Biology subjects

Suzuki, A.

Publications and source records attributed to Suzuki, A..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

The Golgi-associated microtubule cross-linking protein MTCL2 promotes the multipolar extension of dendrites in cerebellar granule neurons.

The dynamic regulation of neuronal polarity is essential for the formation of neural networks during brain development. Primary cultures of rodent neurons recapitulate several aspects of this polarity regulation, providing valuable insights into the molecular mechanisms underlying axon specification, dendrite formation, and neuronal migration. However, the process by which the preexisting bipolarity of migrating neurons is disrupted to form multipolar dendrites remains to be elucidated. In this study, we demonstrate that MTCL2, a microtubule-crosslinking protein associated with the Golgi apparatus, plays a crucial role in this type of polarity transformation observed during the differentiation of cerebellar granule neurons (CGNs). MTCL2 is highly expressed in CGNs and gradually accumulates in dendrites as the cells develop polarity. MTCL2 knockdown resulted in the generation of longer and fewer dendrites by suppressing the bipolar-to-multipolar transition of dendrite extension observed in the normal polarization process. During this process, the Golgi apparatus shifts from the base of the preexisting bipolar neurites to the lateral or apical side of the nucleus in the cell body. There, it forms a close association with the microtubule cage that wraps around the nucleus. The resulting upward extension of the Golgi apparatus is tightly coupled with the randomization of its position in the x-y plane. Knockdown and rescue experiments demonstrated that MTCL2 promotes these Golgi position changes in a microtubule- and Golgi-binding activity-dependent manner. These results suggest that MTCL2 promotes the development of multipolar short dendrites by sequestering the Golgi apparatus into the microtubule cage from the base of the preexisting neurite. Significance StatementPrevious studies have shown that neurons polarize the localization of the Golgi apparatus, thereby facilitating the development of asymmetrically elongated dendrites. In contrast, the present study demonstrated that to symmetrically extend multiple dendrites, cerebellar granule neurons sequester the Golgi apparatus within a microtubule cage surrounding the nucleus. This represents a novel mechanism through which neurons suppress polarized vesicle transport. These findings also reveal an entirely novel function of microtubule cages, which have only been reported for their role in neuronal cell migration. The present study also revealed the involvement of the novel microtubule-regulating protein MTCL2, which links the Golgi apparatus to microtubules, and the LINC complex, which links microtubules to the nuclear membrane, in this process.

cell biology↗

bioRxiv2024

Reversible and effective cell cycle synchronization method for studying stage-specific investigations

The cell cycle is a crucial process for cell proliferation, differentiation, and development. Numerous genes and proteins play pivotal roles at specific cell cycle stages to regulate these events precisely. Studying the stage-specific functions of the cell cycle requires accumulating cell populations at the desired cell cycle stage. Cell synchronization, achieved through the use of cell cycle kinase and protein inhibitors, is often employed for this purpose. However, suboptimal concentrations of these inhibitors can result in reduced efficiency, irreversibility, and undesirable cell cycle defects. In this study, we have optimized effective and reversible techniques to synchronize the cell cycle at each stage in human RPE1 cells, utilizing both fixed high-precision cell cycle identification methods and high-temporal live-cell imaging. These reproducible synchronization methods are invaluable for investigating the regulatory mechanisms specific to each cell cycle stage.

cell biology↗

bioRxiv2024

3D-Aligner: An advanced computational tool designed to correct image distortion in expansion microscopy for precise 3D reconstitution and quantitative analysis

