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Xu, F.

Publications and source records attributed to Xu, F..

At least 37 records · Page 2Linked to original sources

Volumetric montaging of optical coherence tomography in human retinas

Optical coherence tomography (OCT) has transformed clinical eye care by providing high-resolution volumetric imaging of the retina. Recently, ultrawide-field-of-view (FOV) OCT played an increasingly significant clinical role; however, most clinical OCT systems offer only a rather limited FOV. We increased the FOV of clinical OCT by volumetrically montaging multiple OCT datasets in three dimensions (3D). We performed volumetric montaging by representing the internal limiting membrane (ILM) and retinal pigment epithelium (RPE) in each volume as point clouds and using these point clouds to compute transformations that map each volume to a common reference frame. We validated our methodology using datasets from three institutions with different OCT hardware and data-acquisition procedures. Using the mean surface distance between point clouds, we found the error in montaging was less than the lateral pixel size. Our method enabled existing clinical OCT to achieve ultrawide FOV imaging without any hardware modification.

bioengineering↗

ProteinConformers: large-scale and energetically profiled descriptions of protein conformational landscapes

Modeling protein conformational landscapes is essential for understanding dynamics, allostery, and drug discovery, yet existing resources lack diverse conformational coverage, energetic annotations, or benchmarking standards. ProteinConformers (https://zhanggroup.org/ProteinConformers) provides 2.7 million geometry-optimized conformations generated with a multi-seed molecular dynamics strategy, paired with 13.7 million energy evaluations and 5.5 million similarity annotations. It delivers continuous landscapes from non-native to near-native states, benchmarking framework for multi-conformation generators, and an interactive analysis platform.

bioinformatics↗

Nab-paclitaxel fused with the de novo designed receptor binder exhibits enhanced tumor targeting and therapeutic efficacy

Chemotherapy has been widely used in cancer treatment, but most of the chemotherapeutic drugs rely mainly on passive accumulation due to lack of target specificity, which may lead to systemic toxicity and limited clinical utility. Recent advances in artificial intelligence-based protein design provide new opportunities for developing precision therapeutics. Here we modify the albumin-bound paclitaxel (Nab-PTX), one of the most widely used drugs in chemotherapies, by applying the fusion proteins of albumin with the de novo designed protein binders targeting human EGFR or HER2. The resulting particles, EGFRmb-Nab-PTX and HER2mb-Nab-PTX, retain the similar physicochemical properties of Nab-PTX while acquiring the receptor-specific binding capacities. The in vitro assays show that both binder-modified Nab-PTX particles have increased uptake and inhibitory effects significantly in the cancer cell lines with high receptor expression levels. Furthermore, the data from a xenograft model, including tumor growth, excised tumor analysis, organ histology, and fluorescence imaging, show that the binder-modified Nab-PTX enhances tumor accumulation, improves tumor suppression, and reduces off-target toxicity compared with the conventional Nab-PTX, suggesting that they may have promising clinical potential in cancer treatment. Overall, this strategy provides an adaptable modular platform for generating albumin-based chemotherapeutic drugs with target specificities, which can be readily customized with diverse target binders to enable precise cancer therapies.

cancer biology↗

Isthmin-1 is a Key Regulator of Induced Pluripotent Stem Cell-Derived Cardiomyocytes Maturation through Activation of p53 Signaling

