Biology subjects

Pei, X.

Publications and source records attributed to Pei, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Fungal microbial enrichment method enables fungal metagenomics directly from human clinical samples

Fungi play important roles in health and disease, but current methods such as culture, PCR, and amplicon sequencing cannot provide genome-level characterization directly from clinical samples. Although metagenomic sequencing could overcome these limitations, it remains impractical in clinical samples where fungal DNA is present at low abundance relative to human DNA. Here, we extend a recently described microbial enrichment method (MEM)(1) to fungi (fungal Microbial Enrichment Method; fMEM) and test the method in bronchoalveolar lavage (BAL) samples to demonstrate direct-from-sample fungal metagenomic analysis and metagenome-assembled genome (MAG) recovery. In BAL samples, fMEM depleted human DNA by more than 1000-fold while preserving fungal DNA within 10-fold, enabling shotgun sequencing from samples with fungal biomass as low as 10 pg fungal DNA per 200 {micro}L BAL. fMEM enabled de novo recovery of fungal MAGs from three of four sequenced BAL samples, including two near-complete MAGs (>90% BUSCO completeness) and one 82.1% complete MAG, with low BUSCO-estimated contamination ([≤]1.5%). Fungal MAGs recovered by fMEM also resolved potentially clinically-relevant genes, not fully predictable from taxonomy alone and revealed genomic content absent from currently-available same-species reference genomes. fMEM is compatible with a whole-genome amplification (including long-read sequencing workflows). Long reads from fMEM-processed samples provided high coverage (>10X) over fungal assemblies. fMEMs compatibility with long-read sequencing enables recovery of genes that would be difficult to assemble with short reads alone. fMEM may enable new insights into the role of human-associated fungi, impacting public health, clinical management, and research into complex diseases with suspected fungal roles. ImportanceFungi influence human health, infectious disease, and the microbiome, but direct genome analysis from clinical samples has remained impractical because fungal DNA is often overwhelmed by human DNA. We developed a fungal microbial enrichment method (fMEM) that enables direct-from-sample fungal metagenomic sequencing and genome recovery from bronchoalveolar lavage samples without requiring culture for genome assembly. fMEM recovers genome-level features not predicted by taxonomy or current same-species reference genomes and is compatible with long-read sequencing workflows that can recover loci missed by short-read sequencing. fMEM opens new opportunities for culture-independent fungal genomics, clinical microbiology, comparative genomics, and mechanistic studies of human-associated fungi.

bioengineering↗

bioRxiv2026

Extracranial lymphatic-venous anastomosis remodels the choroid plexus-vascular axis in Alzheimer's disease

Coordination of brain fluid transport, proteostasis and vascular function is essential for neural homeostasis, yet whether extracranial lymphatic outflow can actively shape central neurovascular states remains poorly understood. Here we identify a lymphatic-choroid plexus signaling axis through which extracranial drainage regulates intracranial proteostatic and vascular remodeling. Using cervical lymphatic-venous anastomosis (LVA) as a gain-of-function approach in an Alzheimers disease (AD) rat model, we show that enhancement of extracranial lymphatic outflow rapidly stabilizes cerebrospinal fluid-associated ventricular dynamics, selectively reduces oligomeric amyloid-{beta} burden and improves locomotor performance. Single-cell transcriptomic profiling further reveals broad remodeling of the hippocampal neurovascular niche, marked by attenuation of inflammatory microglial programs and reinforcement of vascular communication networks. Mechanistically, LVA induces a secretory response in choroid plexus epithelial (CPE) cells characterized by co-upregulation of clusterin (CLU) and vascular endothelial growth factor (VEGF). This CLU-VEGF epithelial program links amyloid chaperoning to microvascular remodeling, accompanied by increased choroid plexus microvessel density and vascular caliber, preserved cerebral perfusion and restoration of neurovascular homeostasis. Together, these findings define the choroid plexus as a biomechanical-molecular transducer that connects extracranial lymphatic drainage with central proteostasis and vascular regulation. The lymphatic-choroid plexus axis provides a new framework for understanding how peripheral fluid drainage shapes brain homeostasis and suggests novel mechanism of action for treating neurodegenerative diseases.