Expansion Microscopy (ExM) is an innovative and cost-effective super-resolution microscopy technique that has become popular in cell biology research. It achieves super-resolution by physically expanding specimens. Since its introduction, ExM has undergone continuous methodological developments to enhance its resolution and labeling capabilities. However, ExM imaging often encounters sample drift during image acquisition due to the physical movement of the expanded hydrogel, posing a significant challenge for accurate image reconstruction. Despite many proposed experimental solutions to mitigate sample drift, a universal solution has yet to be established. In response to this challenge, we developed 3D-Aligner, an advanced and user-friendly image analysis tool designed to computationally correct drift in ExM images for precise three-dimensional image reconstruction and downstream quantification. We demonstrate that 3D-Aligner effectively determines and corrects drift in ExM images with different expansion rates and various fluorescently labeled biological targets, showcasing its capabilities and robustness in drift correction. Additionally, we validate the precision of 3D-Aligner by comparing drift values across different labeled targets and highlight the importance of drift correction in quantification of biological structures.

cell biology↗

bioRxiv2024

ImmunoCellCycle-ID: A high-precision immunofluorescence-based method for cell cycle identification

The cell cycle is a fundamental process essential for cell proliferation, differentiation, and development. It consists of four major phases: G1, S, G2, and M. These phases collectively drive the reproductive cycle and are meticulously regulated by various proteins that play critical roles in both the prevention and progression of cancer. Traditional methods for studying these functions, such as flow cytometry, require a substantial number of cells to ensure accuracy. In this study, we have developed a user-friendly, immunofluorescence-based method for identifying cell cycle stages, providing single-cell resolution and precise identification of G1, early S, late S, early G2, late G2, and each sub-stage of the M phase using fluorescence microscopy. This method provides high-precision cell cycle identification and can serve as an alternative to, or in combination with, traditional flow cytometry to dissect detailed substages of the cell cycle in a variety of cell lines.

cell biology↗

bioRxiv2024

Pyruvate kinase modulates the link between β-cell fructose metabolism and insulin secretion

2Glucose triggers insulin secretion from pancreatic {beta}-cells through intracellular glucose metabolism, ATP production, and closure of ATP-sensitive K+ channels (KATP channels). Fructose also stimulates insulin secretion, but the underlying mechanisms remain unclear. This study investigated the contribution of phospholipase C (PLC) signaling and fructose metabolism to fructose-stimulated insulin secretion (FSIS) using MIN6-K8 clonal {beta}-cells and mouse islets. Fructose-induced PLC activation, assessed by inositol 1-phosphate accumulation, was reduced in fructose-unresponsive {beta}-cell models, such as diabetic mouse islets and KATP channel-deficient {beta}-cells, suggesting that {beta}-cell fructose responsiveness is primarily determined by PLC signaling. Although FSIS was dependent on KATP channels and Ca2+ influx, the ATP/ADP ratio was unexpectedly lowered by fructose, and suppression of intracellular fructose metabolism hardly affected FSIS. Metabolic flux analysis revealed that the accumulation of fructose 1-phosphate (F1P) suppressed pyruvate kinase (PK) activity, contributing to ATP depletion. Strikingly, a small-molecule PK activator, TEPP-46, antagonized F1P-mediated PK suppression, prevented the drop in the ATP/ADP ratio, and restored FSIS in MIN6-K8 cells, normal mouse islets, and fructose-unresponsive diabetic mouse islets. These findings revealed the metabolic effects of fructose in {beta}-cells and identified PK as a key regulator linking {beta}-cell fructose metabolism and FSIS, thereby providing new insights into the mechanisms of insulin secretion and potential therapeutic targets for fructose-associated metabolic diseases. 1 GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=124 SRC="FIGDIR/small/608033v2_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@11ce1e9org.highwire.dtl.DTLVardef@1339f22org.highwire.dtl.DTLVardef@1493a5org.highwire.dtl.DTLVardef@e97026_HPS_FORMAT_FIGEXP M_FIG C_FIG Left: Fructose-stimulated insulin secretion (FSIS) is driven by sweet taste receptor (STR)-mediated PLC signaling in pancreatic {beta}-cells. Meanwhile, fructose metabolism does not promote FSIS because fructose causes accumulation of fructose 1-phosphate (F1P), which suppresses pyruvate kinase M2 (PKM2), lowering the ATP/ADP ratio. Right: A small-molecule PK activator counteracted F1P-mediated PKM2 inhibition, prevented ATP decrease, and substantially enhanced FSIS in normal and diabetic mouse {beta}-cells. Thus, PK has been identified as a key regulator linking {beta}-cell fructose metabolism and FSIS.

