Biology subjects

Chen, B.

Publications and source records attributed to Chen, B..

At least 145 records · Page 8Linked to original sources

bioRxiv2024

Ascorbate depletion increases quiescence and self-renewal potential in hematopoietic stem cells and multipotent progenitors

Ascorbate (vitamin C) limits hematopoietic stem cell (HSC) function and suppresses leukemia development by promoting the function of the Tet2 tumor suppressor. In humans, ascorbate is obtained from the diet while in mice it is synthesized in the liver. In this study, we show that deletion of the Slc23a2 ascorbate transporter severely depleted ascorbate from hematopoietic cells. Slc23a2 deficiency increased HSC reconstituting potential and self-renewal potential upon transplantation into irradiated mice. Slc23a2 deficiency also increased the reconstituting and self-renewal potential of multipotent hematopoietic progenitors (MPPs), conferring the ability to long-term reconstitute irradiated mice. Slc23a2-deficient HSCs and MPPs divided much less frequently than control HSCs and MPPs. Increased self-renewal and reconstituting potential were observed particularly in quiescent Slc23a2-deficient HSCs and MPPs. The effect of Slc23a2 deficiency on MPP self-renewal was not mediated by reduced Tet2 function. Ascorbate thus regulates quiescence and restricts self-renewal potential in HSCs and MPPs such that ascorbate depletion confers MPPs with long-term self-renewal potential. KEY POINTSO_LIDeletion of the ascorbate transporter, Slc23a2, increases quiescence and self-renewal potential in HSCs and multipotent progenitors C_LIO_LIAscorbate depletion is sufficient to confer long-term self-renewal potential upon multipotent hematopoietic progenitors C_LI

cell biology↗

bioRxiv2024

Functional characterization of Lipid storage droplets 1 (LSD1) in growth and lipolysis of Hermetia illucens

As intracellular organelles in adipose tissue, lipids droplets manage the balance between triglyceride accumulation and energy consumption in animals. Perilipin family members, associated with surface of lipid droplets, participate the regulation of lipid metabolism. Lipid storage droplet-1 (LSD1)/Perilipin-1 acts as a gatekeeper for adipose lipid storage in animals. Despite extensive studies in fruit fly, the function of LSD1 in insect larval stage remain indistinct. In this study, we characterized the function of LSD1 in black soldier fly Hermetia illucens, a nova resource insect to recycle organic wastes. We found that LSD1 was broadly present in dipteran species and evolved with divergence between mosquitos and flies. We further constructed in vivo mutagenesis mediated by CRISPR/Cas9 and found that mutations in LSD1 increased the larval weight and did not bring any defects in development. Raw fat content was also not significantly influenced in late larval stage and new-emerged adults. Our results not only extend our knowledge of LSD1 in insects, but also help for better understanding of the lipid homeostasis in BSF.

zoology↗

bioRxiv2024

ELO-6 expression predicts longevity in isogenic populations of Caenorhabditis elegans

Variations of individual lifespans within genetically identical populations in homogenous environments are remarkable, with the cause largely unknown. Gene expression changes with age, and the transcriptome changes correlate with chronological aging. Here, we show that in Caenorhabditis elegans, the expression dynamic of the fatty acid elongase ELO-6 during aging predicts individual longevity in isogenic populations. The expression of elo-6 is reduced with age. From adult day 5, ELO-6 expression level exhibits variation between individuals, and the expression level is positively correlated with adult lifespan and health span. Interventions that prolong longevity enhance the expression stability of ELO-6 during aging from adult day 4 to adult day 8, indicating ELO-6 is also a populational lifespan predictor. We performed transcriptome analysis in short-lived and long-lived isogenic worms and identified differentially expressed genes, which are enriched for PQM-1 binding sites. Decreasing pqm-1 expression in young adults improved the homogeneity of ELO-6 levels between individuals and enhanced health span. Furthermore, we found reducing the expression of genes that are highly expressed in short-lived individuals, including PQM-1 target genes, enhanced ELO-6 expression stability with age and extended lifespan. Thus, our study identified ELO-6 as a predictor of individual and populational lifespan and revealed the role of pqm-1 in restricting health span and possibly causing individual lifespan variation.

physiology↗

bioRxiv2024

Complete telomere-to-telomere assemblies of two sorghum genomes to guide biological discovery

