Biology subjects

Lyu, M.

Publications and source records attributed to Lyu, M..

At least 19 recordsLinked to original sources

bioRxiv2026

A cross-modal generative model for incomplete and degradedprostate MRI with multicentre clinical validation

Missing or degraded sequences can limit prostate multiparametric MRI. We developed MSCNet, a sequence-conditioned cross-modal generative framework for reconstructing unavailable contrasts and restoring degraded acquisitions. Across ten completion tasks, task-specific MSCNet achieved mean structural similarity of 0.818 versus 0.798 for the strongest task-matched comparators; matched-capacity analyses showed larger differences in lesion fidelity and boundary preservation. In a blinded 1,000-case reader study, overall image quality met the prespecified non-inferiority criterion for DWI, ADC and T2W completion, but not T1W. In a separate 200-case diagnostic assessment, AUCs for clinically significant cancer were 0.860 with acquired images, 0.841 with MSCNet and 0.797 with baseline-generated images. A locked 186-case three-hospital cohort supported multicentre transportability. These retrospective results support quality-controlled cross-modal reconstruction as an adjunct to acquired prostate MRI.

bioengineering↗

bioRxiv2026

BMSC-Laden PEGDA/HAMA Dual-Crosslinked Hydrogels with Distinct Stiffness Profiles for Osteochondral Defect Repair

This study aimed to develop a BMSC-laden polyethylene glycol diacrylate/methacrylated hyaluronic acid (PEGDA/HAMA) dual-crosslinked hydrogel and evaluate its effects on osteochondral defect repair. Two PEGDA concentrations, 3.75% and 7.5% (w/v), were used to prepare representative soft and stiff hydrogel formulations, respectively. The hydrogels were characterized in terms of morphology, cytocompatibility, and compressive behavior, and their ability to support BMSC-associated matrix deposition was evaluated in vitro. Repair outcomes were further assessed in a rat osteochondral defect model at 4 and 8 weeks. The 7.5% PEGDA/HAMA hydrogel exhibited higher stiffness than the 3.75% formulation and supported BMSC viability and matrix deposition in vitro. In vivo, the stiff hydrogel group showed improved defect filling and subchondral bone remodeling compared with the soft hydrogel and defect groups. However, histological and immunohistochemical analyses revealed predominant collagen type I deposition and limited collagen type II expression in the repair region, indicating fibrocartilaginous rather than hyaline-like cartilage repair. These findings suggest that BMSC-laden PEGDA/HAMA hydrogels may provide a useful platform for osteochondral defect repair, while further optimization of degradation behavior, matrix maturation, and collagen type II deposition is required to improve hyaline cartilage-oriented repair.

bioengineering↗

bioRxiv2026

New insights into the evolution of spider silk proteins illuminated by long-read transcriptomes

Spider silk has long fascinated scientists because of its exceptional mechanical properties, yet the evolutionary origins and diversification of spider silk proteins (spidroins) remain incompletely understood. By analyzing long-read spidroin transcripts from spiders representing key evolutionary lineages, we identify two ancestral proteins present in basal spiders: an alanine-serine-rich (AS-type) protein and a glycine-serine-rich (GS-type) protein. These ancestral proteins likely served as primary evolutionary templates for the diversification of modern spider silks. We show that the AS-type ancestral spidroin remained relatively conserved and ultimately gave rise to the specialized tubuliform spidroin (TuSp) used in eggcase silk. In contrast, the GS-type protein underwent extensive functional radiation, evolving into differentiated minor ampullate spidroins (MiSp) through the acquisition of distinct terminal domains and {beta}-sheet-associated structural innovations. Our results further suggest that major ampullate spidroins (MaSp) may have originated from MiSp, with the GS motif representing an evolutionarily favorable genetic substrate for the emergence of high-performance silk proteins. Finally, we propose a revised evolutionary trajectory for flagelliform spidroins (Flag), suggesting that they were co-opted as components of ampullate silk during functional degeneration in modern non-web-weaving RTA clade spiders. Together, these findings provide a high-resolution framework for understanding the genetic innovations that drove the diversification of spider silk.

