Biology subjects

Qin, Y.

Publications and source records attributed to Qin, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2023

Molecular Evolution and Interaction of 14-3-3 Proteins with H+-ATPases in Plant Abiotic Stresses

Environmental stresses severely affect plant growth and crop productivity. Regulated by 14-3-3 proteins (14-3-3s), H+-ATPases (AHA) are important proton pumps that can induce diverse secondary transport via channels and co-transporters for the abiotic stress response of plants. Many studies demonstrated the roles of 14-3-3s and AHAs in coordinating the processes of plant growth, phytohormone signaling, and stress responses. However, the molecular evolution of 14-3-3s and AHAs has not been summarized in parallel with insights across multiple plant species. Here, we review the roles of 14-3-3s and AHAs in cell signaling to enhance plant responses to diverse environmental stresses. We analyzed the molecular evolution of key proteins that are associated with 14-3-3s and AHAs in plant growth and hormone signaling. The results revealed evolution, duplication, contraction, and expansion of 14-3-3s and AHAs in green plants. We also discussed the stress-specific expression of those 14-3-3s and AHAs in a eudicot (Arabidopsis thaliana), a monocot (Hordeum vulgare) and a moss (Physcomitrium patens) under abiotic stresses. We propose that 14-3-3s and H+-ATPases respond to abiotic stresses through many important targets and signaling components of phytohormones, which could be promising to improve plant tolerance to single or multiple environmental stresses. HighlightWe review the response and adaptation of 14-3-3s and AHAs to diverse environmental stimuli and we analyze the evolutionary features and molecular functions of 14-3-3s and AHAs.

plant biology↗

bioRxiv2023

Hypoxia-induced circSTT3A maintains Breast Cancer Stem Cell formation by Stabilizing PGK1 protein

BackgroundHypoxia is a key feature of tumor microenvironment that can cause fundamental changes in cancer cells, and may also lead to the development of breast cancer stem cells (BCSCs) with self-renewal ability. However, the mechanism of hypoxia in inducing BCSCs is not fully understood. MethodsPerforming RNA sequence and bioinformatics analysis, a hypoxia specific circular RNA (circRNA), named circSTT3A, was identified in hypoxic breast cancer cells and tissues. The clinical significance of circSTT3A was investigated in breast cancer (BC) tissues and tissue array. The loss and acquisition of circSTT3A were carried out in vivo and in vitro to confirm its functional roles in BCSC stemness maintenance. HIF1 droved circSTT3A expression was evaluated by chromatin immunoprecipitation and dual luciferase reporter assays. RNA pull-down, RNA immunoprecipitation, silver staining detection, mass spectrographic analysis, co-immunoprecipitation assays and western blotting were exerted to determine circSTT3A directly binding with HSP70 and PGK1 proteins. CircSTT3A-mediated serine metabolism was determined by UHPLC-QTRAP-MS system and ELISA kit. BC mouse model was used to assess the effects of circSTT3A/Hsp70/PGK1 on tumorigenesis and chemotherapy resistance in vivo. ResultsA novel hypoxia specific circSTT3A was significantly upregulated in clinical breast cancer tissues, and was related to the clinical stage and poor prognosis of BC patients. The hypoxia inducible factor 1 alpha (HIF1)-regulated circSTT3A has remarkable effect on mammosphere formation in breast cancer cells. Our work revealed that circSTT3A directly interacting with nucleotide-binding domain of heat shock protein 70 (HSP70) increases the ability of HSP70 to recruit phosphoglycerate kinase 1 (PGK1) via its substrate-binding domain, which reduces the ubiquitination of PGK1 and increases the stability of PGK1. The enhanced PGK1 catalyzes 1,3-diphosphoglycerate (1, 3-BPG) into 3-phosphoglycerate (3-PG) leading to 3-PG accumulation and increase of serine synthesis, thus to facilitate BCSC enrichment under hypoxic microenvironment. Loss of circSTT3A or PGK1 substantially induces suppression in tumor initiation and tumor growth, which dramatically increases tumor sensitivity to Doxorubicin treatment in mice. ConclusionsHypoxia induced circSTT3A/HSP70/PGK1 axis plays a critical role in maintaining BCSC properties and may be meaningful for treating patients with breast cancer.

