Biology subjects

Yang, C.

Publications and source records attributed to Yang, C..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Multiple-level organizational logic of the locus coeruleus-norepinephrine system in structure and function

The locus coeruleus (LC) regulates various neural processes through a limited number of norepinephrine (NE)-releasing neurons with widespread axon projections. However, how the LC is organized to exert brain-wide regulatory functions remain elusive. Utilizing larval zebrafish as a whole-brain-scale model, we reveal that morphologically heterogenous but physiologically comparable LC-NE neurons assemble complementarily to implement region-specific regulation of brain-wide neural dynamics. Individual LC-NE neurons exhibit diverse axon projections with ipsilateral bias and region preference, but share comparable electrophysiological properties, sensory responses and neural function-related genes expression. Moreover, population LC-NE neurons display bilaterally symmetrical yet regionally different axon projections and fire synchronously, causing regionally patterned NE release. Along with the regional comparability of NE receptor expression, these enable the LC to tune brain-wide neural dynamics in an inverted-U manner with region difference. Thus, our study provides a comprehensive understanding of the organizational logic of the LC system.

neuroscience↗

bioRxiv2025

Treatment Resistant Persister Cells Exploit Macrophage Lipid Metabolism to Sustain Glioblastoma Growth

Glioblastoma (GBM) displays pronounced intratumoral heterogeneity, posing significant challenges to understanding its biology and developing effective treatments. Using spatial multi-omics, in vivo functional assays, and systems-level analysis, we delineate the diverse metabolic and immune architecture of GBM. We identify a lipid-dependent lineage of treatment-resistant persister cells (TRPCs) that engage tumor-associated macrophages (TAMs) in a spatially organized, metabolically specialized crosstalk. TRPCs co-opt CCR2, CSF1R, CD163+ TAMs for lipid scavenging and acquisition, promoting a pro-tumorigenic and immunosuppressive microenvironment. This cooperative axis is critically dependent on lipid chaperones like FABPs, whose targeting disrupts TAM recruitment, remodels immune composition, and suppresses tumor growth. Retrospective clinical analyses reveal that elevated TRPC-associated transcriptome may serve as stratification criteria to identify patients benefiting from lipid-lowering therapies like statins. Our findings uncover a targetable immunometabolic circuit between TRPCs and TAMs and support the development of precision therapies that disrupt lipid-fueled tumor-immune cooperation in GBM. In briefTreatment-resistant persister cells (TRPCs) in glioblastoma spatially engage TAMs to facilitate lipid transfer, thereby sustaining tumor growth and promoting immune evasion. Targeting this TRPC-TAM metabolic axis reprograms the immunosuppressive microenvironment and improves therapeutic outcomes, revealing a clinically actionable metabolic vulnerability with potential for precision immune-metabolic interventions in GBM. HighlightsO_LIGBM exhibits spatially resolved heterogeneity revealing correlative metabolic and immune micro-niches C_LIO_LITRPC lineage promotes a pro-tumorigenic and immunosuppressive microenvironment by recruiting lipid-specialized TAMs C_LIO_LITRPC lineage hijacks TAMs for metabolic support via stimulating lipid transfer and acquisition C_LIO_LIDisruption of the TRPC-TAM lipid axis, including through FABP3 targeting, reprograms the immune landscape, limits TAM recruitment, and impairs tumor progression C_LIO_LITRPC lineage and associated micro-niche transcriptomic profiles can serve as criteria for patient stratification and identification of responders to lipid-lowering therapies, such as statins C_LI

cancer biology↗

bioRxiv2025

Structural and temporal dynamics analysis on PANoptosis in sepsis: a bibliometric analysis