evolutionary biology↗

bioRxiv2026

The E. coli clamp loader sharply bends DNA to load β-clamp onto small gaps

DNA sliding clamps are essential for processive DNA synthesis in all domains of life and are loaded by ATP-dependent clamp loaders that recognize recessed 3' ends. How clamp loaders function at nicks and small ssDNA gaps--common intermediates during DNA repair--remains incompletely understood. Here, we show that the bacterial Escherichia coli DnaX clamp loader employs a fundamentally different mechanism from its eukaryotic counterpart. Whereas eukaryotic RFC unwinds DNA at the recessed 3' end and stabilizes the 5'-dsDNA at a dedicated shoulder site, the bacterial DnaX-complex neither unwinds DNA nor stably binds the 5'-dsDNA in vitro. Instead, cryo-EM structures reveal that the {beta}-clamp itself contains a conserved external DNA-binding site that enables sharp bending of gapped DNA by [~]150{degrees}, promoting insertion of the 3'-dsDNA into the clamp. This DNA-bending mechanism allows efficient {beta}-clamp loading at nicks and small gaps and reveals a distinct bacterial strategy for clamp loading. Because small DNA gaps are frequently associated with DNA damage, clamps loaded at these sites are likely important for DNA repair. In briefZheng et al. show that the bacterial clamp loader DnaX-complex uses a DNA-bending mechanism--rather than DNA unwinding--to load the {beta}-clamp at nicks and small gaps, revealing a clamp-loading strategy distinct from eukaryotic RFC and relevant to DNA damage repair. HighlightsO_LIThe bacterial DnaX clamp loader lacks a stable shoulder DNA-binding site C_LIO_LIUnlike eukaryotic RFC, DnaX does not unwind DNA at nicks and small gaps C_LIO_LIThe E. coli {beta}-clamp contains a conserved external DNA-binding site absent in PCNA C_LIO_LISharp DNA bending enables {beta}-clamp loading at nicks and small ssDNA gaps C_LI

biochemistry↗

bioRxiv2025

A whole-organ multi-scale in silico framework for human kidney haemodynamics informed by hierarchical phase-contrast tomography

Studying human kidney haemodynamics has been limited by the absence of complete vascular maps of the whole organ. Here we utilise previously generated multi-resolution hierarchical phase-contrast tomography (HiP-CT) coupled with a hybrid anatomically-grounded synthetic reconstruction to generate a full arterial-glomerular network of an intact human kidney comprising 1.6 million vessels and over 800,000 glomeruli. Using this anatomically comprehensive structure, we apply physics-based zero-dimensional haemodynamic modelling to quantify blood pressure, flow and simulated filtration rate across the entire organ. We show that the reconstructed human kidney vascular network exhibits order-dependent branching behaviour similar to that of rat kidneys, and that physiologically plausible pressure and flow patterns are recovered only when the full vascular network is represented. We further demonstrate how the kidney responds to macrovascular and microvascular perturbations, including stenosis of the large renal arteries and narrowing or ablation of afferent arterioles. Stenosis and arteriole narrowing exhibit threshold-type behaviour, with kidney perfusion and simulated glomerular filtration rate remaining largely preserved up to [~]50% narrowing, followed by sharp nonlinear declines beyond [~]70%. These predictions emerge in the absence of autoregulatory mechanisms, indicating that vascular geometry and resistance scaling alone contribute to kidney functional deterioration. Together, our framework provides the first organ-wide, data-driven model of human kidney haemodynamics and offers a foundation for future studies of kidney physiology and disease.

bioengineering↗

bioRxiv2025

Chimeric Immunoglobulin and human Immunoglobulin M structures provide insights on joining-chain independent assembly and function

