Biology subjects

Ma, N.

Publications and source records attributed to Ma, N..

At least 19 recordsLinked to original sources

bioRxiv2026

Kinetochore Proteins CENPB and LIC2 are critical for Episome Persistence and Replication of Kaposis's Sarcoma-Associated Herpesvirus

Kaposi's sarcoma-associated herpesvirus (KSHV) establishes lifelong latency by maintaining its genome as circular episomes tethered to host chromatin and faithfully segregated during mitosis. This process is primarily mediated by the latency-associated nuclear antigen (LANA), which interacts with host chromosome-associated factors to ensure viral genome persistence. Several kinetochore proteins, including CENP-F, Bub1, BubR1, Aurora B, Survivin, and NuMA, have been implicated in this process, yet the broader contribution of kinetochore components remains poorly defined. We performed a systematic shRNA-based screen of the 37 host genes encoding kinetochore-associated proteins to evaluate their role in KSHV episome maintenance. We validated involvement of previously reported factors and identified Centromere Protein B (CENP-B) and Light Intermediate Chain 2 of the dynein complex (LIC2) as novel kinetochore-associated proteins critical for KSHV episome persistence. Loss of these proteins significantly reduced episome stability, highlighting previously unrecognized host-virus interactions at the chromosome segregation machinery. These findings identify critical host factors that expand the repertoire of kinetochore proteins co-opted by KSHV for episome maintenance and provide new mechanistic insights into how viral episomes exploit host chromosome segregation pathways for long-term persistence. Our work underscores kinetochore proteins as a broader class of host dependency factors in gamma-herpesvirus biology and suggests potential therapeutic targets for KSHV-associated malignancies.

microbiology↗

bioRxiv2026

Microbial Metabolites Potentiate MAIT Cell Anti-Tumor Immunity Against Solid Tumors

Mucosal-associated invariant T (MAIT) cells sense riboflavin metabolites through the monomorphic antigen-presenting molecule MR1, providing a unique opportunity to therapeutically mobilize a broadly shared T cell population without genetic engineering. Here, we show that the highly potent microbial metabolites, 5-OP-RU and 5-OE-RU, can be exploited as pharmacologic precision immune activators to drive human MAIT cell responses against solid tumors. Ligand stimulation in human co-culture systems elicited robust MAIT cell cytotoxicity, inflammatory cytokine secretion, and transcriptional states transformation. In vivo administration of riboflavin ligands 5-OP-RU significantly suppressed tumor growth in xenograft liver cancer models. Metabolite-driven MAIT activation also reprogrammed the local immune landscape, enhancing effector function and overcoming features of the immunosuppressive niche by markedly eliminating tumor-associated macrophages (TAMs) and myeloid-derived suppressor cells (MDSCs) within the tumor microenvironment (TME). These findings reveal that microbial riboflavin metabolites can power and redirect MAIT cells to solid tumors, establishing MR1-metabolite signaling as a tractable therapeutic axis for liver cancer and other solid malignancies.

cancer biology↗

bioRxiv2026

Allosteric Gating Mechanism Regulates Odorant Selectivity and Antagonism in Odorant Receptors

Odorant receptors (ORs) belong to class A G protein coupled receptors that detect diverse small molecules, yet the steps that link odorant association to receptor mediated selectivity remains incompletely defined. Here we combined 1.26 milliseconds of all-atom odorant association Molecular Dynamics simulations with Markov state modeling and cell-based cAMP measurements to examine two human ORs receptors that recognize chemically distinct odorants. In the class I receptor OR51E2, propionate associates via two extracellular pathways gated for selectivity by residues in the extracellular loop 2 and 3. The longer alkyl chain heptanoate occupies this gate and reduces propionate association and signaling which is consistent with the observed antagonist behavior of heptanoate. Pocket-expanding mutations at F155 and L158 allosterically regulate ECL2-ECL3 gate by permitting longer-chain fatty acids to adopt fully inserted poses that support gate closure, while also attenuating propionate responses. In the class II receptor OR1A1, hydrophobic odorants partition into the membrane and reach the orthosteric site mostly through multiple transmembrane paths. A mutational scan of gating residues and analysis of intermediate-state occupancies suggest that an orthosteric substitution at G108 can allosterically bias odorant association path choice. Together, these results support a model in which odorant association paths and gate residence, together with allosteric coupling between the orthosteric site and entry gates, contribute to odorant specificity and antagonism in odorant receptors.

