Biology subjects

Xue, X.

Publications and source records attributed to Xue, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Integrating Histology with Spatial Molecular Programs Using a Multimodal Foundation Model

Histopathological assessment remains central to cancer diagnosis and stratification, yet its mechanistic interpretation remains limited without molecular context. To address this, we developed SQUALL, a multimodal foundation model integrating histology with spatial molecular programs. For pretraining, we assembled histMol, a large-scale corpus of 1.76 billion paired histology-spatial transcriptomics spots/bins across 33 tissues and 12 platforms from 3,446 tissue sections. Following pretraining, SQUALL enables transcriptome-wide virtual biomarker profiling, prognostically relevant spatial niches discovery, and integrative disease progression modeling. Leveraging its multimodal embeddings, SQUALL identifies niches associated with tertiary lymphoid structure (TLS) maturation and ovarian cancer relapse, reconstructs molecular trajectories of breast cancer invasion across 325,112 spots, and uncovers underlying transcriptional programs. Applied to whole-slide images from 898 patients, SQUALL outperforms existing pathology foundation models in outcome prediction while enabling interpretable risk stratification. Together, these results establish spatially aligned multimodal pretraining as a new paradigm for extending molecular insights into pathology images.

bioinformatics↗

bioRxiv2026

A Synthetic Platform for Antibody Junctional Diversification Beyond Natural Constraints

Antibody junctional diversity in jawed vertebrates arose from RAG transposon domestication, generating CDR3-focused V(D)J recombination with lymphocyte specificity--a constrained system limiting engineered antibody diversity. To overcome these limitations, we developed ARESEC (Antibody Reprogram and Expression System in Engineered Cells), a synthetic platform that enables programmable V(D)J recombination in non-lymphoid HEK293T cells. Through engineered recombination signal sequences (RSS) and optimized RAG1/2 expression, ARESEC enables RSS-guided DNA recombination across all three complementarity-determining regions (CDR1/2/3). Co-expression of terminal deoxynucleotidyl transferase (TdT) enhanced junctional sequence diversity by 41.5-86.3% across 3 CDRs. The platform enables native IgG production by coupling mammalian surface display with FACS-based functional screening. Using clinical-grade antibodies (Nivolumab and Durvalumab) as high-affinity starting scaffolds, we achieved further efficient affinity maturation through focused CDR diversification (library complexity >103). From these diversification libraries, we identified optimized variants including the anti-PD-L1 Dur1 with 2.01-fold enhanced binding, demonstrating the systems capacity for rapid antibody optimization from minimal diversity sampling. Collectively, ARESEC establishes a synthetic paradigm that transcends natural V(D)J constraints, generating multi-CDR diversification in non-lymphoid cells to enable rapid discovery of affinity-matured antibodies, effectively bridging immune evolution with modern antibody engineering demands.

synthetic biology↗

bioRxiv2026

RNABag: A Generalizable Transcriptome Foundation Model for Precision Oncology across Biopsy Modalities

Transcriptomic data is highly sensitive to cancer state and progression, making transcriptome-based foundation models a great promise for diverse clinical ontological inference. However, analyses of transcriptome are conventionally hindered by technical batch effects and limited generalization across platforms. Here, we introduce RNABag, a foundation model designed to generalize well to external datasets. In particular, the model only focuses on highly variable genes to reduce noise; and extensive data augmentation was utilized to pretrain RNABag to learn robust representations, invariant to batch variations. We demonstrate that RNABag achieves superior performance in pan-cancer tissue-of-origin classification and cancer detection in internal validation sets, as well as in zero-shot generalization to external cohorts and in-house clinical samples. Furthermore, RNABag, after specialized finetuning, exhibits strong capabilities in a wide range of clinical applications. The model effectively stratifies patient survival and predicts relapse risks, highlighting key molecular pathways driving tumor progression. Crucially, we extend RNABags utility to liquid biopsies, achieving high diagnostic accuracy in plasma cfRNA and tumor-educated platelets (TEPs), thereby supporting its application in non-invasive cancer monitoring. Interpretability analysis revealed pivotal role of tumor immune escape in the cancer induced plasma cfRNA signals. In summary, our study indicates that cancer states and progression may be monitored in details and precision via comprehensive modeling of transcriptome across biopsy modalities.

bioinformatics↗

bioRxiv2026

Bayesian rhythmic model for jointly detecting circadian biomarkers and predicting molecular circadian time in human post-mortem brain transcriptome