AimsHuman induced pluripotent stem cell-derived cardiomyocytes (iPSC-CMs) exhibit an immature structural and metabolic phenotype that limits their utility for cardiac disease modeling and regenerative therapy. Although multiple extrinsic strategies have been proposed to enhance iPSC-CM maturation, intrinsic molecular regulators governing this process remain incompletely defined. This study aimed to identify and characterize a novel molecular factor that promotes cardiomyocyte maturation. Methods and ResultsCross-species transcriptomic analyses comparing adult versus fetal hearts and hypertrophic cardiomyopathy versus healthy myocardium identified Isthmin-1 (ISM1) as a conserved maturation-associated gene. In human iPSC-CMs, ISM1 overexpression enhanced sarcomere organization, mitochondrial oxidative phosphorylation, ATP production, and calcium-handling properties, whereas ISM1 knockdown impaired these maturation features. RNA sequencing revealed global transcriptional reprogramming toward an adult-like state, characterized by suppression of cell-cycle-related gene programs and activation of oxidative metabolic pathways. KEGG pathway enrichment, GSVA, and GSEA consistently identified p53 signaling as the most significantly activated pathway in ISM1-overexpressing iPSC-CMs. Mechanistically, ISM1 directly interacted with p53, enhanced its protein stability, promoted nuclear localization, and increased transcription of p53 downstream targets involved in metabolic remodeling and cell-cycle exit. Pharmacological inhibition of p53 abolished ISM1-induced structural and metabolic maturation, demonstrating that ISM1 promotes cardiomyocyte maturation in a p53-dependent manner. ConclusionsISM1 is a previously unrecognized molecular driver of cardiomyocyte maturation that promotes structural, metabolic, and functional maturation of iPSC-CMs through activation of p53-dependent transcriptional programs. These findings provide new mechanistic insight into cardiomyocyte maturation and identify ISM1 as a promising target for improving the maturity of stem cell-derived cardiomyocytes. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=142 SRC="FIGDIR/small/698535v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@15daca3org.highwire.dtl.DTLVardef@f1396dorg.highwire.dtl.DTLVardef@f13400org.highwire.dtl.DTLVardef@18d0b41_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

Kilohertz-rate two-photon voltage imaging of population dynamics in vivo

Understanding how neural circuits compute requires capturing voltage dynamics across large neuronal populations with millisecond resolution in vivo. However, two-photon voltage imaging remains fundamentally limited by a trade-off among imaging speed, field of view, and excitation efficiency. We introduce HS2PM, a hybrid scanning two-photon microscope that overcomes this bottleneck, enabling kilohertz-rate imaging over a 650 x 524 m2 field of view at single-cell resolution while preserving the photon efficiency of single-point excitation. HS2PM stably records deep-layer membrane potentials from over 160 neurons simultaneously, with minimal photobleaching and phototoxicity. It resolves both spikes and subthreshold voltage dynamics in vivo, revealing how these jointly shape sensory adaptation and population coding. Beyond voltage imaging, HS2PM supports high-speed fluorescence lifetime and vascular flow imaging, establishing a multimodal platform for dissecting fast circuit dynamics with precision previously inaccessible to optical methods.

neuroscience↗

Metabolic dysfunction related to specific genetic variant sites of methylmalonic acidemia

Methylmalonic acidemia (MMA) is a genetic metabolic disease, with mut (mut-MMA, caused by MMUT gene variation) and cblC (cblC-MMA, caused by MMACHC gene variation) being the predominant subtypes. MMA patients carrying c.729_730insTT and c.609G>A exhibit severe clinical manifestations and have poorer outcomes. Little information is known on the potential mechanism. The metabotypes of MMA patients carrying c.729_730insTT and c.609G>A were profiled. The potential effect of genetic variation sites on the metabolism were explored. Leveraging the gene variation spectrum and the targeted metabolomics, propionic acid, indolelactic acid, myristoleic acid, tetradecenoic acid, tridecanoic acid, and oxoadipic acid showed strong enrichment in c.729_730insTT carrying mut-MMA patients. Whereas mutation c.609G>A caused adipic acid, pimelic acid, fructose, AMP, hexanylcarnitine, and methionine significnatly altered in cblC-MMA patients. Furthermore, the metabolomic profiles were obviously different in c.729_730insTT and non-c.729_730insTT carrying mut-MMA patients after treatment. Different metabolic alterations in cblC-MMA patients carrying c.609G > A and non-c.609G > A under treatment were also observed. Our findings provide unique insights into the metabolic basis of MMA specific subtypes and its implications across different variants.

molecular biology↗

Ribosomal Epistatic Interactions Drive the Emergence of High-Level Streptomycin Resistance in Escherichia coli