biophysics↗

bioRxiv2026

Walking on the Moon: Hypogravity drives the emergence of a proprioception-dependent locomotor state

Animals must adapt locomotion to changing environmental conditions, but how the nervous system flexibly controls movement remains unclear. Gravity provides a powerful perturbation because it alters body loading, limb dynamics, and proprioceptive feedback. Apollo astronauts often skipped on the Moon, adopting an asymmetric gait rarely used on Earth, yet the sensorimotor basis of this behaviour is unknown. Here, by studying hypogravity locomotion in humans and mice, we show that reduced gravity reveals a conserved proprioception-dependent mechanism for locomotor state expression. In humans, skipping in simulated lunar gravity is generated through flexible temporal reconfiguration of existing motor modules rather than construction of a new motor architecture. In mice, simulated lunar gravity elicited a skipping-like locomotor state, and genetic elimination of muscle proprioceptors abolished this response. Thus, hypogravity reveals how proprioceptive feedback enables flexible expression of locomotor states.

neuroscience↗

bioRxiv2026

BaSiCPy: Scalable and Robust Shading Correction for Optical Microscopy Images

Quantitative fluorescence microscopy is frequently confounded by spatially varying illumination and temporal intensity drift. Although BaSiC is a widely adopted retrospective correction method, it can fail when foreground content is strongly correlated across images--a common regime in time-lapse, tiled and volumetric acquisitions--and its application often requires manual parameter tuning that limits reproducibility and scalability. We introduce BaSiCPy, a foreground-aware implementation of BaSiC that improves illumination profile estimation under correlated foreground structures, provides automatic hyperparameter selection and accelerates large-scale processing through GPU support. BaSiCPy is distributed as an open-source Python package with graphical and programmatic interfaces, facilitating integration into contemporary bioimage analysis workflows.

bioengineering↗

bioRxiv2026

Vascularized Human Cardiac Organoids Reveal Endothelial-Cardiomyocyte Crosstalk and Mechanisms of Carfilzomib-Induced Cardiotoxicity

Human cardiac organoids (hCOs) provide a powerful platform for modeling heart development and disease, yet their lack of vasculature limits physiological relevance. Here, we generate vascularized human cardiac organoids (vhCOs) by assembling hCOs with blood vessel organoids, enabling the self-organized formation of unified tissues with extensive vascular networks and substantially enhanced cardiomyocyte (CM) maturation. Single-nucleus multiomic profiling reveals CM state resembling the 17-week human fetal heart, while endothelial cells (ECs) acquire cardiac-specific and arterial-like identities. Integrative cell-cell communication analyses and experimental validation identify CM-derived Laminin-2 as a driver of arterial EC specification, while reciprocal EFNB2 signaling from arterial ECs promotes CM maturation, uncovering bidirectional cardiac-vascular crosstalk. Modeling carfilzomib-induced cardiotoxicity in vhCOs reveals ATF4-dependent endoplasmic reticulum (ER) stress and IL8-mediated inflammatory responses that are blunted in non-vascularized hCOs. Pharmacological attenuation of ER stress alleviates carfilzomib-induced cardiotoxicity. Altogether, vhCOs provide a developmentally advanced and physiologically faithful human cardiac model.

cell biology↗

bioRxiv2026

Kindlin-2-Moesin interaction orchestrates sprouting angiogenesis via modulating endothelial membrane mechanics and VEGF signaling