cell biology↗

bioRxiv2024

PDPN/CLEC-2 axis modulates megakaryocyte subtypes in a hematopoietic stem cell-regulating megakaryocyte-dominant manner

IntroductionMegakaryocytes are classified into several subtypes including LSP1-positive immune-skewed, MYLK4-positive hematopoietic stem cell (HSC)-regulating, and BMAL1-positive platelet-producing megakaryocytes. Podoplanin (PDPN)-expressing stromal cells generate a microenvironment that promotes megakaryopoiesis in the bone marrow. In this context, PDPN interacts with C-type lectin-like receptor-2 (CLEC-2) on megakaryocyte progenitors, which induces megakaryocyte proliferation. However, the megakaryocyte subtypes developed by the regulation of the PDPN/CLEC-2 axis have not yet been elucidated. Materials and MethodsWe established an immortalized bone marrow PDPN-expressing stromal cell line and a PDPN-knockout line (PDPN WT and KO feeder cells, respectively). Bone marrow hematopoietic progenitors were committed to megakaryocytes in co-culture with PDPN WT or KO feeder cells. The number and ploidy of megakaryocytes, resultant platelets, and the polarization of megakaryocyte subtypes were investigated. ResultsThe number of megakaryocytes was significantly increased in the co-culture with PDPN WT feeder cells compared to that with PDPN KO feeder cells. The megakaryocytes on the PDPN WT and KO feeders showed their main ploidy at 16N[~]32N and 8N[~]16N, respectively. The number of platelets decreased in the co-culture with the PDPN WT feeder compared to those in the co-culture with the PDPN KO feeder. Megakaryocyte subtypes were immunocytochemically detected in in vitro differentiated CD41-positive megakaryocytes. For each megakaryocyte subtype, the percentage of MYLK4-positive megakaryocytes significantly increased and the percentage of BMAL1-positive megakaryocytes significantly decreased when co-cultured with the PDPN WT feeder. ConclusionThe PDPN/CLEC-2 axis modulates megakaryocyte subtype differentiation, with a predominance of HSC-regulating megakaryocytes.

cell biology↗

bioRxiv2024

One step 4x and 12x 3D-ExM: robust super-resolution microscopy in cell biology

Super-resolution microscopy has become an indispensable tool across diverse research fields, offering unprecedented insights into biological architectures with nanometer scale resolution. Compared to traditional nanometer-scale imaging methods such as electron microscopy, super-resolution microscopy offers several advantages, including the simultaneous labeling of multiple target biomolecules with high specificity and simpler sample preparation, making it accessible to most researchers. In this study, we introduce two optimized methods of super-resolution imaging: 4-fold and 12-fold 3D-isotropic and preserved Expansion Microscopy (4x and 12x 3D-ExM). 3D-ExM is a straightforward expansion microscopy method featuring a single-step process, providing robust and reproducible 3D isotropic expansion for both 2D and 3D cell culture models. With standard confocal microscopy, 12x 3D-ExM achieves a lateral resolution of under 30 nm, enabling the visualization of nanoscale structures, including chromosomes, kinetochores, nuclear pore complexes, and Epstein-Barr virus particles. These results demonstrate that 3D-ExM provides cost-effective and user-friendly super-resolution microscopy, making it highly suitable for a wide range of cell biology research, including studies on cellular and chromatin architectures.

cell biology↗

bioRxiv2024

HIV-1 Vif disrupts phosphatase feedback regulation at the kinetochore, leading to a pronounced pseudo-metaphase arrest