cancer biology↗

bioRxiv2023

xQTLbiolinks: a comprehensive and scalable tool for integrative analysis of molecular QTLs

Genome-wide association studies (GWAS) have identified thousands of disease-associated non-coding variants, posing urgent needs for functional interpretation. Molecular quantitative trait loci (xQTLs) such as eQTLs serve as an essential intermediate link between these non-coding variants and disease phenotypes and have been widely used to discover disease-risk genes from many population-scale studies. However, mining and analyzing the xQTLs data presents several significant bioinformatics challenges, particularly when it comes to integration with GWAS data. Here, we developed xQTLbiolinks as the first comprehensive and scalable tool for xQTLs data retrieval, quality controls, and pre-processing from 75 human tissues and cell types. In addition, xQTLbiolinks provided a robust colocalization module through integration with GWAS data. The result generated by xQTLbiolinks can be flexibly visualized or stored in standard R objects that can easily be integrated with other R packages and custom pipelines. We applied xQTLbiolinks to cancer GWAS summary statistics as case studies and demonstrated its robust utility and reproducibility. xQTLbiolinks will profoundly accelerate the interpretation of disease-associated variants, thus promoting a better understanding of disease etiologies. xQTLbiolinks is available at https://github.com/lilab-bioinfo/xQTLbiolinks.

bioinformatics↗

bioRxiv2023

Substrate specificity and functional conservation of SWEET10 transporter in pineapple

O_LISWEET transporters are a unique class of sugar transporters that play vital roles in various developmental and physiological processes in plants. C_LIO_LIWhile the functions of SWEETs have been well established in model plants such as Arabidopsis, their functions in economically important fruit crops like pineapple have not been well studied. C_LIO_LIThis study investigated the substrate specificity of pineapple SWEETs by comparing the protein sequences of known glucose and sucrose transporters in Arabidopsis to those in pineapple. C_LIO_LIGenome-wide approach and 3D structure comparison showed that the Arabidopsis SWEET8 homolog in pineapple, AcSWEET10, shares similar sequences and protein properties responsible for glucose transport. To determine the functional conservation of AcSWEET10, its ability to complement glucose transport mutants in yeast, its expression in stamens, and its impact on the microspore phenotype and seed set in transgenic Arabidopsis were analyzed. C_LIO_LIAcSWEET10 was found to be functionally equivalent to AtSWEET8 and plays a critical role in regulating microspore formation through the regulation of CalS5. C_LIO_LIManipulating SWEET transporter activity could have important implications for improving fruit crop yield and quality. C_LI

plant biology↗

bioRxiv2023

Thalamic regulation of ocular dominance plasticity in adult visual cortex

Experience-dependent plasticity in the adult visual system is generally thought of as a cortical process. However, several recent studies have shown that perceptual learning or monocular deprivation can also induce plasticity in the adult dorsolateral geniculate nucleus (dLGN) of the thalamus. How plasticity in the thalamus and cortex interact in the adult visual system is ill understood. To assess the influence of thalamic plasticity on plasticity in primary visual cortex (V1), we made use of our previous finding that during the critical period, ocular dominance (OD) plasticity occurs in dLGN and requires thalamic synaptic inhibition. Using multielectrode recordings we find that this is also true in adult mice, and that in the absence of thalamic inhibition and plasticity, OD plasticity in adult V1 is absent. To study the influence of V1 on thalamic plasticity we silenced V1 and show that during the critical period, but not in adulthood, the OD shift in dLGN is partially caused by feedback from V1. We conclude that during adulthood, the thalamus plays an unexpectedly dominant role in experience-dependent plasticity in V1. Our findings highlight the importance of considering the thalamus as a potential source of plasticity in learning events that are typically thought of as cortical processes.

neuroscience↗

bioRxiv2023

Design and characterization of porous poly(glycerol-dodecanedioate) scaffolds for cartilage repair