PANoptosis, as a new type of programmed cell death, is characterized by pyroptosis, apoptosis and necroptosis, and is a key mechanism causing a variety of inflammatory diseases. Despite the growing number of studies indicating the crucial role of PANoptosis in sepsis, there has been no bibliometric analysis of the research hotspots and trends in this field. Therefore, this study aims to explore the history, research hotspots and emerging trends of PANoptosis in sepsis related research in the past 20 years from the perspective of structure and temporal dynamics. The articles related to PANoptosis in sepsis were retrieved from the Web of Science Core Collection (WoSCC) database from 2000 to 2024. CiteSpace and HistCite were used to analyse the historical features, the evolution of active topics, and emerging trends about PANoptosis in sepsis. 6165 original articles and reviews on PANoptosis in sepsis were included in the bibliometric analysis. In the last 20 years, the number of published documents is increasing year by year and reaches a peak in 2022. At the same time, many activation themes have emerged at different times, as evidenced by a total of 96 categories, 865 keywords and 629 reference bursts. Keyword clustering anchored eight emerging research subfields, namely 0# oxidative stress, 1#pyroptosis, 2#sepsis-associated encephalopathy, 3#acute kidney injury, 4#immunosuppression, 5#necroptosis, 7#lung injury and 8#extracellular vesicles. The keyword alluvial map shows that the most persistent research concepts in this field are phosphatase. And the emerging keywords are toll_like_receptors, regulatory T cells, recognition, etc. In a timeline visualization based on the time span of the citations, we find five relevant emerging topics, namely 1# immunosuppression, 2# sepsis-induced cardiomyopathy, 3# pyroptosis, 4# acute kidney injury, and 13# COVID-19. Our study provides a comprehensive bibliometric analysis and summary about the current status and trends on PANoptosis in sepsis, which will aid researchers in conducting further scientific research in this field.

bioinformatics↗

bioRxiv2025

Targeting HMGA1-driven leukemic transformation in myeloproliferative neoplasms with pacritinib

Progression of myeloproliferative neoplasms (MPNs) to secondary acute myeloid leukemia (sAML) is a lethal transition lacking reliable early biomarkers and effective therapies. Integrating multi-omics analyses, a cohort of 240 patient biopsies, and functional studies, we identify High Mobility Group A1 (HMGA1) as a critical driver and predictor of this transformation. HMGA1 expression, readily detectable by immunohistochemistry, progressively increases from chronic MPN phases to sAML, outperforming established markers (CD34/CD117) in predicting impending leukemic transformation (AUC = 0.96). Mechanistically, HMGA1 cooperates with JAK2V617F and TP53 mutations to promote leukemogenesis. Clinically, high HMGA1 levels correlate with resistance to first-generation JAK inhibitors and portend poor overall survival. Importantly, the next generation JAK2/FLT3 inhibitor pacritinib abrogates HMGA1-driven proliferation and significantly extends survival in preclinical models, offering an immediate therapeutic strategy for this high-risk population. Our findings establish HMGA1 as an actionable biomarker for risk stratification and early intervention, and a therapeutic target to overcome therapeutic resistance in MPN-sAML. HighlightsO_LIHMGA1 IHC staining serves as a readily implementable biomarker, outperforming existing marker for early prediction of MPN progression to sAML and identifying patients at high risk. C_LIO_LIElevated HMGA1 expression correlates with resistance to first-generation JAK inhibitors and predicts poor overall survival in MPN-sAML patients, highlighting a critical unmet therapeutic need. C_LIO_LIThe next-generation JAK2 inhibitor pacritinib effectively overcomes HMGA1-driven aggressive disease and therapy resistance, offering a rational, clinically available treatment strategy for HMGA1-high MPN-sAML. C_LI O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=117 SRC="FIGDIR/small/657170v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@18b835org.highwire.dtl.DTLVardef@e5b31dorg.highwire.dtl.DTLVardef@5245caorg.highwire.dtl.DTLVardef@163f5de_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗

bioRxiv2025

AURKA inhibition amplifies DNA replication stress to foster WEE1 kinase dependency and synergistic antitumor effects with WEE1 inhibition in cancers

Highly elevated expression of the oncogene Aurora kinase A (AURKA) occurs in numerous human cancers harboring defective p53, nominating AURKA as a potential vulnerability in TP53-mutated cancer. However, clinical trials have indicated modest monotherapy activity of AURKA inhibitors. Here, we demonstrate that AURKA inhibition promotes phosphorylation of Replication Protein A (RPA), resulting in stalled DNA replication fork progression and eliciting a replication stress response in multiple TP53-mutated models, creating a druggable dependence on the mitotic checkpoint kinase WEE1. Combined inhibition of AURKA and WEE1 synergistically enhanced replication stress, tumor-specific apoptotic cell death, and mitotic catastrophe, and lead to marked tumor regression in cell line- and patient-derived xenograft models of TP53-mutated cancer. Our findings define enhanced DNA replication stress as underlying the strong synergy between AURKA and WEE1 inhibitors and offer preclinical confirmation of efficacy, indicating high potential for clinical translation of this synthetic lethal strategy for TP53-mutated carcinomas. Statement of significanceWe demonstrate that a small molecule AURKA inhibitor amplifies DNA replication stress in TP53-mutated carcinomas. This amplification of DNA replication stress can be leveraged this for synthetic lethal therapy in a combination with WEE1 inhibition that enhances antitumor effects in in vitro, in xenografts and in patient-derived xenograft models, advancing a promising novel combination therapy.