neuroscience↗

bioRxiv2026

Ultra-low biomass sequencing workflow (LBV-Seq) enables de novo metagenomic reconstruction of DNA and RNA viral genomes

Genome-resolved virome analysis remains inaccessible for many samples, including those with clinical relevance, because viral nucleic acid recovered after enrichment is often too scarce to support de novo genome assembly. As a result, many analyses are limited to sparse read-level detection, which cannot recover divergent viruses, resolve strains, or interpret gene-level variation. Here, we developed Low Biomass Viral Sequencing (LBV-Seq), a workflow that couples low-input viral sample handling with modified primary template-directed amplification and short- or long-read sequencing to enable de novo reconstruction of DNA and RNA viral genomes from sub-femtogram to nanogram inputs. LBV-Seq reproducibly captures the same relative community composition, amplifies diverse viruses, and achieved broad genome coverage across nearly all targets regardless of viral genome structure, Baltimore class, abundance, or input mass. Short-read assemblies recovered near-complete genomes from femtogram-scale inputs. Long-read sequencing provided orthogonal support for genome structure, with PacBio HiFi reads spanning large portions of viral genomes and, in some cases, complete small viral genomes. Applied to virus-enriched human duodenal biopsy eluates, LBV-Seq provided proof-of-feasibility for recovering both bacteriophage and eukaryotic viral genomes from low-input biopsy-derived material. In the eluates tested, LBV-Seq recovered co-occurring Alphatorquevirus and Betatorquevirus genomes estimated to be present at roughly 10 copies/{micro}L and at viral masses below 0.1 fg/{micro}L. LBV-Seq enables genome-resolved virome analysis in samples previously limited to detection-based viromics, supporting viral discovery and strain-resolved analyses in settings where viral mass is low, including viruses enriched from human tissue biopsies.

genomics↗

bioRxiv2026

Near completely reversing the γ- to β-globin switch by enhancer release, retargeting and reinforcing

The {gamma}- to {beta}-globin switch is intricately regulated during human ontogeny, and this process is manipulated for therapeutic approaches to treat {beta}-hemoglobinopathies by activating {gamma}-globin expression. Several genetic strategies to reactivate HbF have partially reversed the {gamma}- to {beta}-globin switch and ameliorated the clinical symptoms of {beta}-hemoglobinopathies. However, whether the {gamma}- to {beta}-globin switch can be completely reversed remains unknown. Completely reversing the {gamma}- to {beta}-globin switch requires a thorough redirection of the locus control region (LCR) from interacting with the {beta}-globin gene (HBB) to interacting with the {gamma}-globin gene (HBG). Here, we found that disrupting the KLF1-mediated HBB-LCR interaction by mutating the CACCC motif in HBB leads to the release of the LCR and its retargeting to other {beta}-like globin genes. Moreover, simultaneously disrupting the KLF1-mediated HBB-LCR interaction and the epigenetic repression of HBG by combined editing of the CACCC motif in HBB and the TGACCA motif in HBG reinforces the HBG-LCR interaction, resulting in almost exclusive {gamma}-globin expression while nearly absent {beta}-globin expression, achieving near complete reversal of the {gamma}- to {beta}-globin switch. This finding demonstrates the comprehensive regulation of the {gamma}- to {beta}-globin switch by gene competition and gene silencing mechanisms. This finding also suggests that silenced genes can be fully activated through the redirection of enhancer-promoter contacts and that the specificity of enhancer-promoter contact within chromosomal domains is achieved through the transcription factor clusters binding to enhancers and promoters. Combined editing of the CACCC&TGACCA motifs also offer a more optimal therapeutic strategy for {beta}-hemoglobinopathies.