Membrane mechanics play a crucial role in cellular signaling and fate determination, yet their impact on angiogenesis remains poorly understood. Here, we identify Kindlin-2 as a key regulator of sprouting angiogenesis via regulating endothelial membrane tension through its interaction with Moesin, a crucial linker protein between the cell membrane and the actin cortex. Mechanistically, Kindlin-2 binds to the N62 residue of Moesin, limiting its overactivation and maintaining proper membrane tension to facilitate VEGFR2 endocytosis and downstream signaling. Using both developmental and pathological models, we demonstrate that the interaction of Kindlin-2 and Moesin is enhanced in high angiogenic conditions, and endothelial Kindlin-2 deletion reduces angiogenesis. Furthermore, mutation of Moesin at N62 phenocopies the effects of Kindlin-2 loss. Together, these findings uncover a previously unrecognized mechanism linking membrane tension regulation to angiogenesis and provide new insights into targeting the Kindlin-2-Moesin axis for therapeutic intervention in neovascular diseases.

developmental biology↗

bioRxiv2026

Conserved Residues in the Gα interface show subtype specificity in Gβγ coupling

Although the structural basis of selective G-protein coupling to G protein coupled receptors (GPCRs) is well characterized, the mechanisms underlying selective interactions between distinct G subtypes (Gs, Gi, Gq, and G12/13) and G{beta}{gamma} remain poorly understood. While conserved residues in G subtypes are often assumed to have similar functions, they may instead modulate coupling selectivity by altering the frequency and stability of contacts at the G:G{beta}{gamma} interface. Using molecular dynamics (MD) simulations combined with the interpretable machine learning method, Bayesian Network Model (BNM), and protein-protein proximity (BRET) assays, we show that conserved residues in the two closely related Gi/o and Gq/11 subfamilies contribute differentially to G{beta}{gamma} coupling. These conserved residue "hotspots" on Gi and Gq produced divergent functional effects on G{beta}{gamma} coupling, indicating that conservation does not ensure functional equivalence. These findings suggest that local microenvironment and paralog-specific allosteric coupling shape how conserved interface residues contribute to protein-protein coupling. The framework provides a systematic approach for dissecting subtype-specific mechanisms, with implications for drug design and for annotating the functional relevance of disease-associated variants. The computational methods used here are broadly applicable to other homologous protein families.

molecular biology↗

bioRxiv2025

Focal adhesion prevention on nanoparticle substrates upregulates stemness gene expression in primary melanocytes

HypothesisCell focal adhesions are initiated by interactions of cell surface integrins with extracellular matrix (ECM) proteins, and cells which lack focal adhesions have been associated with an intermediate adhesive state, which is more labile towards cell reprogramming. We hypothesized that cells cultured under conditions where they exhibit reduced focal adhesions will assume an intermediate adhesive state with a more stem cell-like transcriptional profile. ExperimentsTo recreate culture conditions for cells to exhibit reduced focal adhesions, we synthesized PMMA nanoparticles by evaporation-induced self-assembly (EISA), employing varying conditions of surfactant concentrations, and allowed them to self-assemble into nanoparticle substrates. Following guidelines from previous work, we selected nanoparticle substrates of dimensions [~]70nm, suitable for the prevention of focal adhesion formation. Primary human melanocytes were cultured on these substrates to verify the reduction of their focal adhesions; following that the cultures were characterized in terms of their expression of distinct sets of genes related to stemness and differentiation. FindingsThe melanocytes showed reduced focal adhesions on both non-coated and fibronectin-coated nanoparticle substrates, when compared to melanocytes cultured on TCPs. Accompanying the reduction in focal adhesions, the cells exhibited an increase in the expression of general as well as melanocyte-specific stemness related genes such as OCT4, LIN28, NANOG and PAX6 and a concurrent downregulation of genes expressed by differentiated melanocytes, such as TYR, TRP1 and MITF. These observations support our hypothesis.

bioengineering↗

bioRxiv2025

A gastric microbial chromatin remodeler drives gastric cancer progression and immune evasion by reprogramming the host epigenome