cancer biology↗

bioRxiv2025

Highly reproduceable tapered fiber optoacoustic emitters by in-situ photothermal curing of PDMS for single neuron stimulation

Precise neural modulation is an important tool in neuroscience research for intervene of specific neural pathways. Photoacoustic is an emerging technology enabling high precision non-genetic neural stimulation in vitro and in vivo. In this paper, we report a new method to prepare a Candle Soot - Tapered Fiber based Optoacoustic Emitter (CSTFOE) through an in-situ photothermal curing process. The emitter created was found with high spatial resolution and efficiency for neuromodulation. In the meanwhile, the in-situ photothermal curing procedure is highly reproducible and allows for fabricating the photoacoustic coating on the tiny tip of the tapered fiber with a diameter less than 20 m. With the high efficiency and reproducibility, we designed an integrated photoacoustic neuromodulation system incorporating the CSTFOE, a nanosecond pulsed laser for photoacoustic generation, and a function generator for synchronization, achieving effective neuromodulation in vitro.

neuroscience↗

bioRxiv2025

Mechanism-driven screening of membrane-targeting and pore-forming antimicrobial peptides

The rise of antibiotic resistance has generated an urgent demand for the discovery of new antimicrobial peptides (AMPs), prompting the development of various screening strategies. However, the specific function mechanisms of AMPs are often overlooked during the screening and optimization processes. In this study, we introduce a mechanism-driven screening approach that employs machine learning-based computational models to identify peptide sequences that target membranes and form pores. This approach explicitly considers critical factors such as structural features, membrane ainity, and the ability of peptides to oligomerize. Our method was applied to the metaproteomes of poison frogs, African clawed frogs, and human skin, followed by experimental validation. Seven peptides were successfully screened, each demonstrating antimicrobial activity with minimal hemolysis and cytotoxicity. These peptides exhibited membrane disruption capabilities in liposome leakage assays, with three showing broad-spectrum antimicrobial activity. Furthermore, single-molecule experiments indicated that these peptides can oligomerize on membranes, while electrophysiological measurements detected pore formation, confirming the effectiveness of our screening strategy. Therefore, our screening approach can effectively identify AMP sequences that act through membrane-targeting and poreforming mechanisms, offering a promising, mechanism-driven strategy for the discovery of new antimicrobial agents to combat antibiotic resistance.

biophysics↗

bioRxiv2025

High-Throughput Machine Learning-Aided Antibody Discovery for Cell Surface Antigens

Machine learning (ML) has the potential to revolutionize antibody design and selection, but its success depends on access to extensive, well-curated datasets of antibody-antigen interactions. To address this need, we developed a synthetic Fab yeast display library optimized for seamless ML integration, focusing on sequence diversity within the CDRH3 loop. The library incorporates key sequence features derived from human B cell repertoires essential for efficient antibody generation captured in a compact antigen recognition module (ARM) format. Built using the VH1-69 heavy chain and four light chains, the library was evaluated against ten human and murine cell surface antigens, including PD-L1, TIGIT, and ROBO1. This approach yielded hundreds of antibodies with robust biophysical properties, validated for functional performance in flow cytometry and immunohistochemistry. Furthermore, ML analysis identified additional antibodies for ROBO2 and PD-L2 from the aggregate sequencing data, demonstrating utility for hybrid in silico and experimental workflows. We provide a publicly accessible dataset comprising more than 68,000 Fab sequences and 486 characterized antibodies. This study establishes an ML-compatible framework designed to accelerate and streamline antibody discovery and development.

biophysics↗

bioRxiv2025

The HORMA-domain protein ASY1 recruits the plant-specific cyclin SDS to promote DMC1-mediated meiotic recombination