molecular biology↗

bioRxiv2025

DNA replication errors drive genome-wide small inverted triplication dynamics

Structural variants (SVs) have a profound impact on phenotype and diversity and are associated with human diseases. To explore the origination of SVs, we have analyzed 1,340 cancer genomes with annotation of 4,608 novel small inverted triplication (SIT) events and found that FEN1 is strongly associated with SIT incidence. Then, we performed long-read sequencing and developed PacBioR to annotate SITs in yeast FEN1 mutant cells. We found that SIT structures mimic classic inverted triplications but with a smaller DUP/IN/DUP structure of 184/160/184 bp on average, with a spacer sequence of 30 bp and breakpoint junction of 6 bp. We further showed that breakpoints of SITs preferentially occurred at nucleosome midpoints, aligned with Okazaki fragment termini, and those harbored in plasmids were precisely eliminated via DNA polymerase slippage over SIT-derived hairpin structures. This study provides mechanistic insight into SIT origination and offers practical tools for future studies on genome rearrangements.

genetics↗

bioRxiv2025

Oncometabolite fumarate impairs ATR-CHK1 signaling by succinating RPA1 in Fumarate Hydratase-deficient renal cell carcinoma cells

Abnormal accumulation of oncometabolite fumarate drives susceptibility in fumarate hydratase-deficient renal cell carcinoma (FH-dRCC), but the precise mechanisms remain not fully understood. In this study, we demonstrate that high fumarate levels impair activation of ATR-CHK1 signaling in response to replication stress and DNA damage. Mechanistically, fumarate modifies RPA1, an essential factor for ATR-CHK1 activation through succination, a post-translational modification. Succination of RPA1 occurs mainly at cysteine residues 481 and 486, which reduces its binding affinity for single-stranded DNA (ssDNA). RPA1 succination leads to deficient recruitment of TOPBP1 to ssDNA, resulting in attenuated CHK1 activation and defective cell cycle arrest in response to DNA damage. Succinated RPA1 compromises homologous recombination-mediated DNA repair. Our findings establish that fumarate-induced succination of RPA1 impairs DNA repair and cell cycle control, promoting genomic instability in FH-dRCC. This work reveals a novel mechanism by which oncometabolites contribute to genomic instability.

cancer biology↗

bioRxiv2025

Vascular and Lymphatic Dysregulation via Non-EndoMT Col2a1 Signaling in Bisphosphonate-Related Osteonecrosis of the Jaw

Bisphosphonate-related osteonecrosis of the jaw (BRONJ) is one of the most severe complications of antiresorptive therapy. Although impaired angiogenesis is commonly observed in BRONJ, the underlying vascular mechanisms remain poorly understood, impeding the development of effective treatments. In this study, we integrated whole-organ tissue-clearing imaging, single-cell transcriptomics, and proteomics to construct a multimodal atlas of the mandibular microenvironment in both mouse and human BRONJ. Our findings revealed gross vascular and lymphatic rarefaction in BRONJ, along with 4 endothelial subtypes uniformly exhibiting aberrant upregulation of Col2a1. Moreover, fibroblasts and macrophages emerged as key endothelial interactors, collectively underscoring dysregulation of the endothelium-matrix-immune axis. Unlike homeostatic Dmp1/Tfap2a fibroblasts and Stab1 macrophages, BRONJ lesions featured pathological Lrrc15/Chad fibroblasts and Il6 macrophages, which promote ectopic chondrogenesis and inflammation. Mechanistically, BRONJ activated the COL2A1-CD44 axis (EC-to-fibroblast/macrophage signaling) and COL2A1-SDC4 axis (EC-to-fibroblast signaling), whereas lineage tracing excluded endothelial-to-mesenchymal transition (EndoMT), implicating extracellular matrix remodeling as the driver of dysfunction. Cross-species validation in human mandibles further confirmed vascular-lymphatic dysregulation, inflammatory activation, and aberrant chondrogenesis. Overall, this study establishes vascular and lymphatic dysfunction as a central pathological hallmark of BRONJ, driving matrix remodeling dysregulation and immune-inflammatory imbalance, and identifies the COL2A1-CD44/SDC4 axis as a potential therapeutic target for BRONJ.

cell biology↗

bioRxiv2025

Light-Activated Nucleic Acid Amplification Systems Using Photo-caged DNA Polymerase or Primers