The widespread use of antibiotics has raised serious concerns about the emergence and dissemination of antibiotic resistance in the environment. Studies reveal that environmental exposures to antibiotics and other non-antibiotic pollutants can promote the development of high-level antibiotic resistance via de novo mutations. However, specific genotypes conferring strong resistance in resistant mutants, particularly the roles of co-occurring mutations, remained poorly understood. This study fills this knowledge gap by constructing site-specific Escherichia coli mutants and demonstrating that it was the epistatic interactions that conferred the observed strong streptomycin resistance in native E. coli isolates. Three ribosomal mutations (rpsED142N, rpsLR86S and rsmGW150fs), which co-evolved under environmentally relevant selection pressures, acted synergistically to confer resistance far exceeding that of each individual mutation. The interactions between the rsmG frameshift mutation and other reported rpsL point mutations were also investigated. The findings unravel the essential but previously overlooked role played by specific co-evolving mutations in the acquisition of both high-level streptomycin resistance and fitness compensation. The findings also underscore a strong and increasing need to investigate whole genomes of antibiotic-resistant bacteria and identify potential epistatic mutations conferring resistance phenotypes. The integration of those genetic mutations as antibiotic resistance biomarkers will complement with the resistome profiling and enable more accurate antibiotic resistance monitoring and environmental risk assessment. SynopsisMultiple ribosomal mutations co-evolved under environmentally relevant exposure conferred high-level streptomycin resistance via epistatic interactions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/694165v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@e47b2borg.highwire.dtl.DTLVardef@525e27org.highwire.dtl.DTLVardef@1a36e4dorg.highwire.dtl.DTLVardef@9eaf34_HPS_FORMAT_FIGEXP M_FIG Table of Contents Graphic C_FIG

microbiology↗

Exploring multi-level microbial interactions from individual 3D genomes to community networks

Microbial communities interact with their hosts through complex genomic networks that influence ecosystem stability and disease progression. Here, we present FindMeta3D, a computational framework that simultaneously identifies microbial three-dimensional (3D) genome structures and cross-domain interaction networks. Applying this approach to 528 Hi-C samples, we resolved 3D genome structures of 344 microbial species, revealing five evolutionarily conserved chromatin folding patterns linked to intrinsic sequence features. Further analyses demonstrated distinct microbial-host interaction preferences and identified functional interaction hotspots that are critical for infection. Experimental deletion of such hotspots in the EBV genome resulted in significant infection defects, demonstrating their essential role in viral infectivity. Additionally, we constructed the first Cross-domain Microbial Interaction Network (CMIN), which uncovered pathogen-specific subnetworks and demonstrate dramatic restructuring of gut microbial communities in neutropenic patients, including enhanced Klebsiella-phage interactions. Subnetwork analysis identified potential phage therapy targets, such as Klebsiella phage ST16-OXA48phi5.4. These findings provide fundamental insights into microbial 3D genomics and establish FindMeta3D as a powerful platform for studying microbial genome structure and communities and developing antimicrobial strategies.

microbiology↗

ALKBH1 activity in vitro and human cell lines by isotope dilution mass spectrometry

AlkB homolog 1 (ALKBH1) is a member of the AlkB family of Fe(II) and -ketoglutarate (-KG)-dependent dioxygenases, known for its enzymatic activity on various nucleic acid substrates. Its known targets include N1-methyladenosine (m1A), N6-methyladenosine (m6A), N3-methylcytidine (m3C), and 5-methylcytosine (m5C) in RNA, as well as N6-methyladenine (N6-mA, 6mA) in DNA and the histone protein H2A. Moreover, dysregulation or dysfunction of ALKBH1 has been implicated in a broad spectrum of human diseases. In order to shed further light on the substrate scope and role of ALKBH1, we used quantitative mass spectrometry to assess its activity in vitro and in human cell lines. To study ALKBH1 activity on defined substrates in vitro, we enzymatically generated tRNAs specifically carrying the m3C32 (tRNA-ThrUGU and tRNA-SerUCN) and i6A37 (tRNA-SerUCN) modifications. Here we show that ALKBH1 reduces m3C, m1A and m5C in vitro in total extracts of tRNAs, but does not impact on rRNA modifications in human cell lines. However, upon overexpression or siRNA-mediated knock-down of alkbh1 in human cell lines no impact on the modification of total tRNA extracts or specifically enriched RNAs could be observed. In addition, varying the glucose and fetal bovine serum (FBS) concentration in the growth medium of HEK293T cells, in combination with alkbh1 siRNA-mediated knock-down, also shows no impact on the tRNA modification spectra. Based on our data, we conclude that in human cells lines grown under optimal conditions ALKBH1 does not play an important role in the demethylation of tRNAs.