The chromosome axis is a proteinaceous scaffold essential for crossover formation in meiosis. While the axis associated HORMA-domain protein ASY1 is known to be necessary for the localization of the recombinase DMC1 to the axis, the molecular mechanism linking ASY1 to DMC1 loading remains unclear. Here, we demonstrate that ASY1 directly recruits the plant-specific cyclin SDS to chromosomes, which ensures efficient DMC1 localization and interhomolog recombination. Live-cell imaging and immunodetection revealed that SDS localizes to chromosomes from leptotene to zygotene and dissociates from chromosomes after pachytene resembling DMC1 dynamics. Biochemical assays demonstrated a direct interaction between ASY1 and SDS. Further analyses revealed that ASY1s closure motif, a conformational regulatory element, is required for SDS recruitment despite being dispensable for ASY1s own chromosome association. Moreover, unlike in sds mutants, depletion of the DMC1 inhibitor FIGL1-FLIP complex failed to restore DMC1 foci in asy1 mutants, positioning ASY1 upstream of both positive (SDS) and negative (FIGL1-FLIP) regulators of DMC1. These findings establish ASY1 as a key coordinator of meiotic recombination, bridging chromosome axis architecture with recombinase dynamics to control crossover formation and genome stability.

plant biology↗

bioRxiv2025

Specific Pathogen Free Ten Gene-Edited Pig Donor for Xenotransplantation

Xenotransplantation has entered the clinical phase to fulfill the global organ shortage. However, recent clinical studies revealed that the xenograft from current gene-edited (GE) pigs still poses the risk of immune rejection, and biosafety concerns. In this study, we successfully constructed a large batch of 10- (GTKO/CMAHKO/ {beta}4GalNT2KO/hCD46/hCD55/hCD59/hTBM/hEPCR/hCD39/hCD47) GE cloned (GEC) donor pigs by utilizing gene editing and somatic cell cloning technology, and successfully obtained F1 generation. Phenotypic characterization of 10-GEC pigs showed the deletion of three xenoantigens along with expression of seven human transgenes in various tissues. Digital droplet polymerase chain reaction, and whole genome sequencing indicated 2 copies of hCD46/hCD55/hCD59/hTBM/hCD39 and 1 copy of hEPCR/hCD47 in pig genome without significant off-target and damage to the porcine own functional genes. The validation results showed that 10-GEC pigs effectively inhibited the attacks of human antibodies, complement, and macrophages on porcine endothelial cells and alleviated the coagulation abnormalities between pigs and humans. 10-GEC pigs were negative for all zoonotic pathogens (48) including cytomegalovirus, except streptococcal infections. Kidney, heart, and liver xenografts from these 10-GE pigs were transplanted to non-human primates (NHP), which started working normally without hyperacute rejection. Among them, the heart and liver transplant recipient died without resuscitation due to unexpected interruption of oxygen supply, while the 2 kidney transplant recipients survived for 23 and 16 days, respectively. Pathological analysis showed that 10-GE pig kidney xenografts showed mesenchymal congestion, and fibrosis, cellular hyperplasia, with minor antibody and complement deposition, and significantly reduced the infiltration of CD68+ macrophage. In summary, we successfully produced a group of specific pathogen free GEC donor pigs that effectively mitigated immune rejection upon multi-organ transplantation to NHP.

immunology↗

bioRxiv2025

Novel HIV-1 fusion peptide immunogens using glycan-engineered alphavirus-like particles

Immunofocusing on conserved, subdominant epitopes is critical for vaccines against highly diverse viruses such as HIV-1, influenza, and SARS-CoV-2. The eight-residue N-terminus of the HIV-1 fusion peptide (FP) is one such example of a promising yet small target. We developed new FP immunogens using three alphavirus-like particles (VLPs) and introduced additional glycans to mask shared carrier-specific epitopes. In two independent guinea pig studies, sequential immunization with heterologous carriers enhanced FP-directed antibody titers, which were further improved with glycan engineering. Separately, using diverse FP variants sharing the same N-terminal six amino acids increased neutralizing antibody titers. When combined, these two strategies led to higher FP-directed titers and, after Env trimer boosting, induced FP-directed neutralizing antibodies against multi-clade wild-type HIV-1 in nearly all animals. These findings established the importance of minimizing recurrent off-target epitopes across immunizations and support the engineered VLPs as a promising platform for peptide immunization. HighlightsO_LINovel HIV-1 fusion peptide immunogens using glycan-engineered alphavirus-like particles C_LIO_LIImproved FP-directed response by minimizing recurrent carrier-specific epitopes across immunizations C_LIO_LIImproved neutralizing response by sequential immunization with diverse FP variants C_LIO_LIFP-directed antibodies neutralizing multi-clade wildtype viruses in nearly all animals C_LI