Virion Infectivity Factor (Vif) of the Human Immunodeficiency Virus type 1 (HIV-1) targets and degrades cellular APOBEC3 proteins, key regulators of intrinsic and innate antiretroviral immune responses, thereby facilitating HIV-1 infection. While Vifs role in degrading APOBEC3G is well-studied, Vif is also known to cause cell cycle arrest, but the detailed nature of Vifs effects on the cell cycle has yet to be delineated. In this study, we employed high-temporal single-cell live imaging and super-resolution microscopy to monitor individual cells during Vif-induced cell cycle arrest. Our findings reveal that Vif does not affect the G2/M boundary as previously thought. Instead, Vif triggers a unique and robust pseudo-metaphase arrest, distinct from the mild prometaphase arrest induced by Vpr. During this arrest, chromosomes align properly and form the metaphase plate, but later lose alignment, resulting in polar chromosomes. Notably, Vif, unlike Vpr, significantly reduces the levels of both Protein Phosphatase 1 (PP1) and 2A (PP2A) at kinetochores, which regulate chromosome-microtubule interactions. These results unveil a novel role for Vif in kinetochore regulation that governs the spatial organization of chromosomes during mitosis.

microbiology↗

bioRxiv2024

Single-cell analysis of human diversity in circulating immune cells

Lack of diversity and proportionate representation in genomics datasets and databases contributes to inequity in healthcare outcomes globally1,2. The relationships of human diversity with biological and biomedical phenotypes are pervasive3, yet remain understudied, particularly in a single-cell genomics context. Here we present the Asian Immune Diversity Atlas (AIDA), a multi-national single-cell RNA-sequencing (scRNA-seq) healthy reference atlas of human immune cells. AIDA comprises 1,265,624 circulating immune cells from 619 healthy donors and 6 controls, spanning 7 population groups across 5 countries. AIDA is one of the largest healthy blood datasets in terms of number of cells, and also the most diverse in terms of number of population groups. Though population groups are frequently compared at the continental level, we identified a pervasive impact of sub-continental diversity on cellular and molecular properties of immune cells. These included cell populations and genes implicated in disease risk and pathogenesis as well as those relevant for diagnostics. We detected single-cell signatures of human diversity not apparent at the level of cell types, as well as modulation of the effects of age and sex by self-reported ethnicity. We discovered functional genetic variants influencing cell type-specific gene expression, including context-dependent effects, which were under-represented in analyses of non-Asian population groups, and which helped contextualise disease-associated variants. We validated our findings using multiple independent datasets and cohorts. AIDA provides fundamental insights into the relationships of human diversity with immune cell phenotypes, enables analyses of multi-ancestry disease datasets, and facilitates the development of precision medicine efforts in Asia and beyond.

genomics↗

bioRxiv2024

Spatial domain analysis to estimate spatiotemporal pathological mechanisms in microenvironment with single-cell spatial omics data

Single-cell spatial omics analysis requires consideration of biological functions and mechanisms in a microenvironment. However, microenvironment analysis using bioinformatic methods is limited by the need to detect histological morphology. In this study, we developed SpatialKNife (SKNY), an image-processing-based toolkit that detects spatial domains that potentially reflect histology and extends these domains to the microenvironment. The SKNY algorithm identified tumour spatial domains from spatial transcriptomic data of breast cancer, followed by clustering of these domains, trajectory estimation, and spatial extension to the tumour microenvironment (TME). The results of the trajectory estimation were consistent with the known mechanisms of cancer progression. We observed endothelial cell and macrophage infiltration into the TME at mid-stage progression. Our results suggest that analysis using the spatial domain as a unit reflects pathological mechanisms in the TME. This approach may be applicable to the biological estimation of diverse microenvironments.

bioinformatics↗

bioRxiv2024

Tissue growth associated transition of podoplanin-expressing stromal cells in the postnatal mouse femur