Sorghum is a C4 crop well-known for its high efficiency of biomass accumulation and adaptation to drought and hot environments. This study reports the assembly of complete genome sequence of two sorghum genomes using a combination of ultra-long reads from Oxford Nanopore Technology, high-fidelity long reads from Pacbio and Hi-C reads. The accuracy and completeness of the T2T assemblies were comprehensively validated using a range of parameters, including coverage depth assessment, BUSCO, LTR assembly index, ect. Our T2T assembly of BTx623 identified 36.25 Mb of new sequence, in addition to dozens of misoritation and mispositioning of large DNA segments in the BTx623-v3. Correcting these assembly errors in the reference genome is critical for exploiting genetic information in these complex regions in sorghum. Comparison of the two T2T genomes shed new insights on variation of centromeres in sorghum. The two high-quality T2T genomes represent an important resource for sorghum improvement and gene discovery. They would serve as the new reference genomes to unlock the full potential of global sequence variation of this valuable crop.

genomics↗

bioRxiv2024

Extended culture of 2D gastruloids to model human mesoderm development

Micropatterned human pluripotent stem cells (hPSCs) treated with BMP4 (2D gastruloids) are among the most widely used stem cell models for human gastrulation. Due to its simplicity and reproducibility, this system is ideal for high throughput quantitative studies of tissue patterning and has led to many insights into the mechanisms of mammalian gastrulation. However, 2D gastruloids have only been studied up to 48h. Here we extended this system to 96h. We discovered a phase of highly reproducible morphogenesis during which directed migration from the primitive streak-like region gives rise to a mesodermal layer beneath an epiblast-like layer. Multiple types of mesoderm arise with striking spatial organization including lateral mesoderm-like cells on the colony border and paraxial mesoderm-like further inside the colony. Single cell transcriptomics showed strong similarity of these cells to mesoderm in human and non-human primate embryos. However, our data suggest that the annotation of the reference human embryo may need to be revised. This illustrates that extended culture of 2D gastruloids provides a powerful model for human mesoderm differentiation and morphogenesis. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=44 SRC="FIGDIR/small/585753v1_ufig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@6411fborg.highwire.dtl.DTLVardef@1d8a834org.highwire.dtl.DTLVardef@10afa27org.highwire.dtl.DTLVardef@1ad1f2e_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

developmental biology↗

bioRxiv2024

Adaptive Optics in an Oblique Plane Microscope

Adaptive optics (AO) can restore diffraction limited performance when imaging beyond superficial cell layers in vivo and in vitro, and as such is of interest for advanced 3D microscopy methods such as light-sheet fluorescence microscopy (LSFM). In a typical LSFM system, the illumination and detection paths are separate and subject to different optical aberrations. To achieve optimal microscope performance, it is necessary to sense and correct these aberrations in both light paths, resulting in a complex microscope system. Here, we show that in an oblique plane microscope (OPM), a type of LSFM with a single primary objective lens, the same deformable mirror can correct both the illumination and fluorescence detection. Besides reducing the complexity, we show that AO in OPM also restores the relative alignment of the light-sheet and focal plane, and that a projection imaging mode can stabilize and improve the wavefront correction in a sensorless AO format. We demonstrate OPM with AO on fluorescent nanospheres and by imaging the vasculature and cancer cells in zebrafish embryos embedded in a glass capillary, restoring diffraction limited resolution and improving the signal strength twofold.

cell biology↗

bioRxiv2024

Functional characterization of fatty acid synthase in Hermetia illucens

Fatty acid synthase (FAS) is a key role in de novo lipogenesis (DNL) in most lives. In insects, type I FAS functions in homodimer, activated by a phosphopantetheine transferase (PPT), to de novo produce essential saturated fatty acid for cellular processes. In a nova insect species Hermetia illucens (Diptera: Stratiomyidae), different from most animals and insects, lauric acid (LA) accumulates to a noticeable level, near content of that in coconut oil or palm kernel oil. However, the origin of LA, from de novo biosynthesis or as degraded products from long chain fatty acid, was still ambiguous. Here, in this study, we mined a FAS genes (HiOGS16234) from H. illucens genome and initially characterized its abilities of LA production in a free-fatty-acid producible yeast. After clear the yeast metabolites background of fatty acid by deletion of ScFAS1 and ScELO1 sequentially, which responsible for fatty acid genesis and elongation respectively, functions of HiOGS16234 from H. illucens was in vitro elucidated by analyzing its product portfolio. Through protein domain swap in HiOGS16234, we found the ketoacyl synthase domain and thioesterases domain were responsible for the different product portfolio of HiOGS16234, compared with DmFASN1. Through in vitro assay in yeast, the origin of LA in BSF was firstly elucidated at molecular level, which support DNL origin hypothesis in BSF.