immunology↗

bioRxiv2025

Automatic Individual Cortical Parcellation for the Human Connectome Project

The original Human Connectome Project multimodal cortical parcellation (HCP_MMP1.0) used MRI-derived local features and long-distance functional connectivity measures to define a multimodal parcellation at the group level, accompanied by an automated areal classifier, to create subject-specific mappings of the human cerebral cortex. These mappings, referred to as individual (cortex) parcellations, aim to capture individual variability in areal organization by learning from both structural and functional data. However, a strict supervised learning approach using the group parcellation as labels would have no incentive to learn individual differences that registration is unable to reconcile (e.g., atypical 55b topologies). Furthermore, there are many types of resting state network (RSN) feature maps, and it is unclear which type would most accurately or effectively classify areas, or even what should be the primary criteria for evaluating classification performance. Here, we introduce an Areal Recognition Ensemble with Nested Approach (ARENA) classifier that learns from uncertain labels, using a novel application of weakly supervised learning to this type of problem. Additionally, in comparing multiple candidate RSN decompositions, temporal ICA and PROFUMO maps outperformed the original spatial ICA-based approach based on objective criteria. With these refinements, the ensemble classifier achieved a reliable individual variability score of 8380, an average areal detection rate of 97.8%, and test-retest reproducibility of 73.3%, outperforming a retrained version of the original Multi-layer Perceptron (MLP) model (whose reliable individual variability score was 3128, average areal detection rate was 97.2%, and test-retest reproducibility was 71.6% on the same dataset). Furthermore, the ARENA classifier demonstrated stronger generalization for all three measures when applied to task fMRI data that were not part of the training dataset. Using the refined classifier and leveraging all 1071 HCP-Young Adult subjects, we identified new types of atypical organization of language-related area 55b. Here we provide the fully data-driven HCP_MMP1.0_1071_MPM (Maximum Probability Map) group parcellation and a summary of area 55b organization in both hemispheres. Our automated individual parcellation pipeline powered by the novel ARENA classifier is now integrated into the HCP pipelines, offering a user-friendly tool for the neuroimaging community.

neuroscience↗

bioRxiv2025

Disentangling complex language contact and admixture in the broad Gansu-Qinghai region

Language evolution in the Gansu-Qinghai (GQ) region provides a key perspective for understanding cultural development along the Silk Road. Previous genetic and archaeological studies revealed complex multiethnic interactions shaped by migration and sociocultural exchange. However, the lack of structured linguistic data and computational tools for studying language contact has limited rigorous analysis of sociocultural evolution in this area. Here, we presented a new hybrid dataset of phonological and morpho-syntactic features from languages sampled across the GQ region. We introduced a computational framework to assess language contact and admixture, allowing us to quantify interaction among GQ languages and trace their origins. Our results showed that GQ languages have distinct contact patterns in their phonological and morphosyntactic systems, with some languages exhibiting clear evidence of mixture. Using a new statistical method, Trait Sharing Test (TS-TEST), based on tree topology, we identified significant influences from Sinitic, Tibetan, Mongolic, and Turkic languages in shaping GQ linguistic diversity. These findings highlight the GQ region as a linguistic convergence zone on the Silk Road and provide a foundation for quantitative research on language contact and admixture. Our work strengthens the linguistic perspective on cultural evolution in the GQ region and supports future interdisciplinary studies integrating languages, genes, and material cultures.

evolutionary biology↗

bioRxiv2025

ZMS-6659, a selective Polθ helicase inhibitor, demonstrates anti-tumor activity as monotherapy and synergy effect with PARP inhibitors and topoisomerase inhibitors

