Biology subjects

Lu, M.

Publications and source records attributed to Lu, M..

At least 109 records · Page 6Linked to original sources

bioRxiv2023

Ribonucleotide Reductase Subunit Switching in Hepatoblastoma Drug Response and Relapse

Prognosis of children with high-risk hepatoblastoma (HB), the most common pediatric liver cancer, remains poor. In this study, we found ribonucleotide reductase (RNR) subunit M2 (RRM2) was one of the key genes supporting cell proliferation in high-risk HB. While standard chemotherapies could effectively suppress RRM2 in HB cells, they induced a significant upregulation of the other RNR M2 subunit, RRM2B. Computational analysis revealed distinct signaling networks RRM2 and RRM2B were involved in HB patient tumors, with RRM2 supporting cell proliferation and RRM2B participating heavily in stress response pathways. Indeed, RRM2B upregulation in chemotherapy-treated HB cells promoted cell survival and subsequent relapse, during which RRM2B was gradually replaced back by RRM2. Combining an RRM2 inhibitor with chemotherapy showed an effective delaying of HB tumor relapse in vivo. Overall, our study revealed the distinct roles of the two RNR M2 subunits and their dynamic switching during HB cell proliferation and stress response.

cancer biology↗

bioRxiv2022

SGC-CLK-1 (CAF-170) a chemical probe for the Cdc2-Like kinases CLK1, CLK2, and CLK4

Small molecule modulators are important tools to study both basic biology and the complex signaling of protein kinases. The cdc2-like kinases (CLK) are a family of four kinases that have garnered recent interest for their involvement in a diverse set of diseases such as neurodegeneration, autoimmunity, and many cancers. Targeted medicinal chemistry around a CLK inhibitor hit identified through screening of a kinase inhibitor set against a large panel of kinases allowed us to identify a potent and selective inhibitor of CLK1, 2 and 4. Here, we present the synthesis, selectivity, and potential binding site of this compound - SGC-CLK-1. We further show CLK2 has the highest binding affinity, and high CLK2 expression correlates with a lower IC50 in a screen of multiple cancer cell lines. Finally, we show that SGC-CLK-1 not only reduces serine arginine rich (SR) protein phosphorylation, but also alters SR protein and CLK2 subcellular localization in a reversible way. Therefore, we anticipate that this compound will be a valuable tool for increasing our understanding of CLKs and their targets, SR proteins, at the level of phosphorylation and subcellular localization.

cancer biology↗

bioRxiv2022

Exploring the interaction between immune cells in testicular microenvironment of azoospermia combining RNA-seq and scRNA-seq

Non-obstructive azoospermia is the most serious cause of male infertility. The testis has a special immunological environment, but the relationship between immune cells in the testicular microenvironment is still unclear. Therefore, it is urgent to identify the interaction mechanism and molecular determinants of immune cells in the testicular microenvironment. To further elucidate the etiology of azoospermia and provide a reference for the treatment of azoospermia. The GSE145467 and GSE9210 datasets were analyzed by Limma package, and then the differential genes were analyzed by enrichment analysis and protein-protein interaction analysis. In addition, we combined single-cell analysis(scRNA) to identify immune cell types and verified the expression of Hub genes in these immune cells. Finally, CellChat was used for cell-to-cell communication analysis. We found the distribution of immune cells in the microenvironment of Y chromosome AZF region microdeletions (AZFa_Del), idiopathic NOA (iNOA), and Klinefelter syndrome (KS) was significantly different from that of normal adults, especially monocytes/macrophages. In normal subjects, monocytes/macrophages mainly played the role of the signal source, while in patients with azoospermia, monocytes/macrophages mainly received signals from other immune cells. Monocytes/macrophages in AZFa_Del, iNOA, and KS communicated with other immune cells mainly through MDK-LRP1, PTN-NCL, and MDK-NCL ligand-receptor pairs respectively. Our research provides new ideas for the pathogenesis and treatment of azoospermia. Author SummaryThis article uses the datasets in the public database, including RNA-seq and scRNA-seq. It is a secondary analysis of these databases. Previous studies have found the destruction of Sertoli cells in the testicular microenvironment using scRNA datasets. We have analyzed immune cells in the testicular microenvironment based on previous studies. Found huge changes in macrophages and abnormal macrophages communication through cell communication analysis, The receptor-ligand pairs were screened to provide a basis for the study of macrophages in the testicular microenvironment and the treatment of azoospermia.

