Biology subjects

Zhu, M.

Publications and source records attributed to Zhu, M..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Natural genetic and transcriptomic variation in photosynthesis associated pathways contribute to adaptive traits variation in worldwide Arabidopsis thaliana population

Photosynthesis is the most important reaction underlying carbon fixation. Despite its potential in boosting carbon assimilation, nature variations underlying genes in photosynthesis pathway and their role in adaptive traits variation remains elusive. In this study, we investigated the genetic, transcriptomic variation of 1103 genes in photosynthesis associated pathways, including 82 photosynthesis core genes, 24 plastid-encoded RNA polymerase related genes, 2 nucleus-encoded RNA polymerase-related genes, 34 photomorphogenesis-related genes, 40 genes involved in transcription and translation (TAC) and 938 other nuclear-encoded chloroplast-targeted genes. By de novo assembling the chloroplast genomes of 28 representative accessions and leveraging whole-genome, transcriptome sequencing data from the 1001 Genome Project, we revealed extensive natural genetic and transcriptome variations these genes in worldwide Arabidopsis thaliana population. 34.0% of them were identified with regulatory variations in expression quantitative locus mapping (eQTL) mapping, including key components of Rubisco (RBCS1B, RBCS2B), and Rubisco activase (RCA). Genome-wide and transcriptome-wide association analysis (GWAS/TWAS) showed that these genetic and transcriptomic variations made considerable contribution to variation of adaptive traits. Overall, our study provides insight into the natural genetic variation of these genes among worldwide Arabidopsis thaliana accessions and their role in complex traits variation and adaptation.

plant biology↗

bioRxiv2024

Asynchronous mouse embryo polarization leads to heterogeneity in cell fate specification

The first lineage allocation in mouse and human embryos separates the inner cell mass (ICM) from the outer trophectoderm (TE). This symmetry breaking event is executed through polarization of cells at the 8-cell stage and subsequent asymmetric divisions, generating polar (TE) and apolar (ICM) cells. Here, we show that embryo polarization is unexpectedly asynchronous. Cells polarizing at the early and late 8-cell stage have distinct molecular and morphological properties that direct their following lineage specification, with early polarizing cells being biased towards producing the TE lineage. More recent studies have also implicated heterogeneities between cells prior to the 8-cell stage in the first lineage allocation: cells exhibiting reduced methyltransferase CARM1 activity at the 4-cell stage are predisposed towards the TE fate. Here, we demonstrate that reduced CARM1 activity and upregulation of its substrate BAF155 promote early polarization and TE specification. These findings provide a link between asymmetries at the 4-cell stage and polarization at the 8-cell stage, mechanisms of the first lineage allocation that had been considered separate.

developmental biology↗

bioRxiv2024

The role of YAP/TAZ signaling in dendritic cell-mediated pathogenesis of insulin resistance and non-alcoholic fatty liver disease

Obesity and insulin resistance (IR) are global health challenges linked to metabolic diseases, such as type 2 diabetes and non-alcoholic fatty liver disease (NAFLD). High-caloric intake, which is associated to NAFLD, induces adipocyte hypertrophy and inflammation, triggering dendritic cell (DC) activation and systemic inflammation. DC exacerbate inflammation by promoting pro-inflammatory responses, aggravating IR and NAFLD progression. NAFLD is characterized by liver fibrosis, which alters tissue stiffness that can trigger mechanosensing pathways such as the Hippo pathway in immune cell types. In this work we explored the roles of key mediators of the Hippo pathway, YAP and TAZ, in DCs within the context of liver fibrosis, obesity and IR, using a model of NAFLD induced by feeding a high fat high sucrose diet. Our findings indicate that specific deletion of YAP and/or TAZ in DCs had minimal impact on IR development and metabolic tissue inflammation. We conclude that YAP and TAZ have limited and possibly redundant roles in the immune pathophysiology of NAFLD and IR.

immunology↗

bioRxiv2024

Combined HDAC and eIF4A inhibition: A novel epigenetic therapy for pancreatic adenocarcinoma