The repair of DNA double strand break (DSB) is crucial for genome stability. Homologous recombination (HR) is a high-fidelity, error-free DSB repair pathway, and its dysfunction leads to genome instability and can result in tumorigenesis. In HR deficient contexts, microhomology-mediated end joining (MMEJ), dependent on DNA polymerase theta (Pol{theta}), is up-regulated to serve as a backup pathway for DSB repair. Several studies have proved that Pol{theta} inhibition causes synthetic lethality with HR deficiency, and Pol{theta} emerges as a potential DNA damage repair (DDR) target for the treatment of HR deficient tumors both as single agent or in combination with PARP inhibitors (PARPi). In addition, evidences show that the blockage of Pol{theta} can enhance the sensitivity to DNA damage agents. Herein, we characterized ZMS-6659, a highly potent small-molecule Pol{theta} inhibitor targeting the helicase domain. ZMS-6659 induces synthetic lethality in HR deficient models, elicits synergistic effects with even low dose of PARPi and delays PARPi resistance without additional hematotoxicity. Besides, ZMS-6659 also enhance the sensitivity to topoisomerase inhibitors in HR proficient cell lines. These findings support the clinical exploration of ZMS-6659 in combination with PARPi in HR deficient tumors, and suggest a potential application expansion beyond HR deficiency.

cancer biology↗

bioRxiv2025

Exploring non-invasive sexing of early chick embryos in intact eggs using Laser Speckle Contrast Imaging (LSCI) and Deep Neural Network (DNN)

The ability to image blood flow in early-stage avian embryos has significant applications in developmental biology, drug and vaccine testing, as well as determining sex differentiation. In this project, we used our recently developed laser speckle contrast imaging (LSCI) system to non-invasively image extraembryonic blood vessels and used these images to attempt early sex identification of chick embryos. Specifically, we captured images of blood vessels from 1,251 living chicken embryos between day three and day four of incubation. We then applied deep neural network (DNN) models to evaluate whether it is possible to differentiate sex based on vascular patterns. Using ResNetBiT and YOLOv5 models, our results indicate that sex differentiation from extraembryonic blood vessel images was not achievable with sufficiently high accuracy or statistical significance for practical use. Specifically, ResNetBiT had a five-fold cross-validated average accuracy of 59%{+/-}5% (fold-wise p-value, p [≤] 0.3) at day 3 and 61%{+/-}3% (fold-wise, p [≤] 0.04) at day 4. YOLOv5 had a five-fold cross-validated average accuracy of 55%{+/-}3% (fold-wise, p [≤] 0.3) at day 3 and 53%{+/-}3% (fold-wise, p [≤] 0.5) at day 4. Our findings suggest that using vascular pattern imaging alone is inconclusive for reliable early sex identification in chicken embryos.

bioengineering↗

bioRxiv2025

Large Language Model Consensus Substantially Improves the Cell Type Annotation Accuracy for scRNA-seq Data

Different large language models (LLMs) have the potential to complement one another. We introduce an iterative multi-LLM consensus framework for annotating single-cell RNA sequencing data. This framework outperforms the best state-of-the-art method by nearly 15% in mean accuracy (77.3% vs 61.3%) across 50 diverse datasets from 26 tissues, encompassing over 8 million cells. By leveraging cross-model deliberation, our framework quantifies uncertainty, identifies ambiguous clusters for expert review, provides transparent reasoning chains, and minimizes the effort and expertise needed for cell type annotation in large-scale studies. Additionally, our framework enables users to seamlessly integrate new LLMs.

bioinformatics↗

bioRxiv2025

SpatioCell: A Deep Learning Algorithm for High-resolution Single-cell Mapping through Deep Integration of Histology Image and Sequencing Data

Spatial transcriptomics (ST) is a powerful assay to capture gene expression in tissue context. However, due to the limitation of resolution, most existing ST datasets remain at multicellular resolution which hinders comprehensive understanding of the spatial organization. We propose SpatioCell, a computational algorithm to automatically extract both cell type and expression information at single-cell resolution from ST data, through a morpho-transcriptomic spatial reconstruction framework solved via dynamic programming, integrating morphological and transcriptomic information. This framework enables deterministic single-cell spatial reconstruction, assigning cell identities to precise locations rather than inferring spot-level cell-type composition and expression, and further uncovers overlooked microenvironment features while correcting deconvolution errors. Using the ST data from triple negative breast cancer as an example, SpatioCell reveals the significance of the distance between cancer-associated fibroblast (CAF) and tumor or immune cells for disease progression. The establishment of SpatioCell will broaden the biomedical applications of ST and facilitate investigations of single-cell spatial organization.

bioinformatics↗