Synthetic polymeric scaffolds play an important role in establishing the microenvironment for chondrocytes in engineered cartilage. A three-dimensional pore network allows cell accommodation and supports extracellular matrix (ECM) production by chondrocytes. Ligand coating and biomechanical properties of scaffolds guide regeneration of functional cartilage by mediating cell attachment and establishing the local strain environment. Poly(glycerol-dodecanedioate) (PGD) is a novel biodegradable elastomer with nonlinear-elastic properties similar to native cartilage. However, its harsh curing environments limit the feasibility of common strategies for pore creation in polymeric scaffolds. Herein, we developed porous PGD (pPGD) scaffolds with tailorable pore structures using an inverse molding method and evaluated the range of scaffold structural parameters achievable and their subsequent mechanical properties. The influence of coating PGD with various ECM ligands on the cell shape, metabolic activity, and ECM production of human articular chondrocytes (hACs) was evaluated. pPGD scaffolds were created with pore sizes ranging from 250 - 1000 m, resulting in 20 - 50% porosity. The morphology and metabolic activity of hACs on PGD were regulated by the type of ligand coating used. When compared to tissue culture plastic, PGD enhanced ECM production in monolayer cultures. Finite element analysis showed that the tensile strains that developed on the pores surfaces were at levels shown to be anabolic for hACs. The predicted strain profile varied with pore size and porosity under load, demonstrating that the pore structural parameters could be tuned to optimize cellular-level strains. These results suggest that pPGD scaffolds have the potential to guide cartilage regeneration. Statement of SignificancePrevious studies have established the importance of designing pore geometry and surface properties in engineered cartilage tissue constructs. This work reports the development and assessment of pPGD scaffolds with tunable pore and surface parameters for cartilage regeneration. The cellular-level strain that cells may experience inside the pores was influenced by the scaffolds pore geometry. Ligand coating on PGD balanced out the less ideal properties of the material itself and regulated the shape, attachment, metabolic activity, and ECM production of hACs during in vitro culture. These findings highlight how intelligent design of scaffold parameters can optimize chondrocyte function during 3D culture by tuning ligand presentation and cellular-level strain profiles.

bioengineering↗

bioRxiv2023

Transmembrane protein CD69 acts as an S1PR1 agonist

The activation of Sphingosine-1-phosphate receptor 1 (S1PR1) by S1P promotes lymphocyte egress from lymphoid organs, a process critical for immune surveillance and T cell effector activity 1-4. Multiple drugs that inhibit S1PR1 function are in use clinically for the treatment of autoimmune diseases. Cluster of Differentiation 69 (CD69) is an endogenous negative regulator of lymphocyte egress that interacts with S1PR1 in cis to facilitate internalization and degradation of the receptor 5,6. The mechanism by which CD69 causes S1PR1 internalization has been unclear. Moreover, although there are numerous class A GPCR structures determined with different small molecule agonists bound, it remains unknown whether a transmembrane protein per se can act as a class A GPCR agonist. Here, we present the cryo-EM structure of CD69-bound S1PR1 coupled to the heterotrimeric Gi complex. The transmembrane helix (TM) of one protomer of CD69 homodimer contacts the S1PR1-TM4. This interaction allosterically induces the movement of S1PR1-TMs 5-6, directly activating the receptor to engage the heterotrimeric Gi. Mutations in key residues at the interface affect the interactions between CD69 and S1PR1, as well as reduce the receptor internalization. Thus, our structural findings along with functional analyses demonstrate that CD69 acts in cis as a protein agonist of S1PR1, thereby promoting Gi-dependent S1PR1 internalization, loss of S1P gradient sensing, and inhibition of lymphocyte egress.

biophysics↗

bioRxiv2023

Endothelial vacuole membrane enriched aquaporins regulate microvascular lumenization in development and hyperglycemia