Pancreatic ductal adenocarcinoma-(PDAC) needs innovative approaches due to its 12% 5-year survival despite current therapies. We show marked sensitivity of pancreatic cancer cells to the combination of a novel eIF4A inhibitor, des-methyl pateamine A (DMPatA), and a histone deacetylase inhibitor, romidepsin, inducing epigenetic reprogramming as an innovative therapeutic strategy. Exploring the mechanistic activity of this combination showed that with a short duration of romidepsin at low doses, robust acetylation persisted up to 48h with the combination, while histone acetylation rapidly faded with monotherapy. This represents an unexpected mechanism of action against PDAC cells that triggers transcriptional overload, metabolic stress, and augmented DNA damage. Structurally different class I HDAC inhibitors exhibit the same hyperacetylation patterns when co-administered with DMPatA, suggesting a class effect. We show efficacy of this combination regimen against tumor growth in a MIA PaCa-2 xenograft model of PDAC with persistent hyperacetylation confirmed in tumor samples. STATEMENT OF SIGNIFICANCEPancreatic ductal adenocarcinoma, a significant clinical challenge, could benefit from the latent potential of epigenetic therapies like HDAC inhibitors-(HDIs), typically limited to hematological malignancies. Our study shows that a synergistic low dose combination of HDIs with an eIF4A-inhibitor in pancreatic cancer models results in marked pre-clinical efficacy, offering a promising new treatment strategy.

cancer biology↗

bioRxiv2024

TrkA+ sensory neurons regulate osteosarcoma proliferation and vascularization to promote disease progression

Bone pain is a presenting feature of bone cancers such as osteosarcoma (OS), relayed by skeletal-innervating peripheral afferent neurons. Potential functions of tumor-associated sensory neurons in bone cancers beyond pain sensation are unknown. To uncover neural regulatory functions, a chemical-genetic approach in mice with a knock-in allele for TrkA was used to functionally perturb sensory nerve innervation during OS growth and disease progression. TrkA inhibition in transgenic mice led to significant reductions in sarcoma-associated sensory innervation and vascularization, tumor growth and metastasis, and prolonged overall survival. Single-cell transcriptomics revealed that sarcoma denervation was associated with phenotypic alterations in both OS tumor cells and cells within the tumor microenvironment, and with reduced calcitonin gene-related peptide (CGRP) and vascular endothelial growth factor (VEGF) signaling. Multimodal and multi-omics analyses of human OS bone samples and human dorsal root ganglia neurons further implicated peripheral innervation and neurotrophin signaling in OS tumor biology. In order to curb tumor-associated axonal ingrowth, we next leveraged FDA-approved bupivacaine liposomes leading to significant reductions in sarcoma growth, vascularity, as well as alleviation of pain. In sum, TrkA-expressing peripheral neurons positively regulate key aspects of OS progression and sensory neural inhibition appears to disrupt calcitonin receptor signaling (CALCR) and VEGF signaling within the sarcoma microenvironment leading to significantly reduced tumor growth and improved survival. These data suggest that interventions to prevent pathological innervation of osteosarcoma represent a novel adjunctive therapy to improve clinical outcomes and survival.

cancer biology↗

bioRxiv2024

Oligopeptide (FK)4 facilitates the determination of the absolute stereochemistry of chiral organic compounds via NMR Spectroscopy

Molecular chirality plays a crucial role in the fields of chemistry and biology. Various nuclear magnetic resonance (NMR) methods have been employed for assignment of stereochemical configurations. Alignment media for measurements of anisotropic parameters contribute to configuration elucidations, while chiral auxiliaries assist in enantiomer discrimination and chiral recognition. However, each method comes with limitations, and the assignment of absolute configuration by NMR remains challenging. In this study, we explored a combined approach for absolute configuration elucidation with the multifaceted application of the oligopeptide (FK)4, which possesses dual functionalities as an alignment medium for anisotropic NMR measurements and a chiral differentiating agent. As an alignment medium, (FK)4 facilitates the analysis of stereochemical features through residual dipolar couplings (RDC), aiding in the structural elucidation of stereoisomers. Moreover, (FK)4 exhibits unique chiral differentiating properties, interacting distinctly with enantiomers and resulting in observable bifurcation of chemical shift signals, in 13C, 1H and 19F spectra. Using isoleucine and xylose as model compounds, we demonstrate how the dual functionality of (FK)4 enables the identification of stereoisomeric structures via RDC parameters and the assignment of enantiomeric configurations through measurements of t2 relaxation time coupled with theoretical simulations. These findings highlight the potential of versatile chiral media as (FK)4 for approaching the elucidation of absolute configurations of organic molecules via combined NMR spectroscopy approaches, with implications for structural characterization and enantiomer discrimination in chemical applications.

