. A rescuing transgene encoding the longest Bchs BEACH domain isoform not only reverses this defect, but also greatly increases Atg8 compartment number and rescues neuronal death. Although only a small fraction of Bchs colocalizes with these markers under wild-type conditions, the population of Bchs that does associate with autophagosomes shuttles between different locations depending on how autophagy is induced. These observations, together with epistatic relationships between bchs mutant alleles and autophagy-modulating drugs and genetic backgrounds, points to a model whereby BEACH domain isoforms of Bchs participate in the early steps of autophagy by recruiting Atg5 to target substrates for clearance, and that Bchs association with different parts of the autophagy machinery depends upon the type of autophagic stress imposed upon the neuron.

cell biology↗