In vertebral long bones, such as the femur, bone formation involves endochondral ossification. Endochondral ossification first occurs in the central region of the fetal diaphysis, the primary ossification center. Podoplanin (PDPN) is a transmembrane mucin-like glycoprotein, and PDPN-positive cells play key roles in various organ/tissue development. In adult mice, osteolineage PDPN-positive cells are associated with femoral microarchitecture. However, specific roles of PDPN in fetal bone development remain unclear. Therefore, in this study, we aimed to investigate the spatiotemporal dynamics and physiological functions of PDPN-positive cells during fetal femur development. In the fetal femur, PDPN-positive cells first emerged in the primitive cortical bone, termed the bone collar, concurrently with primary ossification center initiation. Several PDPN-positive cells in the bone collar migrated to the marrow cavity and populated the metaphyseal trabecular bone. Most PDPN-positive cells in both the bone collar and trabeculae exhibited osteolineage features, such as osterix expression. Pdpn knockout fetuses exhibited abnormal recruitment of osterix-positive cells and mineral deposition in the dorsal bone collar. Overall, our results suggest that PDPN-positive cells constitute a spatially regulated osteolineage population that contributes to coordinated fetal femur development.

cell biology↗

bioRxiv2024

Glutathione supersulphide regulates T-cell receptor signalling

Immunometabolism regulates functions and fates of immune cells including T cells. Supersulphides, which are universal metabolites containing catenated sulphur atoms, have various physiological functions based on their unique redox properties. Here we found that activation of T-cell receptor (TCR) signalling was accompanied by supersulphide decrease, which suggests a regulatory contribution of sulphur metabolism to immune function. Consistently, inhibiting supersulphide synthesis facilitated TCR activation and exacerbated allergen-induced type 2 inflammation in mice. Supplementation with glutathione trisulphide (GSSSG), a major endogenous supersulphide, suppressed TCR signalling in naive CD4+ T cells and their differentiation and effectively alleviated the inflammation. Docking simulation revealed interaction of GSSSG with CD3{varepsilon} chain in the TCR/CD3 complex, which was supported by mass spectrometry detection of persulphidated glutathionylation at a functionally important CXXC motif of CD3{varepsilon} chain. This study identified a new post-translational modification with supersulfides and demonstrated a critical contribution of sulphur metabolism to TCR signalling regulation.

biochemistry↗

bioRxiv2024

Sildenafil amplifies calcium influx and insulin secretion in pancreatic β cells

Sildenafil, a phosphodiesterase-5 (PDE5) inhibitor, has been shown to improve insulin sensitivity in animal models and prediabetic patients. However, its other metabolic effects remain poorly investigated. This study examines the impact of sildenafil on insulin secretion in MIN6-K8 mouse clonal {beta} cells. Sildenafil is shown to amplify insulin secretion by enhancing Ca2+ influx, an effect that requires other depolarizing stimuli in MIN6-K8 cells but not in KATP channel-deficient {beta} cells, which are already depolarized. These results indicate that the action of sildenafil is dependent on depolarization and is independent of KATP channels. Furthermore, sildenafil-amplified insulin secretion is not inhibited by nifedipine or PDE5 knockdown. Thus, sildenafil stimulates Ca2+ influx independently of L-type voltage-dependent Ca2+ channels (VDCCs) and PDE5, a mechanism that differs from the known pharmacology of sildenafil and conventional insulin secretory pathways. Our results reposition sildenafil as an insulinotropic agent that can be used as a potential anti-diabetic medicine or a tool to elucidate the molecular mechanism of insulin secretion.

cell biology↗

bioRxiv2024

Nobiletin, a Polymethoxyflavonoid, Activates the Desuccinylase Activity of SIRT5 and Prevents the Development of Heart Failure

Nobiletin is a natural compound useful for the prevention and treatment of several diseases. However, the precise role of nobiletin in heart failure is unclear. Nobiletin treatment prevents pressure overload- and myocardial infarction-induced heart failure. Using affinity purification of biotinylated nobiletin from rat heart cell lysates, we identified sirtuin 5 (SIRT5) as a novel nobiletin-binding protein. Nobiletin enhanced the desuccinylase activity of SIRT5 in vitro. Compared to wild-type mice, SIRT5-overexpressing transgenic mice resisted pressure overload-induced systolic dysfunction. Conversely, SIRT5 knockout disrupted the nobiletin-mediated therapeutic effects on heart failure in mice. SIRT5 desuccinylated p300 at lysine 1568 and reduced the histone acetyltransferase (HAT) activity of p300. The desuccinylated p300 mutant suppressed the phenylephrine-induced cardiomyocyte hypertrophic responses. These findings suggest that nobiletin prevents heart failure development through SIRT5-dependent inhibition of p300-HAT activity. Nobiletin, a nontoxic dietary compound, is a potential therapeutic agent for heart failure in humans.