Polymeric (p) immunoglobulins (Igs) play critical roles in vertebrate immunity. IgM is the evolutionarily oldest pIg and functions both in circulation and in the mucosa. pIgM typically comprises between four and six IgM monomers and up to one joining chain (JC), which in mammals facilitates pIg assembly and promotes delivery to mucosal secretions. Bony fish (teleosts) lack JC and assemble tetrameric IgM whereas humans can express JC-containing pentamers and JC-free hexamers. Here we report cryo-electron microscopy structures of two JC-free chimeric IgM, comprising bony fish and human sequences, and the structure of human hexameric IgM. Chimeric IgM structures adopted unique pentameric geometry distinct from both human and fish pIgM whereas the human hexameric IgM structure adopted hexagonal geometry similar to JC-containing pentameric IgM, albeit with structural differences in center of the molecule. Together results provide new insights on how IgM heavy chain motifs contribute to JC-free pIgM assembly and reveal plasticity of this process, which can be manipulated to create pIg structures not observed in nature. Moreover, we found that antigen-targeting chimeric IgM could neutralize C. difficile toxin cytotoxicity, indicating potential to engineer uniquely structured pIgs to prevent or treat disease.

immunology↗

bioRxiv2025

ProteoAutoNet: high-throughput co-eluted protein analysis with robotics and a multi-database search strategy

Co-fractionation mass spectrometry (CF-MS) enables large-scale profiling of endogenous protein-protein interactions. Protein complexes identified by CF-MS using different databases are typically integrated. However, this integration uses varying cutoffs, leading to inconsistencies in protein complex identification. Here, we present ProteoAutoNet, a robotic experimental platform integrating multi-database search strategy into machine learning models, for high-throughput CF-MS analysis. This workflow increases the throughput of sample processing from protein complex to peptide by about two times. We then applied this workflow to map protein interaction networks in thyroid cancer cell lines, identifying significantly upregulated proteasome and prefoldin complexes in lung metastatic follicular thyroid carcinoma cell line FTC238 compared to normal thyroid cell line Nthy-ori 3-1. Notably, we identified a novel protein interaction network comprising PFAS, TGM2, and HK1 that was significantly upregulated in the papillary thyroid carcinoma cell line TPC-1. ProteoAutoNet provides an improved approach for investigating protein-protein interactions and uncovering novel networks, driving advancements in high-throughput proteomics research.

biochemistry↗

bioRxiv2025

Spatial distribution of the proteome in human body and cancers

A comprehensive spatial distribution of the proteome in human body and cancers is fundamental for understanding human biology and diseases including cancers. Here, we present an anatomically resolved human proteome derived from 1781 benign and malignant samples from 58 major tissue types encompassing 251 specific tissues and 25 carcinomas. Based on a spectral library covering over 75% of the human protein-coding genes with 208 understudied and 82 missing proteins characterized, we quantified over 13,000 proteins in these samples using data-independent acquisition proteomics. This data resource presents the so far most comprehensive quantitative proteomic landscape of human tissues and common carcinomas. It allows systematic evaluation of tissue-specific drug responses, identification of drug candidates that may be repurposed as antineoplastics, and discovery of novel targets for anticancer therapy. This resource, available as an online knowledgebase, refines our knowledge of spatial distribution of the human proteome and tumor-specific protein modulation.

systems biology↗

bioRxiv2024

Elucidating the dynamics of Integrin αIIb3 from native platelet membranes by cryo-EM with build and retrieve method