Transcriptomic circadian analysis of human post-mortem brain provides a unique opportunity to characterize in vivo molecular circadian rhythms across brain regions implicated in aging and psychiatric disorders. A primary goal in such analyses is the detection of circadian biomarkers. However, this task is complicated by the frequent mismatch between a subjects recorded circadian clock time and their true molecular circadian time -- arising from observational or recording errors, as well as intrinsic biological variability. Existing methods typically address either biomarker detection or circadian time prediction in isolation. Because errors in one task can degrade performance in the other, the lack of a unified approach remains a key limitation. We propose BayCT -- a Bayesian model for simultaneous circadian marker detection and molecular circadian time estimation. The model extends naturally to repeated measurements from multiple brain regions or organs. For circular data, we employ a von Mises prior distribution, with slice sampling and reversible-jump Markov chain Monte Carlo (MCMC) for Bayesian inference. Through extensive simulations and applications to transcriptomic data from three human brain regions and from 12 mouse organs, BayCT demonstrates superior performance in both biomarker detection and circadian time estimation. Furthermore, we highlight the advantages of integrating data across brain regions, achieving substantial improvements in both tasks.

bioinformatics↗

bioRxiv2025

Decoding the fibroblast/mast cell signaling pathway of acupuncture

Acupuncture has been practiced for thousands of years with documented therapeutic effects, yet its underlying biological mechanisms remain poorly understood. Here, we show that acupuncture stimulation converts local mechanical forces into neuronal signals through defined cellular interactions, establishing a causal axis that links micro-level events at the ST36 acupoint to systemic therapeutic effects. We demonstrate that acupuncture needle manipulation transmits mechanical tension through collagen fibers to local fibroblasts, which subsequently secrete stem cell factor (SCF) and interleukin-33 (IL-33) in the acupoint. SCF recruits mast cells, while IL-33 induces their activation and the release of neuromodulatory molecules. These molecules then engage the nervous system, as evidenced by c-fos expression in the lumbar dorsal horn, demonstrating the transmission of acupuncture-induced peripheral signals into central circuits. Together, these findings define a functional axis linking needle-evoked stimulation to neuronal activation and provide a mechanistic framework for understanding the biological basis of acupuncture and for its evidence-based refinement.

cell biology↗

bioRxiv2025

Curcumin Analogues Trigger HMOX1-Mediated Ferroptosis to Halt Endometrial Cancer Growth

BackgroundAdvanced endometrial cancer remains challenging to treat due to limited therapeutic options and drug resistance. Ferroptosis, an iron-dependent form of cell death, offers a potential strategy for overcoming resistance. Curcumin analogues with improved bioavailability, such as HO-3867 and AKT-100, exhibit potent anti-cancer activity, but their mechanisms remain under-explored. MethodsKLE, Hec50co and Ishikawa endometrial cancer cells were treated with HO-3867 or AKT-100. RNA sequencing, qPCR, and immunoblotting assessed ferroptosis-related gene expression, focusing on HMOX1. Intracellular iron and ROS were measured via FerroOrange and DCFH-DA staining. Cytotoxicity and colony formation were evaluated using CyQUANT assays, with pharmacological inhibitors (ZnPP, Liproxstatin-1, Z-VAD-FMK) and HMOX1 siRNA to dissect the roles of ferroptosis and apoptosis. ResultsBoth analogues upregulated multiple ferroptosis genes, prominently HMOX1. AKT-100 increased intracellular iron and ROS levels. Inhibition of HMOX1, ferroptosis, or apoptosis partially rescued cell viability, while HMOX1 knockdown enhanced clonogenic growth, confirming its key role in AKT-100-mediated cytotoxicity. ConclusionsHO-3867 and AKT-100 induce HMOX1-mediated ferroptosis and apoptosis, effectively suppressing endometrial cancer cell growth. These findings support the therapeutic potential of curcumin analogues and provide a foundation for in vivo studies targeting HMOX1 in endometrial cancer. O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/689080v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@610bcorg.highwire.dtl.DTLVardef@34d8eaorg.highwire.dtl.DTLVardef@18d2a5aorg.highwire.dtl.DTLVardef@d7b4f3_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