Emerging evidence highlights the crucial role of microbial communities in modulating cancer development and progression. In gastric cancer (GC), we identify Streptococcus anginosus (SA) as a tumor-resident oncobacterium that drives both tumor progression and immune evasion. We define a novel mechanism in which SA secretes extracellular vesicles (saEVs) that translocate the bacterial chromatin remodeler saSNF2 into host cell. There, saSNF2 partners with host transcription factor TEAD1--through its ATPase activity and participation in BAF complex assembly--to coordinately activate oncogenic transcription. This transkingdom interaction upregulates the palmitoyltransferase ZDHHC11, which in turn stabilizes PD-L1 via palmitoylation to establish an immunosuppressive niche, while also amplifying other TEAD1 target genes to fuel tumor progression. Functionally, saEVs promote tumor growth and limit CD8+ T-cell infiltration in vivo. Strikingly, pharmacological inhibition of ZDHHC11 reverses immune evasion and synergizes with anti-PD-1 checkpoint blockade. Our results establish SA as a multifaceted driver of GC and reveal the saSNF2-ZDHHC11 axis as a promising target to potentiate immunotherapy.

cancer biology↗

bioRxiv2025

Enterococcus faecalis delivers Obg GTPase via extracellular vesicles to instigate mTOR activity and promote HCC tumorigenesis

Hepatocellular carcinoma (HCC) is a malignant tumor that has been associated with dysbiosis of the gut microbiota. However, how the gut microbiota plays an oncogenic role in HCC remains largely unknown. Here, we show that Enterococcus faecalis (E. faecalis) is highly enriched in liver tumor tissues and is positively correlated with pathogenesis of HCC. E. faecalis promotes liver cancer cell proliferation, protein translation, cell migration and tumorigenesis. Mechanistically, we found that EF-derived extracellular vesicles (EF-EVs) deliver EF-Obg GTPase to activate host mTOR, thereby promoting liver cancer progression. Intriguingly, the EF-Obg protein exerts its influence on the mTOR pathway via a Ras-like G domain involved in GTP binding. EF-Obg exhibits a striking homology with the G1 site of the G domain of Rheb, a key positive regulator of mTOR. Obg gene is critical for E. faecalis to activate mTOR to promote hepatocarcinogenesis based on an engineered obg knockdown strain by CRISPR interference experiment. Clinically, abundant EF-Obg protein expression is correlated with enhanced activation of mTOR, leading to poor overall survival in HCC patients. Significantly, treatment of mTOR inhibitor Everolimus confers effectiveness in EF-colonized liver cancer orthotopic model, suggesting that Everolimus therapeutic approach can be effective for liver cancer patients with enriched E. faecalis. Taken together, we provide mechanistic and functional evidence to verify a direct causal relationship between tumor-resident E. faecalis enrichment and liver carcinogenesis, revealing that EF-Obg functions as a previously unidentified cross-kingdom activator of mTOR to promote liver tumorigenesis.

cell biology↗

bioRxiv2025

In search of nonlipogenic ABCA1 inducers (NLAI): precision coregulator TR-FRET identifies diverse signatures for LXR ligands

APOE4, the major genetic risk factor for Alzheimers disease (AD), and ABCA1, required for lipidation of APOE are gene products of the liver X receptor (LXR) receptor. LXR agonists have been validated in animal models as therapeutics for AD, atherosclerosis, and many other diseases. Clinical progress has been thwarted by unwanted hepatic lipogenesis. Structurally diverse LXR ligands were profiled in coregulator TR-FRET (CRT) assays analyzing ligand-induced coactivator recruitment, coactivator selectivity, corepressor dissociation, and LXR isoform selectivity. A multiplex CRT assay was developed to measure synchronous ligand-induced displacement of corepressor by coactivator. Potency for coactivator recruitment to LXR{beta} correlated with induction of ABCA1 in human astrocytoma cells. Correlation with lipogenic activation of sterol response element (SRE) in hepatocarcinoma cells, was more complex. CRT response was diverse revealing ligands with theoretical full agonist, partial agonist, antagonist, and inverse agonist, and other signatures within the same chemical series, suggesting the scope for precision CRT to guide nonlipogenic LXR agonist design.