BackgroundIn patients with diabetic microvascular complications, decreased perfusion or vascular occlusion, caused by reduced vascular diameter, is a common characteristic that will lead to insufficient blood supply. However, the regulatory mechanism remains undetermined and the treatment approach is lacking. MethodsGene expression of Aquaporin 1 (AQP1) was compared between diabetic and non-diabetic human retina samples. Confocal live imaging analysis of zebrafish was utilized to investigate the hyperglycemia-induced alterations in vascular morphology. Transcriptomic and single-cell RNA sequencing, in situ hybridization, and quantitative PCR were used to analyze gene expressions. Gene knock-out zebrafish and stable transgenic lines were established for functional analysis. Human embryonic stem cells (H1 line), H1-derived endothelial cells (ECs), human umbilical vein endothelial cells (HUVECs), and human retinal microvascular endothelial cells (HRMECs) were used for functional analysis. ResultsFirstly, we found that the expression of human AQP1 was downregulated in diabetic human retina samples (49 healthy vs. 54 diabetic samples) and high-glucose-treated human retinal microvascular endothelial cells. Then, we observed the reduction of vascular diameter and compromised perfusion in high glucose-treated zebrafish embryos. Two aquaporins (aqp1a.1 and aqp8a.1), highly enriched in ECs, were significantly down-regulated under hyperglycemic conditions. Aqp1a.1 and/or aqp8a.1 loss-of-function leaded to reduction in intersegmental vessel diameters, recapitulating the phenotype of the hyperglycemic zebrafish model. Overexpressing aqp1a.1/aqp8a.1 in zebrafish ECs promoted the enlargement of microvascular diameters. Moreover, the reduced vessel diameters induced by high-glucose treatment was rescued by aquaporin overexpression. In addition, both aqp1a.1 and apq8a.1 were localized in the intracellular vacuoles in cultured ECs as well as the ECs of sprouting ISVs, and loss of Aqps caused the reduction of those vacuoles, which was required for lumenization. Loss of AQP1 had no influence on EC differentiation from human stem cells but strongly inhibited the vascular tube formation of differentiated ECs. ConclusionsEC-enriched aquaporins regulate intracellular vacuole-mediated blood vessel diameter hyperglycemia. All of these suggest that EC-expressed aquaporins might be potential targets for gene therapy to cure diabetes-related vascular perfusion defects.

cell biology↗

bioRxiv2022

Perinuclear force regulates SUN2 dynamics and distribution on the nuclear envelope for proper nuclear mechanotransduction

The trans-luminal LINC (Linker of Nucleoskeleton and Cytoskeleton) complex plays a central role in nuclear mechanotransduction by coupling the nucleus with cytoskeleton. High spatial density and active dynamics of LINC complex have hindered its precise characterization for the understanding of underlying mechanisms how the linkages sense and respond to mechanical stimuli. In this study, we focus on SUN2, a core component of LINC complex interconnecting the nuclear lamina and actin cytoskeleton and apply single molecule super-resolution imaging to reveal how SUN2 responds to actomyosin contractility. Using stochastic optical reconstruction microscopy (STORM), we quantitated the distribution pattern and density of SUN2 on the basal nuclear membrane. We found that SUN2 undergoes bidirectional translocation between ER and nuclear membrane in response to actomyosin contractility, suggesting that dynamic constrained force on SUN2 is required for its proper distribution. Furthermore, single molecule imaging unveils interesting dynamics of SUN2 molecules that are regulated by both actomyosin contractility and laminA/C network, whereas SUN2 oligomeric states are not affected by actomyosin contractility. Lastly, the mechanical response of SUN2 to actomyosin contractility was found to regulate expression of mechano-sensitive genes located in lamina-associated domains (LADs) and perinuclear heterochromatin. Taken together, our results reveal how SUN2 responds to mechanical cues at the single-molecule level, providing new insights into the mechanism of nuclear mechanotransduction.

cell biology↗

bioRxiv2022

Latitude influences stability via stabilizing mechanisms in naturally-assembled forest ecosystems at different spatial grains

Ecosystem stability reveals how ecosystems respond to global change over time. Yet, the focus of past research on small spatial grains and extents overlooks scale dependence and how broad-scale environmental gradients shape stability. Here, we use forest inventory data covering a broad latitudinal gradient from the temperate to the tropical zone to examine cross-scale variation in stability of aboveground biomass and underlying stabilizing mechanisms. While stability did not shift systematically with latitude at either spatial grain, we found evidence that species asynchrony increased towards the tropics at the small spatial grain while species stability decreased at both spatial grains. Moreover, latitude stabilized forest communities via its effects on both stabilizing mechanisms, which compensated for the weak and destabilizing effects of species richness. Yet, the trade-off in the relative importance of species stability and species asynchrony for stability was not mediated by latitude, suggesting that context-dependent factors - to a greater extent than macroecological ones - underlie large-scale patterns of stability. Our results highlight the crucial role of species asynchrony and species stability in determining ecosystem stability across broad-scale environmental gradients, suggesting that conserving biodiversity alone may not be sufficient for stabilizing naturally-assembled forest ecosystems.