molecular biology↗

bioRxiv2023

Structural and functional insights into the complex formation of a trimeric autotransporter adhesin with a peptidoglycan-binding periplasmic protein

Trimeric autotransporter adhesins (TAAs) are outer membrane (OM) proteins that are widely distributed in gram-negative bacteria and are involved primarily in adhesion to biotic and abiotic surfaces, cell agglutination, and biofilm formation. TAAs consist of a passenger domain, which is secreted onto the cell surface, and a transmembrane domain, which forms a pore in the OM to secrete and anchor the passenger domain. Because the interactions between TAAs and chaperones or dedicated auxiliary proteins during secretion are short-lived, TAAs are thought to reside on the OM without forming complexes with other proteins after secretion. In this study, we aimed to clarify the interactions between an Acinetobacter TAA, AtaA, and a peptidoglycan (PG)-binding periplasmic protein, TpgA. Pull-down assays using recombinant proteins identified the interacting domains. X-ray crystallography at 2.6 [A] resolution revealed an A3B3 heterohexameric complex structure composed of the N-terminal domain of TpgA and the transmembrane domain of AtaA. TpgA-N consists of two short helices and three antiparallel {beta} strands, yielding an {beta}{beta}{beta} topology similar to BamE. However, the regions corresponding to BamE interfaces with BamA and BamD differ in TpgA-N. All-atom molecular dynamics simulations and mutational assays revealed that both electrostatic and hydrophobic interactions contribute to stable complex formation. Bioinformatic analyses indicate that the TAA-TpgA complex occurs in a wide range of species. These findings will contribute to a better understanding of TAAs and the cell envelope. ImportanceGram-negative bacteria have specialized secretion systems (SSs) that translocate molecules from the cytoplasm to the extracellular space. Type V SSs have a simpler structure consisting of a functional passenger domain and a transmembrane domain involved in the secretion and anchoring of the passenger domain. Here, we provide the first direct evidence that a trimeric autotransporter adhesin (TAA) exported by a type Vc system forms a stable complex with a peptidoglycan-binding periplasmic protein. The 2.6 [A] structure of the A3B3 heterohexamer, together with simulation and mutational data, reveals complementary electrostatic and hydrophobic contacts that stabilize flexible loops on the periplasmic face of the TAA transmembrane barrel. Conservation of the taa-tpgA gene cassette and of key interface residues across diverse genera suggests that this coupling is a common strategy for tuning TAA stability and indicates that the envelope architecture of many TAAs, including those related to pathogenicity, is more elaborate than previously appreciated.

microbiology↗

bioRxiv2023

Basement membrane extract potentiates the endochondral ossification phenotype of bone marrow-derived mesenchymal stem cell-based cartilage organoids