pharmacology and toxicology↗

bioRxiv2025

Protein Frustration Reveals Active Sites in Co-Evolved GPCR:G Protein Complexes and in Engineered Targeted Degrader Complexes

The folded structure of a protein is understood to be an optimal energy state. However, previous studies have shown that certain amino acid residue positions that play a critical role in protein function are often in a suboptimal energy state or "frustrated". Here, we leverage over 1200 three-dimensional structures of G protein-coupled receptors (GPCRs) to demonstrate that residues at the interface between GPCR and its ligand or G protein contain a higher density of frustrated residues compared to other structural regions in the receptor. Likewise, the G subunit of the trimeric G proteins shows multiple clusters of highly frustrated residues on its surface that overlap with their effector protein (G{beta}{gamma}, RGS, Adenyl cyclase, Ric8) binding interfaces. Compared to the co-evolved GPCR:G protein complexes, engineered protein complexes, such as those facilitated by molecular degraders, show a much greater density of highly frustrated residues in the degrader interface. Our study highlights the use of protein frustration as an invaluable tool to evaluate both native protein-protein interfaces and design strategies to facilitate engineered protein complexes.

biophysics↗

bioRxiv2025

Insights From Protein Frustration Analysis Of BRD4-Cereblon Degrader Ternary Complexes Show Separation of Strong from Weak Degraders

PROteolysis TArgeting Chimeras (PROTACs), also known as Ligand-Directed Degraders (LDDs), are an innovative class of small molecules that leverage the ubiquitin-proteasome system to induce the degradation of target proteins. Structure based design methods are not readily applicable for designing LDDs due to the dynamic nature of the ternary complexes. This study investigates the dynamic properties of five LDD-mediated BRD4-Cereblon complexes, focusing on the challenges of evaluating linker efficiency due to the difficulty in identifying suitable computational metrics that correlate well with the cooperativity or degradation propensity of LDDs. We uncovered that protein frustration, a concept originally developed to understand protein folding, calculated for the residues in the protein-protein interface of the LDD-mediated ternary complexes recapitulate the strength of degradation of the LDDs. Our findings indicated that hydrophobic residues in the interface are among the highly frustrated residues pairs, and they are crucial in distinguishing strong degraders from weak ones. By analyzing frustration patterns, we identified key residues and interactions critical to the effectiveness of the ternary complex. These insights provide practical guidelines for designing and prioritizing more efficient degraders, paving the way for the development of next-generation LDDs with improved therapeutic potential.

biophysics↗

bioRxiv2024

Frustration in the Protein-Protein interface Plays a Central Role in the Cooperativity of PROTAC Ternary Complexes

Targeted protein degradation of a protein of interest (POI) by Proteolysis Targeting Chimeras (PROTACs) is an attractive approach for dealing with formerly undruggable protein targets. PROTACs are heterobifunctional molecules that connect a POI-binding and an E3-ligase (E3) binding motif with a linker. The simultaneous binding and formation of a ternary POI::PROTAC::E3 complex (TC) induces proximity between the POI and the E3, allowing for POI-ubiquitination and subsequent induction of proteasomal degradation. Despite the availability of many three-dimensional structures of TCs, unveiling the structure-function relationships for the design of PROTACs remains a challenge. This is because the TCs can be dynamic with a complex conformational landscape that individual crystal structures may not capture. In this work, we used SMARCA2 as the POI and VHL as the E3-ligase and solved the X-ray crystal structures of the respective ternary complexes with four different PROTACs. Molecular dynamics (MD) simulations were used to show that the SMARCA2-VHL interface is flexible with multiple energy minima. The protein-protein (POI-E3) interactions are largely formed by residues located in structurally disordered loops in both VHL and SMARCA2. The residue pairs in the SMARCA2-VHL interface are frustrated, i.e., adopt a suboptimal energetic state. The number of frustrated residue pairs averaged over the MD ensemble shows a positive correlation with the experimentally determined cooperativity of the PROTACs. This indicates that protein-protein interface frustration can play an important role in PROTAC function. The TC ensembles of VHL, SMARCA2 and 11 different PROTACs were modeled by comparative modeling followed by MD. The frustration was subsequently calculated from the MD trajectories and correlated with the cooperativity. We found that identification of the dynamic protein-protein contacts and frustrated residue pairs in the interface can provide a rational framework for the structure-based design of PROTACs.