biochemistry↗

Rapid canalization of chromosome conformation-transcription fingerprints during embryogenesis revealed by fully-automated cell identity decoding with CeSCALE

Genome organization into higher-order active and inactive compartments exhibits cell-type specific patterns, which are widely implicated in the regulation of transcriptional activity. During embryogenesis, epigenetic regulation controls cell type specification along cellular lineages with similar transcriptional identities through the coordinated action of chromatin states. However, prevalent single-molecule variability in higher-order chromosome conformation and a lack of precise cell lineage information have previously limited our understanding of the relationship between conformation and transcriptional activity in vivo. Specifically, how the conformation-transcription relationship is inherited along cellular lineages through cell divisions is poorly understood. Here, we developed a novel algorithm for cell lineage identification (C. elegans Sinkhorn-based Cell ALignmEnt, CeSCALE) combined with single cell genomics to reveal that local conformation-transcription fingerprints are associated with, and inherited along the stereotyped cellular lineages of C. elegans embryos. Inspired by Optimal Transport theory, CeSCALE provides a fully automated framework for quantifying lineage-resolved individual cell phenotypes in situ, across a wide developmental window. Combining CeSCALE with single-molecule chromosome tracing uncovered higher-order interchromosomal block associations, which surprisingly coalesce transcriptionally diverse domains and are independent of lineage identity. Instead, by integrating lineage-resolved chromosome conformations with single-cell transcriptomics, we find that local conformation-transcription spatial relationships ( fingerprints), containing both hubs and islands of transcriptional activity, are robustly inherited along lineages. Finally, we find that the canalization of these fingerprints represent the rewiring of chromatin states at key developmental stages. Our results suggest that local chromatin environments, but not large-scale compartments, coordinate the dramatically changing transcriptome during embryogenesis.

developmental biology↗

A spatially-resolved human brain proteome atlas for understanding function and disease

While the brain performs specialized functions across distinct regions, the spatial organization of the human brain proteome remains largely uncharted. Here we present a comprehensive spatially-resolved proteome atlas of the human brain, analyzing over two thousand MRI- guided locations across four individuals. Proteome analysis integrated with transcriptomics reveals extensive post-transcriptional regulation, with cortical regions showing markedly higher protein diversity than transcript. Unsupervised molecular clustering defines distinct brain territories that transcend anatomical boundaries, instead reflecting metabolic demands and functional specialization patterns. Application to epilepsy brain tissue uncovered disrupted astrocyte metabolism, protein homeostasis and therapeutic targets including the seizure-associated purinergic receptor P2RX7. This resource bridges molecular and systems neuroscience to accelerate neurological drug discovery.

neuroscience↗

AAV11 mediates efficient retrograde trans-neuronal transduction of astrocytes

Understanding the mechanisms by which astrocytes regulate neural circuits is crucial for elucidating the mechanisms underlying cognitive and behavioral abnormalities in psychiatric disorders and for exploring potential therapeutic or intervention strategies. Viral tracers are powerful vehicles for comprehending the complex relationship between neurons and astrocytes. Despite adeno-associated virus 1 (AAV1) based anterograde trans-neuronal tools have been successfully applied for identifying astrocytes connected with presynaptic neurons, analogous retrograde trans-neuronal tools for labeling astrocytes connected to postsynaptic neurons remain under development. Here, we first demonstrate that GfaABC1D promoter embedding AAV11 can transfer retrogradely from axons of postsynaptic neurons to astrocytes. Furthermore, we established an AAV11-based dual-viral recombination strategy for labeling astrocytes connected to specific postsynaptic neurons. Finally, by employing targeted neuronal ablation technology to ablate neurons in a specific brain region, we observed that injection of AAV11 into the downstream brain region of this targeted area exhibited minimal labeling of astrocytes functionally associated with the ablated neurons. This finding indicates that AAV11 holds utility for deciphering pathological alterations in disease-related astrocyte-neuron connectivity networks. This work fills a key gap in tools used for studying astrocyte-neuron connectivity networks.