synthetic biology↗

bioRxiv2024

Structural basis for Retriever-SNX17 assembly and endosomal sorting

During endosomal recycling, Sorting Nexin 17 (SNX17) facilitates the transport of numerous membrane cargo proteins by tethering them to the Retriever complex. Despite its importance, the mechanisms underlying this interaction have remained elusive. Here, we report the structure of the Retriever-SNX17 complex determined using cryogenic electron microscopy (cryo-EM). Our structure reveals that the C-terminal tail of SNX17 engages with a highly conserved interface between the VPS35L and VPS26C subunits of Retriever. Through comprehensive biochemical, cellular, and proteomic analyses, we demonstrate that disrupting this interface impairs the Retriever-SNX17 interaction, subsequently affecting the recycling of SNX17-dependent cargos and altering the composition of the plasma membrane proteome. Intriguingly, we find that the SNX17-binding pocket on Retriever can be utilized by other ligands that share a consensus acidic C-terminal tail motif. By showing how SNX17 is linked to Retriever, our findings uncover a fundamental mechanism underlying endosomal trafficking of critical cargo proteins and reveal a mechanism by which Retriever can engage with other regulatory factors.

biochemistry↗

bioRxiv2024

Heterogeneity and evolution of DNA mutation rates in microsatellite stable colorectal cancer

DNA sequence mutability in tumors with chromosomal instability is conventionally believed to remain uniform, constant, and low, based on the assumption that further mutational accrual in a context of marked aneuploidy is evolutionarily disadvantageous. However, this concept lacks robust experimental verification. We adapted the principles of mutation accumulation experiments, traditionally performed in lower organisms, to clonal populations of patient-derived tumoroids and empirically measured the spontaneous rates of accumulation of new DNA sequence variations in seven chromosomally unstable, microsatellite stable colorectal cancers (CRCs) and one microsatellite unstable CRC. Our findings revealed heterogeneous mutation rates (MRs) across different tumors, with variations in magnitude within microsatellite stable tumors as prominent as those distinguishing them from microsatellite unstable tumors. Moreover, comparative assessment of microsatellite stable primary tumors and matched synchronous metastases consistently documented a pattern of MR intensification during tumor progression. Therefore, wide-range diversity and progression-associated evolvability of DNA sequence mutational instability emerge as unforeseen hallmarks of microsatellite stable CRC, complementing karyotype alterations as selectable traits to increase genetic variation. One sentence summaryTumors with chromosomal instability accrue DNA sequence mutations at highly variable rates, which increase during metastatic progression.

cancer biology↗

bioRxiv2024

Molecular chaperone BiP controls activity of the ER stress sensor Ire1 through interactions with its oligomers

The complex multistep activation cascade of Ire1 involves changes in the Ire1 conformation and oligomeric state. Ire1 activation enhances ER folding capacity, in part by overexpressing the ER Hsp70 molecular chaperone BiP; in turn, BiP provides tight negative control of Ire1 activation. This study demonstrates that BiP regulates Ire1 activation through a direct interaction with Ire1 oligomers. Particularly, we demonstrated that the binding of Ire1 luminal domain (LD) to unfolded protein substrates not only trigger conformational changes in Ire1-LD that favour the formation of Ire1-LD oligomers but also exposes BiP binding motifs, enabling the molecular chaperone BiP to directly bind to Ire1-LD in an ATP-dependent manner. These transient interactions between BiP and two short motifs in the disordered region of Ire1-LD are reminiscent of interactions between clathrin and another Hsp70, cytoplasmic Hsc70. BiP binding to substrate-bound Ire1-LD oligomers enables unfolded protein substrates and BiP to synergistically and dynamically control Ire1-LD oligomerisation, helping to return Ire1 to its deactivated state when an ER stress response is no longer required.

biophysics↗

bioRxiv2024

Construction and Application of a Technical Platform for Determining Cell Cycle- and Autophagy-Associated Cellular Uptake of Lipid-Based Nanoparticles