Platelets fulfill their essential physiological roles sensing the extracellular environment through their membrane proteins. The native membrane environment provides essential regulatory cues that impact the protein structure and mechanism of action. Single-particle cryogenic electron microscopy (cryo-EM) has transformed structural biology by allowing high-resolution structures of membrane proteins to be solved from homogeneous samples. Our recent breakthroughs in data processing now make it feasible to obtain atomic-level-resolution protein structures from crude preparations in their native environments by integrating cryo-EM with the "Build-and-Retrieve" (BaR) data processing methodology. We applied this iterative bottom-up methodology on resting human platelet membranes for an in-depth systems biology approach to uncover how lipids, metal binding, post-translational modifications, and co-factor associations in the native environment regulate platelet function at the molecular level. Here, we report using cryo-EM followed by the BaR method to solve the unmodified integrin IIb{beta}3 structure directly from resting human platelet membranes in its inactivated and intermediate states at 2.75[A] and 2.67[A], respectively. Further, we also solved a novel dimer conformation of IIb{beta}3 at 2.85[A] formed by two intermediate-states of IIb{beta}3. This may indicate a previously unknown self-regulatory mechanism of IIb{beta}3 in its native environment. In conclusion, our data show the power of using cryo-EM with the BaR method to determine three distinct structures including a novel dimer directly from natural sources. This approach allows us to identify unrecognized regulation mechanisms for proteins without artifacts due to purification processes. These data have the potential to enrich our understanding of platelet signaling circuitry. Key pointsO_LIWe report the first structural analysis of platelet membrane proteins extracted directly from human platelet membranes. C_LIO_LIOur novel structural-omics approach allowed us to solve integrin IIb{beta}3 structures in two distinct states from resting human platelets. C_LIO_LIRegulatory cues of integrin IIb{beta}3 were preserved from the native resource and revealed on the models with atomic resolutions. C_LIO_LIThis study opens the potential to build the platelet membrane protein atlas to understand platelet physiology. C_LI

biochemistry↗

bioRxiv2024

The Plasmodium falciparum NCR1 membrane protein is a novel antimalarial target that exports cholesterol to maintain membrane homeostasis

Malaria is an extremely devastating parasitic infection that kills over half a million people each year. It is the leading cause of death in many developing countries, in part, due to a lack of resources and readily available therapeutics. Unfortunately, the most prevalent and deadliest causative agent of malaria, Plasmodium falciparum, has developed resistance to nearly all currently available antimalarial drugs. The P. falciparum Niemann-Pick Type C1-related (PfNCR1) transporter has been identified as a druggable target, as it is required for membrane homeostasis of the parasite. However, the structure and detailed molecular mechanism of this membrane protein are not yet available. Here we present three structures of PfNCR1 both in the absence and presence of the functional inhibitor MMV009108 at resolutions between 2.98 [A] and 3.81 [A] using single-particle cryo-electron microscopy (cryo-EM). The data suggest that PfNCR1 binds cholesterol and forms a cholesterol transport tunnel to modulate the composition of the parasite plasma membrane. Cholesterol efflux assays substantiate this as they show that PfNCR1 is an exporter capable of extruding cholesterol from the membrane. Additionally, the inhibition mechanism of MMV009108 appears to be due to a direct blockage of PfNCR1, preventing this transporter from shuttling cholesterol.

biochemistry↗

bioRxiv2024

The dynamic and diverse nature of parenchyma cells in the Arabidopsis root during secondary growth

During the process of secondary growth, the vascular cambium produces the conductive xylem and phloem cells, while the phellogen (cork cambium) deposit phellem (cork) as the outermost protective barrier. Although most of the secondary tissues is made up by parenchyma cells which are also produced by both cambia, their diversity and function are poorly understood. Here we combined single-cell RNA sequencing analysis with lineage tracing to recreate developmental trajectories of the cell types in the Arabidopsis root undergoing secondary growth. By analysing 93 reporter lines, we were able to identify 20 different cell types or cell states, many of which have not been described before. We additionally observed distinct transcriptome signatures of parenchyma cells depending on their maturation state and proximity to the conductive cell types. Our data shows that both xylem and phloem parenchyma tissues are required for normal formation of conductive tissue cell types. Furthermore, we showed that mature phloem parenchyma gradually obtains periderm identity, and this transition can be accelerated by jasmonate or wounding. Thus, our study reveals the remarkable dynamic and diverse nature of parenchyma cells during secondary growth.

plant biology↗

bioRxiv2024

Monocyte-derived fibrocytes contribute to nucleus pulposus fibrosis and intervertebral disc degeneration