neuroscience↗

Vis-OCT Explorer: an open-source software for visible-light optical coherence tomography data processing

Background and objectivesVisible-light optical coherence tomography (vis-OCT) has enabled the visualization of retinal structures and functions beyond the capabilities of conventional OCTs. However, to reconstruct high-quality images, vis-OCT requires special post-processing, including balanced detection. An open-source, standardized vis-OCT data processing software is essential for clinical applications and translation of vis-OCT. MethodsWe developed Vis-OCT Explorer, an open-source, modular Python-based software for processing vis-OCT images. In addition to the standard spectral-domain OCT processing pipeline - including k-space resampling, dispersion compensation, and fast Fourier transformation - Vis-OCT Explorer offers unique dual-spectrometer balanced detection, short-time-Fourier transformation (STFT) based dispersion compensation coefficient optimization, and GPU-accelerated processing. We evaluated the reconstruction performance by quantifying a quality index extracted from individual B-scan images. We also assessed the repeatability of retinal thickness measurements by five operators on images acquired from different testing sites using the intraclass correlation coefficient (ICC) analysis. ResultsBalanced detection and STFT-based dispersion compensation significantly increased the quality index of reconstructed B-scan images. ICC values of the retinal nerve fiber layer (RNFL) and ganglion cell-inner plexiform layer (GCIPL) thickness measurements from four testing sites exceeded 0.8 in 87.5% of the macular-centered images. The ICC of RNFL thickness measurements on all optic nerve head-centered images is above 0.8, showing strong repeatability across users. ConclusionsVis-OCT Explorer provides high-quality image processing and enables highly repeatable measurements on vis-OCT human retinal images. It facilitates future multicenter clinical tests to validate vis-OCTs clinical efficacy.

bioengineering↗

Differential methanogenic archaea-induced TLR8-dependent signaling is governed by NF-κB p65- and STAT1/2-controlled gene classes

Prevalent in the human gut yet lacking canonical cell wall-derived host-recognition motifs found in bacteria, human-associated archaea Methanosphaera stadtmanae and Methanobrevibacter smithii show immune activity and disease links but remain largely underexplored. Time-resolved RNA-seq in human PBMCs identified an immune program shared with bacterial or viral stimuli across both archaeal species, yet their kinetics diverged, with M. stadtmanae inducing earlier and stronger activation and M. smithii eliciting more gradual responses. Among conserved early-upregulated genes, two classes emerged: Class I was preferentially induced by M. stadtmanae, whereas Class II was similarly induced by both species. To investigate the origin of the Class I/II phenotype, we measured uptake and applied TLR8 inhibition, finding greater early uptake with M. stadtmanae and broad TLR8 dependence across readouts. Consistent with this gene-class separation, ChIP-qPCR showed that M. stadtmanae, but not M. smithii, strongly induced NF-{kappa}B p65 binding at representative Class I promoters, while STAT1/2 binding at representative Class II promoters occurred with both stimuli. Dose-response analyses with RNA inputs established distinct activation thresholds, with Class II at low dose (via STAT1/2) and Class I only at higher dose (via p65). Together, these findings support an input-tuned logic in which archaeal inputs and RNA sensing gate TLR8-dependent immune programs.

immunology↗

Nuclear lamina-associated domain biogenesis is regulated by nuclear pore density during embryogenesis and mediates UV protection

Lamina-associated domains (LADs) are critical for genome organization and function, but their formation during development is not well understood. Here, we use DamID and image analysis to reveal the dynamics of LAD biogenesis during C. elegans embryogenesis. At early stages, DNA at the lamina is transcriptionally active and lacks lamina-associated heterochromatin. This state depends on abundant nuclear pores, which prevent heterochromatin accumulation at the nuclear periphery. As development proceeds, pore numbers decline, enabling heterochromatin to access the lamina. Reducing nuclear-pore components induces precocious accumulation of heterochromatin to the lamina. Functionally, we find that heterochromatic LADs confer protection against ultraviolet (UV) radiation. Older embryos are resistant to UV light and concentrate DNA damage at the nuclear periphery, whereas early embryos are UV sensitive and accumulate damage throughout nuclei when unshielded by their mothers in utero. These findings identify embryonic dissipation of nuclear pores as a key step in heterochromatic LAD assembly, allowing older embryos to withstand exposure to UV irradiation.