biochemistry↗

bioRxiv2024

Mapping Somatosensory Afferent Circuitry to Bone Identifies Neurotrophic Signals Required for Fracture Healing

The profound pain accompanying bone fracture is mediated by somatosensory neurons, which also appear to be required to initiate bone regeneration following fracture. Surprisingly, the precise neuroanatomical circuitry mediating skeletal nociception and regeneration remains incompletely understood. Here, we characterized somatosensory dorsal root ganglia (DRG) afferent neurons innervating murine long bones before and after experimental long bone fracture in mice. Retrograde labeling of DRG neurons by an adeno-associated virus with peripheral nerve tropism showed AAV-tdT signal. Single cell transcriptomic profiling of 6,648 DRG neurons showed highest labeling across CGRP+ neuron clusters (6.9-17.2%) belonging to unmyelinated C fibers, thinly myelinated A{delta} fibers and A{beta}-Field LTMR (9.2%). Gene expression profiles of retrograde labeled DRG neurons over multiple timepoints following experimental stress fracture revealed dynamic changes in gene expression corresponding to the acute inflammatory (S100a8, S100a9) and mechanical force (Piezo2). Reparative phase after fracture included morphogens such as Tgfb1, Fgf9 and Fgf18. Two methods to surgically or genetically denervate fractured bones were used in combination with scRNA-seq to implicate defective mesenchymal cell proliferation and osteodifferentiation as underlying the poor bone repair capacity in the presence of attenuated innervation. Finally, multi-tissue scRNA-seq and interactome analyses implicated neuron-derived FGF9 as a potent regulator of fracture repair, a finding compatible with in vitro assessments of neuron-to-skeletal mesenchyme interactions.

cell biology↗

bioRxiv2024

Dual nuclease single-cell lineage tracing by Cas9 and Cas12a

Single-cell lineage tracing based on CRISPR/Cas9 gene editing enables the simultaneous linkage of cell states and lineage history at a high resolution. Despite its immense potential in resolving the cell fate determination and genealogy within an organism, existing implementations of this technology suffer from limitations in recording capabilities and considerable barcode dropout. Here, we introduce DuTracer, a versatile tool, which utilizes two orthogonal gene editing systems to record deep cell lineage history at single-cell resolution in an inducible manner. DuTracer shows the ability of enhanced lineage recording with minimized target dropouts and deepened tree depth. Application of DuTracer in mouse embryoid bodies and neuromesodermal organoids illustrates the lineage relationship of different cell types and proposes potential lineage-biased molecular drivers. Moreover, we have developed an entropy-based approach to quantify the lineage recording ability of DuTracer in cell differentiation models. Together, DuTracer facilitates the precise and regulatory interrogation of cellular lineages of complex biological processes.

developmental biology↗

bioRxiv2024

SEIR: a novel multi-locus GWAS method that provides higher statistical power for fast identifying variant-phenotype associations

Multi-locus genome-wide association study (GWAS) methods have considered the joint effects of multiple variants to more accurately unravel the genetic basis of complex traits. Here, we developed a novel multi-locus GWAS method named Selector-Embedded Iterative Regression (SEIR), which integrates the embedded selector with fast single-marker scanning in an iterative manner. SEIR has excellent adaptability and flexibility under various genetic architectures for qualitative and quantitative traits. Reliability of SEIR was experimentally supported by integrating GWAS with 3D epigenomics in a real trait. Conclusively, SEIR exhibits higher statistical power for fast identifying putative variants compared to other single- and multi-locus methods.

genetics↗

bioRxiv2024

Excessive Dietary Fructose Aggravates Heart Failure via Impairing Myocardial Fatty Acid Oxidation Metabolism in Diet Induced Obese Mouse