Fibrotic remodeling of nucleus pulposus (NP) leads to structural and mechanical anomalies of intervertebral discs that prone to degeneration, leading to low back pain incidence and disability. Emergence of fibroblastic cells in disc degeneration has been reported, yet their nature and origin remain elusive. In this study, we performed an integrative analysis of multiple single-cell RNA sequencing datasets to interrogate the cellular heterogeneity and fibroblast-like entities in degenerative human NP specimens. We found that disc degeneration severity is associated with an enrichment of fibrocyte-like phenotype, characterized by CD45 and collagen I dual positivity, and expression of myofibroblast marker -smooth muscle actin. Refined clustering and classification distinguished the fibrocyte-like populations as subtypes in the NP cells - and immunocytes-clusters, expressing disc degeneration markers HTRA1 and ANGPTL4 and genes related to response to TGF-{beta}. In injury-induced mouse disc degeneration model, fibrocyte-like cells were found recruited into the NP undergoing fibrosis and adopted a myofibroblast phenotype. Depleting the fibrocyte-like cells in CD11b-DTR mice in which monocytic lineages were ablated by diphtheria toxin could markedly attenuate fibrous modeling and myofibroblast formation in the NP of the degenerative discs, and prevent disc height loss and histomorphological abnormalities. Marker analysis supports that disc degeneration progression is dependent on a function of CD45+COL1A1+ and SMA+ cells. Our findings reveal that fibrocyte-like cells play a pivotal role in NP fibrosis and may therefore be a target for modifying disc degeneration and promoting its repair.

physiology↗

bioRxiv2023

The structure of the teleost Immunoglobulin M core provides insights on polymeric antibody evolution, assembly, and function

Polymeric (p) immunoglobulins (Igs) serve broad functions during vertebrate immune responses. Typically, pIgs contain between two and six Ig monomers, each with two antigen binding fragments and one fragment crystallization (Fc). In addition, many pIgs assemble with a joining-chain (JC); however, the number of monomers and potential to include JC varies with species and heavy chain class. Here, we report the cryo-electron microscopy structure of IgM from a teleost (t) species, which does not encode JC. The structure revealed four tIgM Fcs linked through eight C-terminal tailpieces (Tps), which adopt a single {beta}-sandwich-like domain (Tp assembly) located between two Fcs. Remarkably, two of eight heavy chains fold uniquely, resulting in a structure distinct from mammalian IgM, which typically contains five IgM monomers, one JC and a centrally-located Tp assembly. Together with mutational analysis, structural data indicate that pIgs have evolved a range of assembly mechanisms and structures, each likely to support unique antibody effector functions.

immunology↗

bioRxiv2023

Proteomic-based stratification of intermediate-risk prostate cancer patients

Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in Gleason Grade Groups (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or over-treatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomise prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.

cancer biology↗

bioRxiv2022

Droplet microfluidics forward for tracing target cells at single-cell transcriptome resolution

The rapid promotion of single-cell omics in various fields has begun to help solve many problems encountered in research including precision medicine, prenatal diagnosis, and embryo development. Meanwhile, single-cell techniques are also constantly updated with increasing demand. For some specific target cells, the workflow from droplet screening to single-cell sequencing is a preferred option, which also should reduce the impact of operation steps such as demulsification and cell recovery. We developed an all-in-droplet method integrating cell encapsulation, target sorting, droplet picoinjection, and single-cell transcriptome profiling on chips to achieve a labor-saving monitor of TCR-T cells. As a proof of concept, in this research, TCR-T cells were encapsulated, sorted, and performed single-cell transcriptome sequencing (scRNA-seq) by injecting reagents into droplet. It avoided the tedious operation of droplet breakage and re-encapsulation between droplet sorting and scRNA-seq. Moreover, convenient device operation will accelerate the progress of chip marketization. The strategy achieved an excellent recovery performance of single cell transcriptome with a median gene number over 4000 and a cross-contamination rate of 8.2 {+/-} 2%. Furthermore, this strategy allows us to develop a device with high integrability to monitor infused TCR-T cells, which will promote the development of adoptive T cell immunotherapy and their clinical application.

cell biology↗

bioRxiv2022

Gibberellins promote polar auxin transport to regulate stem cell fate decisions in cambium