Precise control over nucleic acid amplification is essential for achieving reliable, quantitative, high-throughput, and multiplexed molecular diagnostics, particularly in point-of-care and field settings. However, conventional isothermal amplification methods, especially rapid assays at ambient temperature such as recombinase-aided amplification (RAA), suffer from spontaneous initiation and lack of synchronization across parallel reactions. Here, we report light-activatable RAA systems employing two distinct photocaging strategies to achieve spatiotemporal control. In the first, a photocaged DNA polymerase was engineered via site-specific incorporation of p-azido-L-phenylalanine and conjugation with a 2-nitrobenzyl-modified ssDNA blocker through click chemistry. This approach offers high stability, making it advantageous for long-term storage and lyophilized formats. In the second, 5'-nitrobenzyl-modified primers were synthesized to block hybridization or extension until UV activation, offering operational simplicity and rapid integration into existing workflows. Both strategies independently suppressed background activity in the dark and restored full amplification efficiency upon 365 nm UV exposure. The systems exhibited high sensitivity, low background, and compatibility with portable diagnostics. A custom-built device integrating UV activation and real-time fluorescence detection enabled seamless, on-demand operation. This modular platform provides flexible light-gated amplification solutions, allowing the selection of polymerase- or primer-based caging according to storage stability or workflow requirements, thereby advancing precise and field-ready molecular diagnostics.

molecular biology↗

bioRxiv2024

Mechanism of Nucleotide-Dependent Allosteric Regulation in Escherichia coli Aspartate Transcarbamoylase

Aspartate transcarbamoylase (ATCase) from Escherichia coli catalyzes a key step in pyrimidine nucleotide biosynthesis and has long served as a model for allosteric regulation. Despite decades of study, how nucleotide binding at distant regulatory sites controls cooperativity between active sites remained unresolved. Here we show that ATCase does not simply interconvert between two conformations, as traditionally depicted, but instead samples a continuum of conformations that tune enzyme cooperativity. Using complementary cryo-electron microscopy, small-angle X-ray scattering, and crystallography under conditions that ensure full assembly of the allosteric sites, we show that ATCase behaves like a flexible balloon whose global "breathing" motions directly regulate activity: compression enforces high cooperativity, inhibiting the enzyme, whereas expansion relieves this cooperativity and activates the enzyme. We further show that all four ribonucleoside triphosphates act in symmetric pairs to tune this motion, with the pyrimidines CTP and UTP compressing the enzyme to limit further pyrimidine production, and the purines ATP and GTP expanding it to balance pyrimidine and purine pools. Together, these findings uncover a dynamic breathing mechanism for long-range allosteric communication in ATCase.

biochemistry↗

bioRxiv2024

YTHDF2 upregulation and relocation dictate CD8 T cell polyfunctionality in tumor immunity

Epigenetic traits impact the antitumor function of CD8 T cells, yet whether and how RNA methylation programs engage in T cell immunity is poorly understood. Here we show that the N6-methyladenosine (m6A) RNA reader YTHDF2 is highly expressed in early effector or effector-like CD8 T cells and is partially distributed in the nucleus. YTHDF2 loss in T cells exacerbates tumor progression and confers unresponsiveness to PD-1 blockade in mice and humans. In addition to initiating RNA decay for mitochondrial fitness, YTHDF2 can orchestrate chromatin regulation to promote T cell polyfunctionality. YTHDF2-mediatd preservation of gene transcription arises from the interaction of YTHDF2 with IKZF1/3. Accordingly, immunotherapy-induced efficacy could be largely restored in YTHDF2-deficient T cells through combinational use of lenalidomide. Moreover, m6A recognition is fundamental for YTHDF2 translocation to the nucleus and autoregulation at the RNA level. Thus, YTHDF2 coordinates epitranscriptional and transcriptional networks to potentiate T cell immunity. HighlightsO_LIYTHDF2 expression and distribution underpin the threshold for bona fide CD8 T cell effector response C_LIO_LICanonical YTHDF2-mRNA decay pathway alleviates mitochondrial stress and CD8 T cell exhaustion C_LIO_LINuclear YTHDF2 sequesters IKZF1/3-mediated transcriptional repression to safeguard CD8 T cell polyfunctionality C_LIO_LIThe tumoricidal activity of YTHDF2-deficient CD8 T cells could be repaired through the synergy of anti-PD-1 and lenalidomide C_LI