ecology↗

bioRxiv2022

Stat3 has a different role in axon growth during development than it does in axon regeneration after injury

Signal transducer and activator of transcription 3 (STAT3) is essential for neural development and regeneration as a key transcription factor and mitochondrial activator. In this study, using zebrafish posterior lateral line (PLL) axons, we demonstrate that Stat3 plays distinct roles in PLL axon embryonic growth and regeneration. In zebrafish stat3 mutants the PLL axons were truncated during embryonic growth. Expressing stat3 in neurons of the PLL ganglion rescued their axon growth suggesting stat3 promoted PLL axon growth in a cell-autonomous manner. Using Jak/Stat signaling inhibitors or modified Stat3, we found Jak/Stat signaling was dispensable for PLL axon growth. We showed that Stat3 was co-localized with mitochondria in PLL axon and lower ATPase activity in stat3 mutant embryos than wild-type embryos. The PLL axon growth was affected by mitochondrial modulators indicating that Stat3 regulated PLL axon growth through mitochondrial Stat3 function. Mutation of stat3 or treating with Jak/Stat signaling inhibitors retarded PLL axon regeneration and Schwann cell migration. Taken together, Stat3 is required for embryonic PLL axon growth by regulating the ATP synthesis efficiency of mitochondria, whereas Stat3 stimulates PLL axon regeneration through regulating Schwann cell migration via Jak/Stat signaling. Our findings show a new mechanism of Stat3 in axon growth and regeneration. Author SummaryNeurons are one of the most specialized cell type in our body. A slender axon used for transmitting information between neuron and target cell extends from the cell body. Axon extension during both development and regeneration is regulated by intrinsic and extrinsic factors. In this study, we used the zebrafish posterior lateral line (PLL) axons which extends a long distance to study the regulation of axon extension. Signal transducer and activator of transcription 3 (STAT3) is a key transcription factor in Jak/Stat signaling and an activator for mitochondria functions. Our results demonstrate that Stat3 plays distinct roles in PLL axons development and regeneration. During embryonic development, Jak/Stat signaling is dispensable for PLL axons extension, whereas the mitochondrial Stat3 is required for embryonic axon growth through promoting ATP synthesis. During PLL axons regeneration, Jak/Stat is essential for Schwann cells migration which mediates axon regeneration.

developmental biology↗

bioRxiv2022

A non-human primate model with Alzheimer's disease-like pathology induced by hippocampal overexpression of human tau

Alzheimers disease (AD) is one of the most burdening diseases of the century with no disease-modifying treatment yet. Non-human primates (NHPs) share genetic, anatomical and physiological similarities with humans, making them an ideal model for investigating the pathogenesis and therapeutics of AD. However, the applications of NHPs in AD research have been hindered by the paucity of spontaneous or induced monkey models for AD due to their long generation time, ethical considerations and technical challenges in making genetically modified monkeys. Here we developed an AD-like NHP model by overexpressing human tau in bilateral hippocampi of adult rhesus macaque monkeys. We evaluated the pathological features of these monkeys with immunostaining, cerebrospinal fluid (CSF) analysis, magnetic resonance imaging (MRI), positron emission tomography (PET) scan, and behavioral tests. We demonstrated that after hippocampal overexpression of human tau, the rhesus macaque monkeys displayed multiple pathological features of AD, including neurofibrillary tangle formation, neuronal loss, hippocampal atrophy, neuroinflammation, A{beta} clearance deficit, blood vessel damage and cognitive decline. This work establishes a human tau-induced AD-like NHP model that may facilitate mechanistic studies and therapeutic treatments for AD.

neuroscience↗

bioRxiv2022

Targeting IRS-1/2 in uveal melanoma inhibits in vitro cell growth, survival and migration, and in vivo tumor growth.