cell biology↗

bioRxiv2022

Reconceptualizing beta diversity: a hypervolume geometric approach

Beta diversity--the variation among community compositions in a region--is a fundamental measure of biodiversity. Despite a diverse set of measures to quantify beta diversity, most measures have posited that beta diversity is maximized when each community has a single distinct species. However, this assumption overlooks the ecological significance of species interactions and non-additivity in ecological systems, where the function and behaviour of species depend on other species in a community. Here, we introduce a geometric approach to measure beta diversity as the hypervolume of the geometric embedding of a metacommunity. This approach explicitly accounts for non-additivity and captures the idea that introducing a unique, species-rich community composition to a metacommunity increases beta diversity. We show that our hypervolume measure is closely linked to and naturally extends previous information- and variation-based measures while providing a unifying geometric framework for widely adopted extensions of beta diversity. Applying our geometric measures to empirical data, we address two long-standing questions in beta diversity research--the latitudinal pattern of beta diversity and the effect of sampling effort--and present novel ecological insights that were previously obscured by the limitations of traditional approaches. In sum, our geometric approach reconceptualizes beta diversity, offering an alternative and complementary perspective to previous measures, with immediate applicability to existing data.

ecology↗

bioRxiv2022

O-GlcNAcylation promotes YTHDF1 cytosolic localization and colorectal cancer tumorigenesis

O-linked N-acetylglucosamine (O-GlcNAc) is an emerging post-translation modification that couples metabolism with cellular signal transduction by crosstalking with phosphorylation and ubiquitination to orchestrate various biological processes. Herein we show that it modifies the N6-methyladenosine (m6A)-mRNA reader YTHDF1 and fine-tunes its nuclear translocation by the exportin protein Crm1. First we present evidence that YTHDF1 interacts with the sole O-GlcNAc transferase (OGT). Second, we verified the YTHDF1 O-GlcNAcylation sites to be Ser196/Ser197/Ser198, as described in previous numerous chemoproteomic studies. Then we constructed the O-GlcNAc-deficient YTHDF1-S196AS197FS198A (AFA) mutants, which significantly attentuated O-GlcNAc signals. Moreover, we revealed that YTHDF1 is a nucleocytoplasmic protein, whose nuclear export is mediated by Crm1. Furthermore, O-GlcNAcylation increases the cytosolic portion of YTHDF1 by enhancing binding with Crm1, thus upregulating the downstream target (e.g. c-Myc) expression. Molecular dynamics simulations suggest that O-GlcNAcylation at S197 might promote the binding between the nuclear export signal motif and Crm1 through increasing hydrogen bonding. Mouse xenograft assays further demonstrate that YTHDF1-AFA mutants decreased the colon cancer mass and size via decreasing c-Myc expression. In sum, we found that YTHDF1 is a nucleocytoplasmic protein, whose cytosolic localization is dependent on O-GlcNAc modification. We propose that the OGT-YTHDF1-c-Myc axis might underlie colorectal cancer tumorigenesis.

biochemistry↗

bioRxiv2022

A continental scale analysis reveals widespread root bimodality

Summary paragraphRecent studies of plant fine roots have greatly advanced our understanding of their geometric properties and symbiotic relationships, but knowledge of how these roots are spatially distributed across the soil matrix lags far behind. An improved understanding of broad-scale variability in root vertical distribution is critical for understanding plant-soil-atmosphere interactions and their influence on the land carbon sink. Here we analyze a continental-scale dataset of plant roots reaching 2-meters depth, spanning 19 ecoclimatic domains ranging from Alaskan tundra to Puerto Rican neotropical forest. Contrary to the common expectation that fine root abundance decays exponentially with increasing soil depth, we found surprising root bimodality at ~20% of 44 field sites --a secondary peak of fine root biomass far beneath the soil surface. All of the secondary root peaks were observed deeper than 60cm (with 33% below 1m), far deeper than the sampling depth commonly used in ecosystem studies and forestry surveys. We demonstrate that root bimodality is more likely in places with relatively low total fine root biomass, and is more frequently associated with shrubland vegetation but less with grassland. Further statistical analyses revealed that the secondary peak of root biomass coincided with unexpected high soil nitrogen contents at depth. By linking roots and nutrient distributions, we further demonstrate that deep soil nutrients tend to be underexploited by plant rooting systems, yet root bimodality offers a unique mechanism by which fine roots can tap into soil resources in the deep. Our findings suggest that empirical practices have often systematically overlooked root dynamics in deep soils, and as a result the current-generation global climate and vegetation models have relied on overly simplistic assumptions for plant rooting distribution.