biophysics↗

bioRxiv2024

BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories

Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical datasets. Concurrently, our ability to perform long-timescale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially. However, the analysis of MD simulation trajectories has not been data-driven but rather dependent on the users prior knowledge of the systems, thus limiting the scope and utility of the MD simulations. Recently, we pioneered using BNM for analyzing the MD trajectories of protein complexes. The resulting BN models yield novel fully data-driven insights into the functional importance of the amino acid residues that modulate proteins function. In this report, we describe the BaNDyT software package that implements the BNM specifically attuned to the MD simulation trajectories data. We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the softwares uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. This provides a powerful and versatile mechanism for users to control the workflow. As an application example, we have utilized this methodology and associated software to study how membrane proteins, specifically the G protein-coupled receptors, selectively couple to G proteins. The software can be used for analyzing MD trajectories of any protein as well as polymeric materials.

bioinformatics↗

bioRxiv2024

CTCF mutation at R567 causes developmental disorders via 3D genome rearrangement and abnormal neurodevelopment

The three-dimensional genome structure organized by CTCF is required for development. Clinically identified mutations in CTCF have been linked to adverse developmental outcomes. Nevertheless, the underlying mechanism remains elusive. In this investigation, we explored the regulatory roles of a clinically relevant R567W point mutation, located within the 11th zinc finger of CTCF, by introducing this mutation into both murine models and human embryonic stem cell-derived cortical organoid models. Mice with homozygous CTCFR567W mutation exhibited growth impediments, resulting in postnatal mortality, and deviations in brain, heart, and lung development at the pathological and single- cell transcriptome levels. This mutation induced premature stem-like cell exhaustion, accelerated the maturation of GABAergic neurons, and disrupted neurodevelopmental and synaptic pathways. Additionally, it specifically hindered CTCF binding to peripheral motifs upstream to the core consensus site, causing alterations in local chromatin structure and gene expression, particularly at the clustered protocadherin locus. Comparative analysis using human cortical organoids mirrored the consequences induced by this mutation. In summary, this study elucidates the influence of the CTCFR567W mutation on human neurodevelopmental disorders, paving the way for potential therapeutic interventions.

molecular biology↗

bioRxiv2024

Integrated multi-omics analysis of Klebsiella pneumoniae revealed the discrepancy in flavonoid effect against strain growth between Rutin and Luteolin

The emergence of drug resistant pathogenic bacteria is increasingly challenging conventional antibiotics. Plant derived flavonoids are always considered as potential alternatives to antibiotics due to their antimicrobial properties. However, the molecular mechanisms by which flavonoids inhibit pathogenic microorganisms growth are not fully understood. In order to better understand the inhibitory mechanism of flavonoids, two flavonoids were used to incubate Klebsiella pneumoniae ATCC700603. After incubation for 4 hours, both the metabolomic and transcriptomic analysis were performed. In present study, 5,483 genes and 882 metabolites were measured. Compared to wild control, the Rutin and Luteolin induced 507 and 374 differentially expressed genes (DEGs), respectively. However, the number of differential abundant metabolites (DAMs) were the same. The correlation between DEGs and DAMs were studied. The top 10 correlated DEGs and DAMs were identified in each comparative groups. Our results showed that, compared to Luteolin, Rutin induced the accumulation of metabolites and suppressed genes expression. Our results provided an explanation for the disparate effects of two flavonoids and demonstrated the inhibitory mechanism of Rutin on strain growth.

bioinformatics↗