BackgroundAn unhealthy diet and a sedentary lifestyle increase the prevalence of cardiometabolic syndrome. Several cardiovascular diseases (CVDs) have been highly linked to excessive added sugar intake, which alters whole-body metabolism, including heart tissue. However, whether specific added sugars can cause and aggravate severe heart dysfunction is still unknown. MethodsWe examined the association between CVDs and added sugar intake using statistical analyses and Mendelian randomization (MR). Then, we evaluated the effect of added sugar on mouse heart function employing a diet-induced obese (DIO) model with transverse aortic constriction (TAC) challenge. We measured the fatty acid and fructose metabolic flux in mouse hearts employing a mass spectrometry-based in vivo double stable isotopic labeling (DSIL) technique. The results of animal models were also confirmed in aortic stenosis (AS) patient samples. ResultsStatistical analyses and MR estimation on public databases indicated that added sugars, especially fructose, are associated with a high risk of heart failure. Feeding on either ingested or drunk fructose could aggravate heart failure and diastolic and systolic dysfunction in TAC challenged DIO mice. Mechanistically, excessive dietary intake of fructose could suppress heart fatty acid oxidation (FAO) metabolism via both shrinkage of the flux rate of FAO and inhibition of the AMPK-ACC axis. Activation of AMPK or deactivation of ACC could limit such heart dysfunction and myocardial hypertrophy. We also obtained plasma from 27 patients with AS and determined that the high fructose level instead of glucose or sucrose was linked to left ventricular ejection fractions (LVEF) and fractional shortening (FS) decline. ConclusionsFindings from epidemiological statistical analyses and investigations of animal models suggested the harmful effect of excessive fructose intake on heart function. Fructose could directly alter heart metabolism by suppressing FAO. Our results implied that targeting AMPK-ACC mediation could effectively attenuate excessive fructose-induced heart failure in DIO mice.

physiology↗

bioRxiv2024

Sacrificing Adaptability for Functionality: The Ivory Tower of Macular Muller Cells

The predilection of many retinal diseases for the macula suggests it may be less resistant to stress than the peripheral retina. Profiling of single-cell level transcriptional changes found that the peripheral retina exhibited more transcriptional changes than the macula in response to stress. One pronounced change was in a subgroup of Muller cells (MCs) that were dominant in the peripheral retina. Genes more abundantly expressed in peripheral MCs were mainly associated with stress responses and were more influenced by light stress. In contrast, genes highly expressed in MCs that predominated in the macula had roles in cellular function and were less influenced by light stress. Metallothionein 1, A Kinase Anchor Protein 12 and MAF BZIP Transcription Factor F were more abundantly expressed in peripheral MCs than in macular MCs. Knockdown of these genes in primary MCs reduced their viability under stress. Our findings indicate that macular MCs are more directed toward maintaining retinal function rather than mounting a stress response when exposed to stress, which may contribute to the maculas vulnerability to degenerative diseases.

neuroscience↗

bioRxiv2024

Control of OPC proliferation and repopulation by the intellectual disability gene PAK1 under homeostatic and demyelinating conditions

Appropriate proliferation and repopulation of oligodendrocyte progenitor cells (OPCs) determine successful (re)myelination in homeostatic and demyelinating brains. Activating mutations in p21-activated kinase 1 (PAK1) cause intellectual disability, neurodevelopmental abnormality, and white matter anomaly in children. It remains unclear if and how PAK1 regulates oligodendroglial development. Here, we report that PAK1 controls proliferation and regeneration of OPCs. Unlike differentiating oligodendrocytes, OPCs display high PAK1 activity which maintains them in a proliferative state by modulating PDGFRa-mediated mitogenic signaling. PAK1-deficient or kinase-inhibited OPCs reduce their proliferation capacity and population expansion. Mice carrying OPC-specific PAK1 deletion or kinase inhibition are populated with fewer OPCs in the homeostatic and demyelinated CNS than control mice. Together, our findings suggest that kinase-activating PAK1 mutations stall OPCs in a progenitor state, impacting timely oligodendroglial differentiation in the CNS of affected children and that PAK1 is a potential molecular target for replenishing OPCs in demyelinating lesions.

neuroscience↗

bioRxiv2024

Circular DNA vcDNA-S7 derived from segmented-dsRNA virus BmCPV attenuated viral infection through RNase H1