ecology↗

bioRxiv2022

The overlooked dimension: soil depth drives microbial community structure and function along a salinity gradient

AimA fundamental challenge in soil macroecology is to understand how microbial community structure shapes ecosystem functions along environmental gradients of land surface (i.e., horizontal dimension). However, little is known of microbial community structure-function relationships along environmental gradients of soil depth (i.e., vertical dimension) in extreme environments. A full understanding of the consequences of environmental change for microbial communities structure and subsequent changes in microbial functions could enable more accurate predictions of extreme environmental change effects. Here, we leveraged a 200-km desert soil salinity gradient that is created by a 12-year saline-water irrigation to evaluate how soil microbial community structure-function relationships change with soil salinity in the horizontal and vertical dimensions. LocationThe Tarim basin of Taklamakan desert. TaxaSoil bacteria and fungi. MethodsWe assessed the prime ecological processes controlling the assembly of microbial communities and the activity of enzymes relevant to carbon, nitrogen, and phosphorus cycling along soil salinity gradients across study sites (horizontal dimension) and soil depths (vertical dimension) by using the general linear model, hierarchical variance partitioning, and path model. ResultsDifferences in soil depth (on the scale of meters) was as important as geographic distance (on the scale of kilometers) in shaping the structure of bacterial and fungal communities, while both the vertical and horizontal variability in enzymatic activity were largely attributed to the increase in the heterogeneity of soil properties, such as soil texture, water content, and pH. Main conclusionsOur results suggest that dispersal limitation and environmental heterogeneity, not soil salinization, along soil depth governs microbial community assembly and enzymatic activity, respectively. This work highlights that conservation efforts of soil macroecology should consider soil depth as a key attribute in the face of ongoing salinization in arid ecosystems.

ecology↗

bioRxiv2022

A Data-Driven Optimization Method for Coarse-Graining Gene Regulatory Networks

One major challenge in systems biology is to understand how various genes in a gene regulatory network (GRN) collectively perform their functions and control network dynamics. This task becomes extremely hard to tackle in the case of large networks with hundreds of genes and edges, many of which have redundant regulatory roles and functions. The existing methods for model reduction usually require the detailed mathematical description of dynamical systems and their corresponding kinetic parameters, which are often not available. Here, we present a data-driven method for coarse-graining large GRNs, named SacoGraci, using ensemble-based mathematical modeling, dimensionality reduction and gene circuit optimization by Markov Chain Monte Carlo methods. SacoGraci requires network topology as the only input and is robust against errors in GRNs. We benchmark and demonstrate its usage with synthetic, literature-based, and bioinformatics-derived GRNs. We hope SacoGraci will enhance our ability to model the gene regulation of complex biological systems.

systems biology↗

bioRxiv2022

Neural Network-Derived Potts Models for Structure-Based Protein Design using Backbone Atomic Coordinates and Tertiary Motifs

AO_SCPLOWBSTRACTC_SCPLOWDesigning novel proteins to perform desired functions, such as binding or catalysis, is a major goal in synthetic biology. A variety of computational approaches can aid in this task. An energy-based framework rooted in the sequence-structure statistics of tertiary motifs (TERMs) can be used for sequence design on pre-defined backbones. Neural network models that use backbone coordinate-derived features provide another way to design new proteins. In this work, we combine the two methods to make neural structure-based models more suitable for protein design. Specifically, we supplement backbone-coordinate features with TERM-derived data, as inputs, and we generate energy functions as outputs. We present two architectures that generate Potts models over the sequence space: TERMinator, which uses both TERM-based and coordinate-based information, and COORDinator, which uses only coordinate-based information. Using these two models, we demonstrate that TERMs can be utilized to improve native sequence recovery performance of neural models. Furthermore, we demonstrate that sequences designed by TERMinator are predicted to fold to their target structures by AlphaFold. Finally, we show that both TERMinator and COORDinator learn notions of energetics, and these methods can be fine-tuned on experimental data to improve predictions. Our results suggest that using TERM-based and coordinate-based features together may be beneficial for protein design and that structure-based neural models that produce Potts energy tables have utility for flexible applications in protein science. CodeCode will be made publically available at https://github.com/alexjli/terminator_public