Uveal melanoma (UM) originating in the eye and metastasizing to the liver is associated with poor prognosis and has only one approved therapeutic option. We hypothesized that liver-borne growth factors may contribute to UM growth. Therefore, we investigated the role of insulin-like growth factor -1 and its receptor (IGF-1/IGF-1R) signaling in UM. We found that the insulin receptor substrate -1 (IRS-1) is overexpressed in UM cells and tumors. Since we previously observed that IGF-1R antibody therapy was not clinically effective in UM, we investigated the potential of NT157, a small molecule inhibitor of IRS-1/2 in blocking this pathway in UM. NT157 treatment in UM cells resulted in reduced cell survival and migration, and increased apoptosis. This treatment also significantly inhibited UM tumor growth in vivo, in the chicken egg chorioallantoic membrane (CAM) and subcutaneous mouse models, validating the in vitro effect. Mechanistically, through reverse phase protein array (RPPA), we identified significant proteomic changes in the PI3K/AKT pathway, a downstream mediator of IGF-1 signaling, with NT157 treatment. Together, these results suggest that NT157 inhibits cell survival, migration in vitro and tumor growth in vivo via inhibiting IGF-1 signaling in UM.

cell biology↗

bioRxiv2022

Bat pluripotent stem cells reveal unique entanglement between host and viruses

Bats have evolved features unique amongst mammals, including flight, laryngeal echolocation, and certain species have been shown to have a unique immune response that may enable them to tolerate viruses such as SARS-CoVs, MERS-CoVs, Nipah, and Marburg viruses. Robust cellular models have yet to be developed for bats, hindering our ability to further understand their special biology and handling of viral pathogens. To establish bats as new model study species, we generated induced pluripotent stem cells (iPSCs) from a wild greater horseshoe bat (Rhinolophus ferrumequinum) using a modified Yamanaka protocol. Rhinolophids are amongst the longest living bat species and are asymptomatic carriers of coronaviruses, including one of the viruses most closely related to SARS-CoV-2. Bat induced pluripotent stem (BiPS) cells were stable in culture, readily differentiated into all three germ layers, and formed complex embryoid bodies, including organoids. The BiPS cells were found to have a core pluripotency gene expression program similar to that of other species, but it also resembled that of cells attacked by viruses. The BiPS cells produced a rich set of diverse endogenized viral sequences and in particular retroviruses. We further validated our protocol by developing iPS cells from an evolutionary distant bat species Myotis myotis (greater mouse-eared bat) non-lethally sampled in the wild, which exhibited similar attributes to the greater horseshoe bat iPS cells, suggesting that this unique pluripotent state evolved in the ancestral bat lineage. Although previous studies have suggested that bats have developed powerful strategies to tame their inflammatory response, our results argue that they have also evolved mechanisms to accommodate a substantial load of endogenous viral sequences and suggest that the natural history of bats and viruses is more profoundly intertwined than previously thought. Further study of bat iPS cells and their differentiated progeny should advance our understanding of the role bats play as virus hosts, provide a novel method of disease surveillance, and enable the functional studies required to ascertain the molecular basis of bats unique traits.

developmental biology↗

bioRxiv2022

A gene expression analysis and immune infiltration between lesioned and preserved subchondral bone in osteoarthritis

BackgroundOsteoarthritis (OA) is a degenerative disease which need more research. The purpose of this study was to performed gene expression analysis and immune infiltration between lesioned and preserved subchondral bone, and validation with datasets and experiment of multiple tissues. MethodsThe different expressed genes(DEGs) of GSE51588 datasets between lesioned and preserved tibial plateaus of OA patients were conducted. Moreover, functional annotation and protein-protein interaction (PPI) network were applied for exploring the potential therapeutic targets in OA subchondral bones between lesioned and preserved sides. In addition, multiple tissues were used to screen out co-expressed genes and the expression levels of identified candidate DEGs was detected by quantitative real-time polymerase chain reaction (qRT-PCR) in OA. Finally, immune infiltration analysis was conducted. ResultsA total of 1010 DEGs were identified, including upregulated 423 genes, 587 downregulated genes. Upregulated genes showed that BP terms were enriched in "skeletal system development", "sister chromatid cohesion","ossification" etc. Pathways were enriched in "Wnt signaling pathway," "Proteoglycans in cancer," Downregulated genes showed that BP terms were enriched in "inflammatory response," "xenobiotic metabolic process", "positive regulation of inflammatory response". Pathways were enriched in "Neuroactive ligand-receptor interaction", "AMPK signaling pathway" etc. JUN, TNF, IL1B,were the hub genes in the PPI network. Col1A1 and LRRC15 were screened out by multiple datasets and validated by experiments. Immune infiltration showed adipocytes and endothelial cells infiltrated less in lesioned samples. ConclusionOur research might provide valuable information for exploring the pathogenesis mechanism of OA and identifying the potential therapy targets for OA diagnosis.