Viral circDNA derived from insect positive-sense single-stranded RNA viruses plays a crucial role in regulating viral infections depending on the RNAi pathway. Our previous research has revealed that Bombyx mori cypovirus (BmCPV), a segmented-dsRNA virus, can generate viral circDNA vcDNA-S7, which can be transcribed to form RNA and further processed into small RNAs to defend against the virus through RNAi. However, whether vcDNA-S7 employs other mechanisms to resist the viruses. Presently, vcDNA-S7 has been found to resist BmCPV infection via a novel mechanism that depends on ribonuclease RNase H1 activity. It was found that the expression level of RNase H1 increased upon BmCPV infection (RNA virus) but not upon B. mori nucleopolyhedrovirus (BmNPV) (DNA virus) infection. RNase H1 has been shown to negatively regulate BmCPV infections. In addition, vcDNA-S7 was found to form a heteroduplex with the viral RNA and subsequently recruit RNase H1 to degrade the viral RNA within the heteroduplex, ultimately leading to the suppression of viral replication. Furthermore, the resistance of vcDNA-S7 to viruses was significantly reduced when cellular RNase H1 gene was silenced. These findings not only reveal a new antiviral mechanism involving circular DNA formed by reovirus but also offer intriguing insights into the antiviral function of RNase H1 in cells.

immunology↗

bioRxiv2024

Multi-Niche Human Bone Marrow On-A-Chip for Studying the Interactions of Adoptive CAR-T Cell Therapies with Multiple Myeloma

Multiple myeloma (MM), a cancer of bone marrow plasma cells, is the second-most common hematological malignancy. However, despite immunotherapies like chimeric antigen receptor (CAR)-T cells, relapse is nearly universal. The bone marrow (BM) microenvironment influences how MM cells survive, proliferate, and resist treatment. Yet, it is unclear which BM niches give rise to MM pathophysiology. Here, we present a 3D microvascularized culture system, which models the endosteal and perivascular bone marrow niches, allowing us to study MM-stroma interactions in the BM niche and model responses to therapeutic CAR-T cells. We demonstrated the prolonged survival of cell line-based and patient-derived multiple myeloma cells within our in vitro system and successfully flowed in donor-matched CAR-T cells. We then measured T cell survival, differentiation, and cytotoxicity against MM cells using a variety of analysis techniques. Our MM-on-a-chip system could elucidate the role of the BM microenvironment in MM survival and therapeutic evasion and inform the rational design of next-generation therapeutics. TEASERA multiple myeloma model can study why the disease is still challenging to treat despite options that work well in other cancers.

cancer biology↗

bioRxiv2024

Gossamer: Scaling Image Processing and Reconstruction to Whole Brains

Neuronal reconstruction-a process that transforms image volumes into 3D geometries and skeletons of cells- bottlenecks the study of brain function, connectomics and pathology. Domain scientists need exact and complete segmentations to study subtle topological differences. Existing methods are diskbound, dense-access, coupled, single-threaded, algorithmically unscalable and require manual cropping of small windows and proofreading of skeletons due to low topological accuracy. Designing a data-intensive parallel solution suited to a neurons shape, topology and far-ranging connectivity is particularly challenging due to I/O and load-balance, yet by abstracting these vision tasks into strategically ordered specializations of search, we progressively lower memory by 4 orders of magnitude. This enables 1 mouse brain to be fully processed in-memory on a single server, at 67x the scale with 870x less memory while having 78% higher automated yield than APP2, the previous state of the art in performant reconstruction.

neuroscience↗

bioRxiv2024

The Transcription Factor OsNAC5 Mediates Cadmium Stress Response and Accumulation in Rice

Cadmium (Cd) is a toxic heavy metal that endangers human health through contaminated rice consumption. Reducing Cd uptake in rice is essential for minimizing grain Cd accumulation. However, the transcriptional regulation of Cd uptake in rice remains largely elusive. This study reveals that the transcription factor OsNAC5 in Oryza sativa positively regulates the Cd transporter gene OsNRAMP1, influencing Cd uptake. OsNAC5 is primarily expressed in roots, localized to the nucleus, and upregulated by Cd-induced H2O2. Knocking out OsNAC5 reduces Cd levels in both shoots and roots and increases Cd sensitivity. OsNRAMP1 expression, enhanced by Cd stress, depends on OsNAC5, which binds to "CATGTG" motifs in the OsNRAMP1 promoter activating its expression. Loss of OsNAC5 function decreases Cd accumulation in rice grains. Our findings elucidate the transcriptional regulation of Cd stress response in rice and suggest biotechnological approaches to reduce Cd uptake in crops. Declaration of Competing InterestThe authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

plant biology↗

bioRxiv2024

Massively parallel combination screen reveals small molecule sensitization of antibiotic-resistant Gram-negative ESKAPE pathogens