biophysics↗

bioRxiv2022

Discovery of unknown quorum-sensing reprogramming factors in Pseudomonas aeruginosa using a dual-acting-gene-blocking approach

LasR is a master regulator of quorum-sensing (QS) in Pseudomonas aeruginosa. LasR-null mutants commonly appear in lung isolates from chronically infected cystic fibrosis (CF) patients. However, numerous such CF isolates have a QS-active phenotype, but factors underlying QS-reprogramming in LasR-null mutants remain largely unknown. Mutations in the transcriptional regulator gene mexT are well known to be responsible for QS-reprogramming in a laboratory LasR-null mutant strain, however, simultaneous occurrence of lasR and mexT mutations is rare in CF isolates. To identify QS-reprogramming determinants, we developed an experimental evolution approach, for which a QS-inactive LasR null mutant with an extra copy of mexT was engineered. In such a strain, spontaneous single mexT mutations are expected to have no or little phenotypic consequences. This novel method, named "targeted gene duplication followed by mutant screening" (TGD-MS), resulted in the identification of QS-active revertants with mutations in genes other than mexT. We characterized a QS-active revertant with a point mutation in rpoA, a gene encoding the -subunit of RNA polymerase. QS activation in this mutant was found to be associated with the down-regulated expression of mexEF-oprN efflux pump genes. Our study therefore uncovers a new functional role for RpoA in regulating QS activity. Furthermore, our results suggest that a regulatory circuit controlling the expression of the mexEF-oprN operon is critical for QS-reprogramming. In conclusion, our study reports on the identification of non-MexT proteins associated with QS-reprogramming in a laboratory strain, shedding light on possible QS activation mechanisms in clinical P. aeruginosa isolates.

microbiology↗

bioRxiv2022

Novel leaf-root coordination driven by leaf water storage tissues in mangroves

Interactions among root and leaf traits (in particular, leaf hydraulic and leaf economics traits) are fundamental in generating diverse strategies in land plants, yet it remains a knowledge gap in mangrove plants that experiences saline stress distinct from most other vascular plants. Here, we tested the trait relationships in mangrove plants and compared them with typical land plants (non-mangrove). Consistent with non-mangrove plants, leaf hydraulic and economics traits were decoupled in mangrove plants. However, mangrove leaf economics traits correlated strongly with root hydraulic traits, which are normally decoupled in non-mangrove plants. Moreover, we observed a unique scaling relationship between leaf dry mass per area and root hydraulic traits in mangroves. The novel coordination between leaves and roots arises from the wide-presence of leaf water storage tissues in mangroves, and this potentially represents a new paradigm with which we look into the ecology, physiology and evolution of this important vegetation.

ecology↗

bioRxiv2022

A Quantitative Evaluation of Topological Motifs and Their Coupling in Gene Circuit State Distributions

One of the major challenges in biology is to understand how gene interactions collaborate to determine overall functions of biological systems. Here, we present a new computational framework that enables systematic, high-throughput, and quantitative evaluation of how small transcriptional regulatory circuit motifs, and their coupling, contribute to functions of a dynamical biological system. We illustrate how this approach can be applied to identify four- node gene circuits, circuit motifs, and motif coupling responsible for various gene expression state distributions, including those derived from single-cell RNA sequencing data. We also identify seven major classes of four-node circuits from clustering analysis of state distributions. The method is applied to establish phenomenological models of gene circuits driving human neuron differentiation, revealing important biologically relevant regulatory interactions. Our study will shed light on a better understanding of gene regulatory mechanisms in creating and maintaining cellular states.

systems biology↗

bioRxiv2022

CryoEM Structures of the Human HIV-1 Restriction Factor SERINC3 and Function as a Lipid Transporter