Vascular cambium contains bifacial stem cells, which produce secondary xylem to one side and secondary phloem to the other. However, how these fate decisions are regulated is unknown. Here, we show that the positioning of an auxin signalling maximum within the cambium determines the fate of stem cell daughters. The position is modulated by gibberellin-regulated, PIN1-dependent polar auxin transport. Gibberellin treatment broadens auxin maximum from the xylem side of the cambium towards the phloem. As a result, xylem-side stem cell daughter preferentially differentiates into xylem, while phloem-side daughter retains stem cell identity. Occasionally, this broadening leads to direct specification of both daughters as xylem, and consequently, adjacent phloem-identity cell reverts to being stem cell. Conversely, reduced gibberellin levels favour specification of phloem-side stem cell daughter as phloem. Together, our data provide a mechanism by which gibberellin regulates the ratio of xylem and phloem production.

plant biology↗

bioRxiv2022

ILC3s select for RORγt+ Tregs and establish tolerance to intestinal microbiota

Microbial colonization of the mammalian intestine elicits inflammatory or tolerogenic T cell responses, but the mechanisms controlling these distinct outcomes remain poorly understood and accumulating evidence indicates that aberrant immunity to intestinal microbiota is causally associated with infectious, inflammatory, and malignant diseases1-8. Here, we define a critical pathway controlling the fate of inflammatory versus tolerogenic T cells that are specific for the microbiota and express the transcription factor ROR{gamma}t. We profiled all ROR{gamma}t+ immune cells at single cell resolution from the intestine-draining lymph nodes of mice and reveal a dominant presence of Tregs and lymphoid tissue-induced (LTi)-like group 3 innate lymphoid cells (ILC3s), which co-localize at interfollicular regions. These ILC3s have interconverting potential with ROR{gamma}t+ extrathymic Aire-expressing cells, abundantly express major histocompatibility complex class II, and are necessary and sufficient to promote microbiota-specific ROR{gamma}t+ Tregs and prevent their expansion as inflammatory T helper (Th)17 cells. This occurs through ILC3-mediated antigen-presentation, interleukin-2 gradients, and v integrin. Finally, single-cell analyses demonstrate that ILC3 and ROR{gamma}t+ Treg interactions are impaired in inflammatory bowel disease. Our results define a novel paradigm whereby ILC3s positively select for antigen specific ROR{gamma}t+ Tregs, and against Th17 cells, to establish immune tolerance to the microbiota and intestinal health.

immunology↗

bioRxiv2021

Prediction of therapy outcomes of CLL using gene expression intensity, clustering, and ANN classification of single cell transcriptomes

BackgroundSingle cell transcriptomics is a new technology that enables us to measure the expression levels of genes from an individual cell. The expression information reflects the activity of that individual cell which could be used to indicate the cell types. Chronic lymphocytic leukemia (CLL) is a malignancy of B cells, one of the peripheral blood mononuclear cells subtypes. We applied five analytical tools for the study of single cell gene expression in CLL course of therapy. These tools included the analysis of gene expression distributions - median, interquartile ranges, and percentage above quality control (QC) threshold; hierarchical clustering applied to all cells within individual single cell data sets; and artificial neural network (ANN) for classification of healthy peripheral blood mononuclear cell (PBMC) subtypes. These tools were applied to the analysis of CLL data representing states before and during the therapy. ResultsWe identified patterns in gene expression that distinguished two patients that had complete remission (complete response), a patient that had a relapse, and a patient that had partial remission within three years of Ibrutinib therapy. Patients with complete remission showed a rapid decline of median gene expression counts, and the total number of gene counts below the QC threshold for healthy cells (670 counts) in 80% of more of the cells. These patients also showed the emergence of healthy-like PBMC cluster maps within 120 days of therapy and distinct changes in predicted proportions of PBMC cell types. ConclusionsThe combination of basic statistical analysis, hierarchical clustering, and supervised machine learning identified patterns from gene expression that distinguish four CLL patients treated with Ibrutinib that experienced complete remission, partial remission, or relapse. These preliminary results suggest that new bioinformatics tools for single cell transcriptomics, including ANN comparison to healthy PBMC, offer promise in prognostics of CLL.

bioinformatics↗