Cellular accumulation of biomedical nanoparticles could be affected by cellular biological properties. However, little is known about the influence of cell cycle and autophagy on nanoparticle accumulation. Whats even more tough is that several long-lasting methodological barriers have hampered the experimental performance and restricted related research progress. Herein, a multi-functional platform was constructed for simultaneously overcoming existing obstacles by integrating several technical approaches, particularly mitotic shake-off, for thorough cell cycle phase separation. Strikingly, application of this platform revealed that G2-phase and M-phase cells, two cell populations previously muddled up together as G2/M-phase cells, respectively exhibited the maximum and minimum accumulation of lipid-based nanoparticles. Moreover, although further verification is needed, we have provided a novel line of evidence for enhanced nanoparticle accumulation by autophagy blockade. Besides providing a technical solution, this study discovered characteristic cell cycle- and autophagy-associated nanoparticle accumulations that may offer new insights for optimization and application of nanomedicines.

cell biology↗

bioRxiv2024

Reverse engineering placebo analgesia

Placebo analgesia is a widely observed clinical phenomenon. Establishing a robust mouse model of placebo analgesia is needed for careful dissection of the underpinning circuit mechanisms. However, previous studies failed to observe consistent placebo effects in rodent models of chronic pain. We wondered whether strong placebo analgesia can be reverse engineered using general anesthesia-activated neurons in the central amygdala (CeAGA) that can potently suppress pain. Indeed, in both acute and chronic pain models, pairing a context with CeAGA-mediated pain relief produced robust context-dependent analgesia, exceeding that induced by morphine in the same paradigm. We reasoned that if the analgesic effect was dependent on reactivation of CeAGA neurons by conditioned contextual cues, the analgesia would still be an active treatment, rather than a placebo effect. CeAGA neurons indeed receive monosynaptic inputs from temporal lobe areas that could potentially relay contextual cues directly to CeAGA. However, in vivo imaging showed that CeAGA neurons were not re-activated in the conditioned context, despite mice displaying a strong analgesic phenotype, supporting the notion that the cue-induced pain relief is true placebo analgesia. Our results show that conditioning with activation of a central pain-suppressing circuit is sufficient to engineer placebo analgesia, and that purposefully linking a context with an active treatment could be a means to harness the power of placebo for pain relief.

neuroscience↗

bioRxiv2024

navigate: an open-source platform for smart light-sheet microscopy.

navigate is a turnkey, open-source software solution designed to enhance light-sheet fluorescence microscopy (LSFM) by integrating smart microscopy techniques into a user-friendly framework. It enables automated, intelligent imaging with a Python-based control system that supports GUI-reconfigurable acquisition routines and the integration of diverse hardware sets. As a comprehensive package, navigate democratizes access to advanced LSFM capabilities, facilitating the development and implementation of smart microscopy workflows without requiring deep programming knowledge or specialized expertise in light-sheet microscopy.

biophysics↗

bioRxiv2024

Clearance of protein aggregates during cell division

Protein aggregates are spatially organized and regulated in cells to prevent deleterious effects of proteostatic stress. Misfolding of proteins in the endoplasmic reticulum (ER) results in aggregate formation, but how the aggregates are processed especially during cell division is not well understood. Here, we induced proteostatic stress and protein aggregation using a proteostasis reporter, which is prone to misfolding and aggregation in the ER. Unexpectedly, we detected solid- like protein aggregates deposited mainly in the nucleus and surrounded by the ER membrane. The membrane-bound aggregates were then cleared as cells progressed through mitosis and cytokinesis. Aggregate clearance depended on Hsp70 family chaperones in the ER, particularly BiP, and proteasomal activity. The clearance culminated at mitotic exit and required cyclin-dependent kinase 1 (Cdk1) inactivation but was independent of the anaphase-promoting complex (APC/C). The ER reorganization that is active during mitosis and cytokinesis was required for the aggregate clearance. Thus, dividing cells reorganize the ER networks to allow BiP to clear the protein aggregates to maintain proteostasis in the newly divided cells.

cell biology↗

bioRxiv2024

RNA Splicing Junction Landscape Reveals Abundant Tumor-Specific Transcripts in Human Cancer