The host proteins SERINC3 and SERINC5 are HIV-1 restriction factors that reduce infectivity when incorporated into the viral envelope. The HIV-1 accessory protein Nef abrogates incorporation of SERINCs via binding to intracellular loop 4 (ICL4). CryoEM maps of full-length human SERINC3 and an ICL4 deletion construct reveal that hSERINC3 is comprised of two - helical bundles connected by a [~]40-residue, tilted, "crossmember" helix. The design resembles non-ATP-dependent lipid transporters. Consistently, purified hSERINCs reconstituted into proteoliposomes flip phosphatidylserine (PS), phosphatidylethanolamine and phosphatidylcholine. SERINC3 and SERINC5 reduce infectivity and expose PS on the surface of HIV-1 and also MLV, which is counteracted by Nef and GlycoGag, respectively. Antiviral activities by SERINCs and the scramblase TMEM16F correlate with the exposure of PS and with altered conformation of the envelope glycoprotein. We conclude that SERINCs are lipid transporters, and we demonstrate that lipid flipping is directly correlated with loss of infectivity. One Sentence SummaryThe HIV-1 restriction factor SERINC3 has a molecular design similar to non-ATP dependent lipid transporters, a function supported by the observation of flipping activity in proteoliposomes and exposure of phosphatidylserine on HIV-1 and MLV particles, which is correlated with loss of infectivity.

biophysics↗

bioRxiv2022

ERnet: a tool for the semantic segmentation and quantitative analysis of endoplasmic reticulum topology for video-rate super-resolution imaging

The topology of endoplasmic reticulum (ER) network is highly regulated by various cellular and environmental stimuli and affects major functions such as protein quality control and the cells response to metabolic changes. The ability to quantify the dynamical changes of the ER structures in response to cellular perturbations is crucial for the development of novel therapeutic approaches against ER associated diseases, such as hereditary spastic paraplegias and Niemann Pick Disease type C. However, the rapid movement and small spatial dimension of ER networks make this task challenging. Here, we combine video-rate super-resolution imaging with a state-of-the-art semantic segmentation method capable of automatically classifying sheet and tubular ER domains inside individual cells. Data are skeletonised and represented by connectivity graphs to enable the precise and efficient quantification and comparison of the network connectivity from different complex ER phenotypes. The method, called ERnet, is powered by a Vision Transformer architecture, and integrates multi-head self-attention and channel attention into the model for adaptive weighting of frames in the time domain. We validated the performance of ERnet by measuring different ER morphology changes in response to genetic or metabolic manipulations. Finally, as a means to test the applicability and versatility of ERnet, we showed that ERnet can be applied to images from different cell types and also taken from different imaging setups. Our method can be deployed in an automatic, high-throughput, and unbiased fashion to identify subtle changes in cellular phenotypes that can be used as potential diagnostics for propensity to ER mediated disease, for disease progression, and for response to therapy.

bioengineering↗

bioRxiv2022

NetAct: a computational platform to construct core transcription factor regulatory networks using gene activity

A major question in systems biology is how to identify the core gene regulatory circuit that governs the decision-making of a biological process. Here, we develop a computational platform, named NetAct, for constructing core transcription-factor regulatory networks using both transcriptomics data and literature-based transcription factor-target databases. NetAct robustly infers regulators activity using target expression, constructs networks based on transcriptional activity, and integrates mathematical modeling for validation. Our in-silico benchmark test shows that NetAct outperforms existing algorithms in inferring transcriptional activity and gene networks. We illustrate the application of NetAct to model networks driving TGF-{beta} induced epithelial-mesenchymal transition and macrophage polarization.

systems biology↗

bioRxiv2022

A CXCL12 morphogen gradient uncovers lung endothelial heterogeneity and promotes distal vascular growth