immunology↗

bioRxiv2024

APOBEC3 mutagenesis drives therapy resistance in breast cancer

Acquired genetic alterations commonly drive resistance to endocrine and targeted therapies in metastatic breast cancer1-7, however the underlying processes engendering these diverse alterations are largely uncharacterized. To identify the mutational processes operant in breast cancer and their impact on clinical outcomes, we utilized a well-annotated cohort of 3,880 patient samples with paired tumor-normal sequencing data. The mutational signatures associated with apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like 3 (APOBEC3) enzymes were highly prevalent and enriched in post-treatment compared to treatment-naive hormone receptor-positive (HR+) cancers. APOBEC3 mutational signatures were independently associated with shorter progression-free survival on antiestrogen plus CDK4/6 inhibitor combination therapy in patients with HR+ metastatic breast cancer. Whole genome sequencing (WGS) of breast cancer models and selected paired primary-metastatic samples demonstrated that active APOBEC3 mutagenesis promoted resistance to both endocrine and targeted therapies through characteristic alterations such as RB1 loss-of-function mutations. Evidence of APOBEC3 activity in pre-treatment samples illustrated a pervasive role for this mutational process in breast cancer evolution. The study reveals APOBEC3 mutagenesis to be a frequent mediator of therapy resistance in breast cancer and highlights its potential as a biomarker and target for overcoming resistance.

cancer biology↗

bioRxiv2024

A drought stress-responsive metabolite malate modulates stomatal responses through G-protein-dependent pathway

Drought stress is a significant environmental threat to global agricultural production and distribution. Plant adaptation to dehydration stress involves intricate biological processes with substantial changes in metabolite composition. In this study, we investigated the role of tricarboxylic acid (TCA) cycle metabolites in drought tolerance in grapevine and Arabidopsis by metabolome, live cell imaging, electrophysiological and pharmacological approaches. Metabolome analysis revealed that amount of malate, citrate, and isocitrate increased over time in detached grapevine leaves. Ca2+ imaging and ion channel measurements indicated that fumarate, malate, and -ketoglutarate induced cytosolic free Ca2+ concentration ([Ca2+]cyt) elevation in guard cells and directly activated a guard-cell anion channel SLAC1. However, only malate induced stomatal closure, which required increases in [Ca2+]cyt in guard cells and activation of SLAC1. Through pharmacological experiments and reverse genetics analyses, G-proteins were identified as essential components of malate signaling by regulating second messenger production. These results indicate that TCA cycle metabolites are sensed individually by guard cells and that malate plays a key role in connecting metabolic regulation and drought tolerance through G-protein-dependent signal cascades.

plant biology↗

bioRxiv2024

EI24-RTRAF interaction represses Nox4 translation, vital for redox balance and insulin production

As a double-edged sword, the content of reactive oxygen species (ROS) is precisely controlled. Disordered actions of ROS contribute to deleterious effects, such as cancer and metabolic dysregulation associated with aging and obesity. Although it is well established that cells have developed evolutionarily conserved programs to sense and adapt to redox fluctuations, it remains unclear how to control the expression of key ROS-producing enzymes to regulate continued ROS production at healthy levels for cells such as neurons and pancreatic beta cells. These cells have weaker antioxidant defense systems but strong secretion ability. Here, we found that the endoplasmic reticulum membrane-localized protein, EI24, controls the translation of nicotinamide adenine dinucleotide phosphate oxidase 4 (NOX4), which constitutively produces hydrogen peroxide (H2O2), by recruiting an RNA transcription, translation, and transport factor (RTRAF) to the 3-UTRs of Nox4. Depletion of EI24 causes RTRAF to relocate into the nucleus, releasing the brake on Nox4 mRNA translation, and thus, the uncontrolled translation of Nox4 leads to a substantial generation of intracellular H2O2. This suppresses the translation of V-maf musculoaponeurotic fibrosarcoma oncogene homolog A (MafA), inhibits its binding to the Ins2 gene promoter, and ultimately hinders insulin transcription. Treatment with a specific NOX4 inhibitor or the antioxidant N-acetyl-cysteine (NAC) restored MafA translation and downstream insulin synthesis while alleviating the diabetic symptoms in pancreatic beta-cell specific Ei24-KO mice. In summary, our study revealed a molecular mechanism that controls the expression of NOX4, a key enzyme responsible for continuous ROS generation. This mechanism ensures low levels of H2O2 and normal biological functions under physiological conditions.