molecular biology↗

bioRxiv2022

Lipids Maintain Genomic Stability and Developmental Potency of Murine Pluripotent Stem Cells

Lipids play vital roles in cellular homeostasis and regulate pluripotency of human stem cells. However, the impact of lipids on murine pluripotent stem cells is unclear. While Mek1/2 and Gsk3{beta} inhibition ("2i") supports the maintenance of murine embryonic stem cells (ESCs) in a homogenous naive state, prolonged culture in 2i results in aneuploidy and DNA hypomethylation that impairs developmental potential. Additionally, 2i fails to support derivation and culture of fully potent female ESCs. Here we find that mouse ESCs cultured in 2i/LIF supplemented with lipid-rich albumin (AlbuMAX) undergo pluripotency transition yet maintain genomic stability and full potency over long-term culture. Mechanistically, lipids in AlbuMAX impact intracellular metabolism including nucleotide biosynthesis, lipid biogenesis, and TCA cycle intermediates, with enhanced expression of ZCAN4 and DNMT3s that prevent telomere shortening and DNA hypomethylation. In concert with 2i, lipids induce a formative-like pluripotent state through direct stimulation of Mek-mediated Erk2 phosphorylation, which also alleviates X chromosome loss in female ESCs. Importantly, both male and female "all-ESC" mice can be generated from de novo derived ESCs using AlbuMAX-based media. Our findings underscore the importance of lipids to pluripotency and link nutrient cues to genome integrity in early development.

developmental biology↗

bioRxiv2022

Bone marrow AdipoQ-lineage progenitors are a major cellular source of M-CSF that dominates bone marrow macrophage development, osteoclastogenesis and bone mass

M-CSF is a critical growth factor for myeloid lineage cells, including monocytes, macrophages and osteoclasts. Tissue resident macrophages in most organs rely on local M-CSF. However, it is unclear what specific cells in bone marrow produce M-CSF to maintain myeloid homeostasis. Here, we identify bone marrow AdipoQ-lineage progenitors, but not bone marrow mature adipocytes or peripheral adipose tissue, as a major cellular source of M-CSF, with these AdipoQ-lineage progenitors producing M-CSF at levels much higher than those produced by osteoblast lineage cells. Deficiency of M-CSF in bone marrow AdipoQ-lineage progenitors drastically reduces the generation of bone marrow macrophages and osteoclasts, leading to severe osteopetrosis in mice. Furthermore, the postmenopausal osteoporosis in a mouse model can be significantly alleviated by the lack of M-CSF in bone marrow AdipoQ-lineage progenitors. Our findings identify bone marrow AdipoQ-lineage progenitors as a major cellular source of M-CSF in bone marrow and reveal their crucial contribution to bone marrow macrophage development, osteoclastogenesis, bone homeostasis and pathological bone loss.

cell biology↗

bioRxiv2022

Application of metallo-supramolecular branched polymer improves particle distribution and orientation in single-particle cryo-EM

Recent technological breakthroughs in single-particle cryo-electron microscopy (cryo-EM) enabled rapid atomic structure determination of biological macromolecules. A major bottleneck in the current single particle cryo-EM pipeline is the preparation of good quality frozen cryo-EM grids, which is mostly a trial-and-error process. Among many issues, preferred particle orientation and sample damage by air-water interface (AWI) are common practical problems. Here we reported a method of applying metallo-supramolecular branched polymer (MSBP) in the cryo-sample preparation for high-resolution single-particle cryo-EM. Our data shows that MSBP keeps a majority of particles away from air-water interface and mitigates preferred orientation as verified by the analyses of apoferritin, hemagglutinin (HA) trimer and various sample proteins. The use of MSBP is a simple method to improve particle distribution for high-resolution structure determination in single-particle cryo-EM.

biophysics↗