In adults, there is a growing amount of data uncovering the cellular diversity of the pulmonary circulation and mechanisms governing vascular repair after injury, however, molecular and cellular mechanisms contributing to the morphogenesis and growth of the pulmonary vasculature during embryonic development are less clear. Importantly, deficits in vascular development lead to a large number of lung diseases in children, indicating a need to uncover fetal programs that promote pulmonary vascular growth. To address this, we used a transgenic mouse reporter for expression of Cxcl12, an arterial hallmark gene, and performed single-cell RNA sequencing on isolated Cxcl12-DsRed+ endothelium to assess cellular heterogeneity within pulmonary endothelium. Combining cell annotation, gene ontology analysis, and spatial transcriptomics allowed us to segregate the developing artery into spatially and functionally distinct novel subpopulations. In addition, expression of Cxcl12 suggests a morphogen gradient from arteries to capillaries, suggesting directed cell migration for pulmonary vascular development. Disruption of this gradient led to abnormal branching and pulmonary vascular hypoplasia. These data provide evidence for arterial endothelial functional heterogeneity and reveal conserved signaling mechanisms essential for pulmonary vascular development.

developmental biology↗

bioRxiv2022

Prime-pull immunization of mice with a BcfA-adjuvanted vaccine elicits mucosal immunity and prevents SARS CoV-2 infection and pathology

Vaccines against SARS-CoV-2 that induce mucosal immunity capable of preventing infection and disease remain urgently needed. We show that intramuscular priming of mice with an alum and BcfA-adjuvanted Spike subunit vaccine, followed by a BcfA-adjuvanted mucosal booster, generated Th17 polarized tissue resident CD4+ T cells, and mucosal and serum antibodies. The serum antibodies efficiently neutralized SARS-CoV-2 and its Delta variant, suggesting cross-protection against a recent variant of concern (VOC). Immunization with this heterologous vaccine prevented weight loss following challenge with mouse-adapted SARS-CoV-2 and reduced viral replication in the nose and lungs. Histopathology showed a strong leukocyte and polymorphonuclear (PMN) cell infiltrate without epithelial damage in mice immunized with BcfA-containing vaccines. In contrast, viral load was not reduced in the upper respiratory tract of IL-17 knockout mice immunized with the same formulation, suggesting that the Th17 polarized T cell responses are critical for protection. We show that vaccines adjuvanted with alum and BcfA, delivered through a heterologous prime-pull regimen, protect against SARS-CoV-2 infection without causing enhanced respiratory disease. SIGNIFICANCEThere remains a need for SARS CoV-2 booster vaccines that generate mucosal immunity and prevent transmission. We show that systemic priming followed by a mucosal booster with a BcfA-adjuvanted subunit vaccine generates neutralizing antibodies and Th17 polarized systemic and tissue-resident immune responses that provide sterilizing immunity against wildtype SARS CoV-2, and a variant of concern. Importantly, in contrast to alum alone, the addition of BcfA prevents respiratory pathology. These results suggest that a BcfA-adjuvanted mucosal booster may elicit mucosal immunity in individuals previously immunized systemically with approved vaccines. This foundational study in mice sets the stage for testing our vaccine regimen in larger animal models as a booster vaccine.

immunology↗

bioRxiv2022

Repressor element 1-silencing transcription factor deficiency yields profound hearing loss through Kv7.4 channel upsurge in auditory neurons and hair cells

Repressor element 1-silencing transcription factor (REST) is a transcriptional repressor that recognizes neuron-restrictive silencer elements in the mammalian genomes in a tissue- and cell-specific manner. The identity of REST target genes and molecular details of how REST regulates them are emerging. We performed conditional null deletion of Rest (cKO) in murine hair cells (HCs) and auditory neurons, spiral ganglion neurons (SGNs). Null-deletion of full-length REST resulted in normal HCs and SGNs development but manifested with progressive hearing loss in adulthood. We found that deletion of REST results in an increased abundance of Kv7.4 channels at the transcript, protein, and function levels. Specifically, we found that SGNs and HCs from Rest cKO mice displayed increased Kv7.4 expression and augmented Kv7 currents; SGNs excitability was also significantly reduced. Administration of Kv7.4 channel activator, fasudil, recapitulated progressive hearing loss in mice. In contrast, inhibition of the Kv7.4 channel by XE991 rescued the auditory phenotype of Rest cKO mice. Previous studies identified some loss-of-function mutations within the Kv7.4-coding gene, Kcnq4, as a causative factor for progressive hearing loss in mice and humans. Thus, the present findings revealed that a critical homeostatic Kv7.4 channel level is required for proper auditory functions.

neuroscience↗