cell biology↗

bioRxiv2023

Analysis of the heterogeneity and complexity of murine extraorbital lacrimal gland via single-cell RNA sequencing

PurposeThe lacrimal gland is essential for maintaining ocular surface health and avoiding external damage by secreting the aqueous layer of the tear film. However, a healthy lacrimal glands inventory of cell types and heterogeneity remains understudied. MethodsHere, 10X genome-based single-cell RNA sequencing was used to generate an unbiased classification of cellular diversity in the extraorbital lacrimal gland (ELG) of C57BL/6J mice. From 48,077 high-quality cells, an atlas of cell heterogeneity was produced, and cell types were defined by classic marker genes. The possible functions of these cells and the pseudotime trajectories for certain cell populations were analyzed through bioinformatics. In addition, a preliminary analysis of the cell-cell communication network in ELG was performed. ResultsOver 41 subclasses of cells were identified, including 9 kinds of glandular epithelial cells, 7 kinds of fibroblasts, 10 kinds of myeloid-derived immune cells, at least 10 kinds of lymphoid-derived immune cells, 3 kinds of vascular-associated cell subsets, and 2 kinds of Schwann cells. Analysis of cell-cell communication networks revealed that innate lymphoid cells were closely associated with other cells. ConclusionsThis study provides the first comprehensive transcriptome atlas and related database of mouse ELG. This resource can aid in a deeper understanding of lacrimal gland biology and pathophysiology of its related diseases.

bioinformatics↗

bioRxiv2023

A Zinc finger (ZnF) transcription factor exerts its multifaceted function through ZnF-regulated phase separation

Zinc finger (ZnF) transcription factors (TFs) consist of ZnF-containing DNA-binding domains (DBDs) and intrinsically disordered region (IDR)-containing activation domains (ADs). Recent studies have suggested that liquid-liquid phase separation (LLPS) is the fundamental mechanism underlying human health and disease, with ZnF TFs activating gene expression through the LLPS capacity of their IDR-containing ADs. However, little is known about how the well-folded DBD of ZnF TFs is involved in their LLPS mechanism. GATA3 is one of the most frequently mutated genes in breast cancer, and its encoded protein GATA3, which contains two ZnFs (ZnF1 and ZnF2) in its DBD, is a master regulator of immunity. Here, we show that GATA3 undergoes LLPS in cells and in vitro, and its DBD plays an important regulatory role. Mechanistically, ZnF2 in the DBD contains two arginine amino acids (R329 and R330) that provide critical charges to regulate GATA3 LLPS and DNA binding by generating multivalent electrostatic interactions. Functionally, we demonstrated that ZnF2-regulated GATA3 LLPS is the mechanism underlying the multifaceted function of GATA3 in breast cancer development and immune regulation, where aberrant GATA3 LLPS caused by artificial or breast cancer-associated ZnF2-defective mutations by reducing Suv39H1 protein stability showed significantly reduced potential in promoting breast cancer development and exhibited remarkably enhanced capacities for activating type I interferon signaling. Since ZnF is a common feature in the DBDs of ZnF TFs, by describing GATA3 as a proof-of-principle, our data suggest that ZnF-regulated LLPS may be a general mechanism underlying the multifaceted function of ZnF TFs in human health and disease.

cancer biology↗

bioRxiv2023

Decoding human in vitro terminal erythropoiesis originating from umbilical cord blood mononuclear cells and pluripotent stem cells