Endochondral ossification is a developmental process in the skeletal system and bone marrow of vertebrates. During endochondral ossification, primitive cartilaginous anlages derived from mesenchymal stem cells (MSCs) undergo vascular invasion and ossification. In vitro regeneration of endochondral ossification is beneficial for research on the skeletal system and bone marrow development as well as their clinical aspects. However, to achieve the regeneration of endochondral ossification, a stem cell-based artificial cartilage (cartilage organoid, Cart-Org) that possesses an endochondral ossification phenotype is required. Here, we modified a conventional 3D culture method to create stem cell-based Cart-Org by mixing it with a basement membrane extract (BME) and further characterized its chondrogenic and ossification properties. BME enlarged and matured the bone marrow MSC-based Cart-Orgs without any shape abnormalities. Histological analysis using Alcian blue staining showed that the production of cartilaginous extracellular matrices was enhanced in Cart-Org treated with BME. Transcriptome analysis using RNA sequencing revealed that BME altered the gene expression pattern of Cart-Org to a dominant chondrogenic state. BME triggered the activation of the SMAD pathway and inhibition of the NK-{kappa}B pathway, which resulted in the upregulation of SOX9, COL2A1, and ACAN in Cart-Org. BME also facilitated the upregulation of genes associated with hypertrophic chondrocytes (IHH, PTH1R, and COL10A1) and ossification (SP7, ALPL, and MMP13). Our findings indicate that BME promotes cartilaginous maturation and further ossification of bone marrow MSC-based Cart-Org, suggesting that Cart-Org treated with BME possesses the phenotype of endochondral ossification. HighlightsO_LIBasement membrane extract (BME) enlarges MSC-based Cart-Org. C_LIO_LIBME activates the SMAD pathway and inhibits the NK-kB pathway of the Cart-Org. C_LIO_LIBME promotes cartilaginous maturation and further ossification of Cart-Org. C_LI

cell biology↗

bioRxiv2023

A single-cell atlas of transcribed cis-regulatory elements in the human genome

Transcribed cis-regulatory elements (tCREs), such as promoters and enhancers, are fundamental to modulate gene expression and define cell identity. The detailed mapping of tCREs at single-cell resolution is essential for understanding the regulatory mechanisms that govern cellular functions. Prior tCRE catalogs, limited by bulk analysis, have often overlooked cellular heterogeneity. We have constructed a tCRE atlas using single-cell 5-RNA-seq, capturing over 340,000 single-cells from 23 human tissues and annotating more than 175,000 tCREs, substantially enhancing the scope and granularity of existing cis-regulatory element annotations in the human genome. This atlas unveils patterns of gene regulation, revealing connections between broadly expressed promoters and cell type-specific distal tCREs. Assessing trait heritability at single-cell resolution with a novel tCRE module-based approach, we uncovered the nuanced trait-gene regulatory relationships across a continuum of cell populations, offering insights beyond traditional gene-level and bulk-sample analyses. Our study bridges the gap between gene regulation and trait heritability, underscoring the potential of single-cell analysis to elucidate the genetic foundations of complex traits. These insights set the stage for future research to investigate the impact of genetic variations on diseases at the individual level, advancing the understanding of cellular and molecular basis of trait heritability.

genomics↗

bioRxiv2023

Identification of novel autophagy inducers by accelerating lysosomal clustering against Parkinson's disease

Autophagy-lysosome pathway plays an indispensable role in the intracellular protein quality control system, degrading abnormal organelles and proteins. Among these proteins is -Synuclein (Syn), which is associated with the pathogenesis of Parkinsons disease (PD). However, the activation of this lysosome-dependent degradation strategy is restricted by enzyme complementation. In this study, we focused on the phase of autophagosome-lysosome fusion around the microtubule organizing center (MTOC) that leads to Syn degradation. Through high-throughput chemical screening, we identified six clinically available drugs that enhance autophagy and can accumulate lysosomes around the MTOC from approximately 1,200 drugs screened. We further demonstrated that these compounds induce lysosomal clustering through a JIP4-TRPML1-dependent mechanism, which is associated with autophagy induction. Among these, the lysosomal clustering compound albendazole was observed to promote the autophagy-dependent degradation of Triton-X-insoluble proteasome inhibitor-induced aggregates (p62). In a cellular PD model, albendazole boosted the degradation of insoluble Syn, an effect that was reversed upon the addition of bafilomycin A1. Our results suggest that lysosomal clustering can facilitate the breakdown of protein aggregates. Therefore, compounds that promote lysosomal clustering may offer a promising therapeutic strategy against neurodegenerative diseases characterized by the presence of aggregate-prone proteins.

cell biology↗