developmental biology↗

Multi-Scale Simulations of Excited-State Energy Transfer Pathways in the C2S2-Type PSII-LHCII Supercomplex of Spinach

Photosystem II-light-harvesting complex II (PSII-LHCII) supercomplex achieves efficient excitation energy transfer (EET), yet how directional transfer emerges from its nearly flat energy landscape has remained unclear. Here, we investigate the C2S2-type spinach PSII-LHCII supercomplex containing 206 pigments by integrating microsecond-scale molecular dynamics, QM/MM site energy calculations, and generalized Forster theory. The computed site energy landscape shows overall downhill gradients from peripheral antennas to the reaction center (RC), with small variations fully explained by dynamic structural fluctuations. Pairwise transfer rates reveal a dense multi-timescale EET network, where fast intra-subunit and interface couplings provide robust channels and slower links maintain global connectivity. Key interface pigments act as energy-funneling hotspots that converge excitations toward the RC. Within the PSII core, both the D1 and D2 branches ultimately transfer energy downhill to ChlD1 and ChlD2, respectively, ensuring thermodynamic feasibility of delivery. Three major transfer pathways were identified, all falling within functional timescales (< 250 ps). Bidirectional dynamics were also observed, with rapid reverse transfers enabling excess excitation to be safely dissipated through peripheral antennas. Together, these results demonstrate that PSII maintains fully downhill energy transfer through the combined effects of structural constraints and dynamic regulation, thereby achieving both efficient energy delivery and photoprotection.

biochemistry↗

Machine-learning-based automated Schlemms canal volumetric segmentation for optical coherence tomography

Volumetric segmentation of Schlemms Canal (SC) in optical coherence tomography (OCT) is time-consuming, creating a barrier to experiments studying glaucoma and the anatomy of the trabecular outflow pathways in vivo. To this end, we developed an automated segmentation tool, Schlemms Canal-Localization and Semantic Segmentation (SC-LSS), for the volumetric segmentation of SC in in vivo mice eyes from visible-light OCT (vis-OCT). SC-LSS first localizes the boundaries of SC and subsequently determines the boundaries of SC within the localized region. We used 324 B-scans from 16 mouse eyes for training, validation, and testing the model, and 203 additional B-scans from 16 mouse eyes to evaluate the models accuracy. We found that the Dice coefficient between segmentations generated by SC-LSS and manual expert graders was 0.70 {+/-} 0.20 and that the Dice coefficient between two expert graders was 0.73 {+/-} 0.18 (p = 0.10). Furthermore, SC-LSS captured decreases in SC size with increasing intraocular pressure, yielding a 51.5% decrease in SC size at 20 mmHg compared to 5 mmHg. SC-LSS also identified a 20.1% increase in SC size following the administration of pilocarpine. We anticipate that SC-LSS will accelerate studies on factors regulating the trabecular outflow pathways and their role in glaucoma development and management.

bioengineering↗

Single-molecule chromosome tracing reveals a diversity of megabase heterochromatin domains

Chromosomes fold into distinct domains that regulate transcription, replication, and repair. Beyond well-characterized TADs and compartments, the diversity of heterochromatin domains remains poorly defined at the sequence level. Using single-molecule tracing of nascent heterochromatin in C. elegans, we identify three classes of megabase-scale domains: (i) sharp-boundary, Condensin I-dependent Topological Associating Domain-like domains (TADLs); (ii) similarly sized, but Condensin-independent, elegans Condensin-Independent Domains (elCIDs); and (iii) weaker, diffuse structures that are abundant in the population. TADLs arise early in development, preceding elCIDs, and both become progressively compacted through H3K9 methylation, which promotes intra- and inter-domain proximity. Condensin mutations disrupt TADLs, yet single molecules can still form domain-like structures, as recapitulated by free polymer simulations. However, these differ markedly in boundary positioning and biophysical properties. Our results uncover previously unrecognized heterochromatin architectures and demonstrate that single-molecule analysis and mutational dissection provide valuable approaches for distinguishing between domain types.

genomics↗