Antibiotic resistance, especially in multidrug-resistant ESKAPE pathogens, remains a worldwide problem. Combination antimicrobial therapies may be an important strategy to overcome resistance and broaden the spectrum of existing antibiotics. However, this strategy is limited by the ability to efficiently screen large combinatorial chemical spaces. Here, we deployed a high-throughput combinatorial screening platform, DropArray, to evaluate the interactions of over 30,000 compounds with up to 22 antibiotics and 6 strains of Gram-negative ESKAPE pathogens, totaling to over 1.3 million unique strain-antibiotic-compound combinations. In this dataset, compounds more frequently exhibited synergy with known antibiotics than single-agent activity. We identified a compound, P2-56, and developed a more potent analog, P2-56-3, which potentiated rifampin (RIF) activity against Acinetobacter baumannii and Klebsiella pneumoniae. Using phenotypic assays, we showed P2-56-3 disrupts the outer membrane of A. baumannii. To identify pathways involved in the mechanism of synergy between P2-56-3 and RIF, we performed genetic screens in A. baumannii. CRISPRi-induced partial depletion of lipooligosaccharide transport genes (lptA-D, lptFG) resulted in hypersensitivity to P2-56-3/RIF treatment, demonstrating the genetic dependency of P2-56-3 activity and RIF sensitization on lpt genes in A. baumannii. Consistent with outer membrane homeostasis being an important determinant of P2-56-3/RIF tolerance, knockout of maintenance of lipid asymmetry complex genes and overexpression of certain resistance-nodulation-division efflux pumps - a phenotype associated with multidrug-resistance - resulted in hypersensitivity to P2-56-3. These findings demonstrate the immense scale of phenotypic antibiotic combination screens using DropArray and the potential for such approaches to discover new small molecule synergies against multidrug-resistant ESKAPE strains. Significance StatementThere is an unmet need for new antibiotic therapies effective against the multidrug-resistant, Gram-negative ESKAPE pathogens. Combination therapies have the potential to overcome resistance and broaden the spectrum of existing antibiotics. In this study, we use DropArray, a massively parallel combinatorial screening tool, to assay more than 1.3 million combinations of small molecules against the Gram-negative ESKAPE pathogens, Acinetobacter baumannii, Klebsiella pneumoniae, and Pseudomonas aeruginosa. We discovered a synthetic small molecule potentiator, P2-56, of the antibiotic rifampin effective in A. baumannii and K. pneumoniae. We generated P2-56-3, a more potent derivative of P2-56, and found that it likely potentiates rifampin by compromising the outer membrane integrity. Our study demonstrates a high-throughput strategy for identifying antibiotic potentiators against multidrug-resistant bacteria.

microbiology↗

bioRxiv2024

Conformational Ensembles Reveal the Origins of Serine Protease Catalysis

Enzymes exist in ensembles of states that encode the energetics underlying their catalysis. Conformational ensembles built from 1231 structures of 17 serine proteases reveal atomic-level changes across their reaction states, identify molecular features that provide catalysis, and quantify their energetic contributions to catalysis. These enzymes precisely position their reactants in destabilized conformers, creating a downhill energetic gradient that selectively favors the motions required for reaction while limiting off-pathway conformational states. A local catalytic motif, the "nucleophilic elbow", has repeatedly evolved, generating ground state destabilization in 50 proteases and 52 additional enzymes spanning 32 distinct structural folds. Ensemble-function analyses reveal previously unknown catalytic features, provide quantitative models based on simple physical and chemical principles, and identify motifs recurrent in Nature that may inspire enzyme design. One sentence summary: Ensemble-function analyses provide a quantitative model for serine protease catalysis, reveal previously unknown conformational features that contribute to their catalysis, and identify a structural motif that underlie these features and has evolved in >100 different enzymes from 32 protein folds.

biophysics↗