RNA splicing is a critical process governing gene expression and transcriptomic diversity. Despite its importance, a detailed examination of transcript variation at the splicing junction level remains scarce. Here, we perform a thorough analysis of RNA splicing junctions in 34,775 samples across multiple sample types. We identified 29,051 tumor-specific transcripts (TSTs) in pan-cancer, with a majority of these TSTs being unannotated. Our findings show that TSTs are positively correlated with tumor stemness and linked to unfavorable outcomes in cancer patients. Additionally, TSTs display mutual exclusivity with somatic mutations and are overrepresented in transposable element-derived transcripts possessing oncogenic functions. Importantly, TSTs can generate neoepitopes that bind to MHC class I molecules for immunotherapy. Moreover, TSTs can be detected in blood extracellular vesicles from cancer patients. Our results shed light on the intricacies of RNA splicing and offer promising avenues for cancer diagnosis and therapy. In briefThis study thoroughly analyzed RNA splicing junctions in 34,775 samples and identified 29,051 tumor-specific transcripts (TSTs), which may serve as novel cancer driver genes, neoantigens, and circulating biomarkers. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/579246v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7e1db2org.highwire.dtl.DTLVardef@1cfbe81org.highwire.dtl.DTLVardef@1e427e1org.highwire.dtl.DTLVardef@1f655f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2024

A self-adaptive and versatile tool for eliminating multiple undesirable variations from transcriptome

Accurate identification of true biological signals from diverse undesirable variations in large-scale transcriptomes is essential for downstream discoveries. Herein, we develop a universal deep neural network, called DeepAdapter, to eliminate various undesirable variations from transcriptomic data. The innovation of our approach lies in automatic learning of the corresponding denoising strategies to adapt to different situations. The data-driven strategies are flexible and highly attuned to the transcriptomic data that requires denoising, yielding significant improvement in reducing undesirable variation originating from batches, sequencing platforms, and bio-samples with varied purity beyond manually designed schemes. Comprehensive evaluations across multiple batches, different RNA measurement technologies and heterogeneous bio-samples demonstrate that DeepAdapter can robustly correct diverse undesirable variations and accurately preserve biological signals. Our findings indicate that DeepAdapter can act as a versatile tool for the comprehensive denoising of the large and heterogeneous transcriptome across a wide variety of application scenarios.

bioinformatics↗

bioRxiv2024

BRD4-mediated epigenetic regulation of endoplasmic reticulum-mitochondria contact sites is governed by the mitochondrial complex III

Inter-organellar communication is critical for cellular metabolic homeostasis. One of the most abundant inter-organellar interactions are those at the endoplasmic reticulum and mitochondria contact sites (ERMCS). However, a detailed understanding of the mechanisms governing ERMCS regulation and their roles in cellular metabolism are limited by a lack of tools that permit temporal induction and reversal. Through unbiased screening approaches, we identified fedratinib, an FDA-approved drug, that dramatically increases ERMCS abundance by inhibiting the epigenetic modifier BRD4. Fedratinib rapidly and reversibly modulates mitochondrial and ER morphology and alters metabolic homeostasis. Moreover, ERMCS modulation depends on mitochondria electron transport chain complex III function. Comparison of fedratinib activity to other reported inducers of ERMCS revealed common mechanisms of induction and function, providing clarity and union to a growing body of experimental observations. In total, our results uncovered a novel epigenetic signaling pathway and an endogenous metabolic regulator that connects ERMCS and cellular metabolism.

cell biology↗

bioRxiv2023

General Anesthesia Activates a Central Anxiolytic Center in the BNST

Low doses of general anesthetics like ketamine and dexmedetomidine have anxiolytic properties independent of their sedative effects. How these different drugs exert these anxiolytic effects is not well understood. We discovered a population of GABAergic neurons in the oval division of the bed nucleus of the stria terminalis that is activated by multiple anesthetics and the anxiolytic drug diazepam (ovBNSTGA). A majority of ovBNSTGA neurons express neurotensin receptor 1 (Ntsr1) and innervate brain regions known to regulate anxiety and stress responses. Optogenetic activation ovBNSTGA or ovBNSTNtsr1 neurons significantly attenuated anxiety-like behaviors in both naive animals and mice with inflammatory pain, while inhibition of these cells increased anxiety. Notably, activation of these neurons decreased heart rate and increased heart rate variability, suggesting that they reduce anxiety through modulation of the autonomic nervous system. Our study identifies ovBNSTGA/ovBNSTNtsr1 neurons as one of the brains endogenous anxiolytic centers and a potential therapeutic target for treating anxiety-related disorders. HIGHLIGHTSO_LIGeneral anesthetics and anxiolytics activate a population of neurons in the ovBNST C_LIO_LIAnesthesia-activated ovBNST neurons bidirectionally modulate anxiety-like behavior C_LIO_LIMost anesthesia-activated ovBNST neurons express neurotensin receptor 1 C_LIO_LIovBNSTNtsr1 neuron activation shifts autonomic responses to an anxiolytic state C_LI

neuroscience↗