Ex vivo RBC production generates unsatisfactory expansion, {beta}-globin expression, and maturation of erythroid cells. The underlying mechanisms behind these limitations and ex vivo terminal erythropoiesis from different origins are largely unexplained. In this study, we mapped an atlas of ex vivo terminally differentiated cells from umbilical cord blood mononuclear cells (UCBMNs) and pluripotent stem cells (PSCs), and observed the differential regulatory dynamics of erythropoiesis from these two origins at a single-cell resolution. We detected the presence of hematopoietic stem progenitor cells (HSPCs), erythroid progenitor (e.g., CFU-E), and non-erythroid cells (e.g., macrophages) in the terminal populations. We observed that UCBMN-derived erythropoiesis is more active than PSC-derived erythropoiesis in terms of the cell cycle, stress erythropoiesis, and autophagy at single cell resolution, which may provide new insights into the limitations in cell expansion, globin expression, and maturation in ex vivo RBC production, respectively. We verified that a stress-erythropoiesis-related gene, TRIB3, increases the expression of globin genes in ex vivo erythropoiesis. As the major unexpected component detected in terminally differentiated cells, CFU-E were further characterized as having high- or low- expansion capacity based on CD99 expression, which generally decreased over erythropoiesis. By inhibiting CD99 gene expression using antagonists, we increased reticulocyte production in the population. Heterogeneous CFU-Es also exist in bone marrow. Moreover, decreased CD99 expression mediates the interactions between macrophages and CFU-E during ex vivo erythropoiesis. Overall, our results provide a reference for facilitating the development of strategies to improve ex vivo RBC regeneration. HighlightsO_LIWe performed scRNA-seq and cell typing of late stage UCBMN- and PSC-derived cells C_LIO_LIStress erythropoiesis, autophagy and cell cycle related gene expression different in two origins C_LIO_LICD99high progenitor cells are a proliferating colony forming unit erythroid subpopulation C_LI

cell biology↗

bioRxiv2023

Disulfiram Exerts anti-pulmonary Fibrosis Effect by Activating PGE2 Synthesis

Idiopathic pulmonary fibrosis (IPF) is marked with the replacement of normal alveolar tissue by thicker and harder fibrous material, damaged exchange ability. Currently, nintedanib and pirfenidone, are the only FDA-approved drugs with limited efficacy for IPF, which indicated an urgent need to explore new therapies. Disulfiram (DSF), an acetaldehyde dehydrogenase inhibitor, used as anti-alcohol treatment. Despite reported with anti-hepatic fibrosis effect of DSF, the underlying mechanism remains unclear. In our study, DSF exhibited regulative impact on abnormal proliferation, EMT and ECM production in cell models of IPF including primary DHLF-IPF cells and TGF-{beta}1-stimulated A549 cells. The absence of COX-2 was restored by DSF treatment, together with elevated prostaglandin biosynthesis both in vitro and in vivo models of IPF. Furthermore, the anti-fibrotic effect of DSF was impeded with COX-2 knockdown or pharmacological inhibition in TGF-{beta}1-stimulated A549 cells, however, exogenous PGE2 reclaimed with anti-EMT function. In established animal model of IPF, DSF ameliorated declined lung function and histopathological changes, and restrained the lung hydroxyproline content. Together, these findings suggest that the anti-fibrotic effect of DSF was achieved through re-activation of COX-2 mediated PGE2 biosynthesis. The above results suggest that DSF can be applied therapeutically in fibrotic conditions.

cell biology↗

bioRxiv2021

Structural and functional characterizations of altered infectivity and immune evasion of SARS-CoV-2 Omicron variant

The SARS-CoV-2 Omicron with increased fitness is spreading rapidly worldwide. Analysis of cryo-EM structures of the Spike (S) from Omicron reveals amino acid substitutions forging new interactions that stably maintain an "active" conformation for receptor recognition. The relatively more compact domain organization confers improved stability and enhances attachment but compromises the efficiency of viral fusion step. Alterations in local conformation, charge and hydrophobic microenvironments underpin the modulation of the epitopes such that they are not recognized by most NTD- and RBD-antibodies, facilitating viral immune escape. Apart from already existing mutations, we have identified three new immune escape sites: 1) Q493R, 2) G446S and 3) S371L/S373P/S375F that confers greater resistance to five of the six classes of RBD-antibodies. Structure of the Omicron S bound with human ACE2, together with analysis of sequence conservation in ACE2 binding region of 25 sarbecovirus members as well as heatmaps of the immunogenic sites and their corresponding mutational frequencies sheds light on conserved and structurally restrained regions that can be used for the development of broad-spectrum vaccines and therapeutics.

biophysics↗