IntroductionEndometriosis (EMS) is an estrogen-dependent inflammatory disorder characterized by immune dysregulation. This condition profoundly affects the quality of life and reproductive health of nearly 200 million women of reproductive age worldwide and poses significant clinical challenges due to lack of diagnosis tools and effective treatment. Peritoneal macrophages play a central role in promoting the initiation and progression of EMS. Bioinformatics studies have indicated that the STimulator of INterferon Gene (STING) was downregulated in the macrophages in EMS, and this influenced their polarization and functional. However, the specific contribution of STING pathway alterations to EMS pathogenesis remains unclear. MethodsWe integrated scRNA-seq data from EMS patients and healthy controls-including lesions, eutopic endometrium, non-lesional tissue, and peritoneal fluid from EMS patients and healthy controls(n = 19,291 total samples)-to analyze macrophage STING expression and function. Mouse EMS model was generated by injecting uterus fragments into WT or STING-/- mice. Peritoneal fluid was collected and macrophage proportions and subtypes were assessed via flow cytometry. Macrophages were depleted in STING-/- mice prior to EMS induction to evaluate their role in disease progression. In vitro, hemin was used to treat macrophages to investigate how heme oxygenase-1 (HO-1) modulates the STING pathway, assessed through immunoblotting, co-immunoprecipitation, ELISA, and multiplex immunofluorescence. ResultsBioinformatic analysis revealed that macrophages within the EMS lesions are primarily derived from peritoneal macrophages and exhibit decreased STING expression, which correlated negatively with HO-1. STING-/- mice developed more numerous and larger EMS lesions, accompanied by a decreased proportion of large peritoneal macrophages and an increase in small peritoneal macrophages. A marked elevation in M2-type macrophages within the lesions was detected in STING-/- mice. In vitro, hemin-induced HO-1 suppressed STING pathway activation in macrophages. Mechanistically, HO-1 inhibited the translocation of STING from the endoplasmic reticulum to the Golgi, thereby suppressing STING signaling and facilitating EMS. ConclusionMacrophages are essential for lesion formation in STING-/- mice. In vitro, hemin promotes EMS progression via HO-1 - mediated suppression of the STING pathway. Our findings identify the heme-HO-1-STING axis as a key immunomodulatory pathway in EMS and suggest its potential as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/683839v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6901beorg.highwire.dtl.DTLVardef@1f18d44org.highwire.dtl.DTLVardef@1716f6forg.highwire.dtl.DTLVardef@4ae22d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract (Created in BioRender.com) Retrograde menstruation leads to the accumulation of heme in the peritoneal cavity, which upregulates HO-1 expression in peritoneal macrophages. HO-1 inhibits the translocation of STING from the endoplasmic reticulum to the Golgi apparatus in macrophages, thereby suppressing the STING pathway and promoting the development and progression of EMS. The progression of EMS, in turn, reinforces this mechanism, creating a self-sustaining vicious cycle. C_FIG

immunology↗

bioRxiv2025

Neural Progenitors as a Novel Pathogenic Mechanism in Microcephaly

Despite their significance, the genetic and molecular bases of neurodevelopmental disorders remain poorly understood. In this study, using human brain organoids and mouse models, we show that loss of NDE1, a gene closely associated with microcephaly, disrupts progenitor identity, prolongs mitosis, and alters regional patterning in the forebrain. NDE1 knockout leads to a caudal identity shift of neural progenitor cells in the organoids and mouse brains, coinciding with aberrant ERK signaling. Notably, downstream activation of the ERK pathway restored rostral PAX6 expression in human brain organoids. Parallel analyses of Nde1 knockout mice confirmed disrupted regional patterning of the forebrain. Together, our data establish NDE1 as a critical regulator of early human brain regionalization and elucidate molecular mechanisms underlying the structural abnormalities observed in NDE1-associated microcephaly.

developmental biology↗

bioRxiv2025

Glucose Metabolism Sustains Aberrant STAT3 Signaling in Colorectal Cancer via Glycosylated Paracrine Factors.

The JAK-STAT3 signaling pathway is a key driver of colorectal cancer (CRC) progression. While STAT3 is canonically activated by cytokines such as IL-6, this activation is typically transient due to negative feedback mechanisms. In CRC, however, STAT3 is aberrantly and persistently activated, promoting tumor cell proliferation and survival. Here, we demonstrate that glucose sustains STAT3 activation independent of cytokine availability. By manipulating glucose metabolism, we show that both glucose and its downstream metabolite, GlcNAc, are essential for maintaining STAT3 activation. Moreover, cells with high basal STAT3 activity produce glucose-dependent glycosylated proteins that can activate STAT3 in neighboring cells via paracrine signaling. Proteomic analysis identified multiple candidate proteins involved in this process; however, no single protein was sufficient to fully activate STAT3, suggesting that a combination of glycosylated proteins likely acts synergistically. In vivo, inhibition of glycolysis reduces STAT3 activation in tumors, and genetic deletion of STAT3 in subcutaneous tumor models significantly decreases tumor growth. Together, these findings uncover a novel mechanism by which glucose metabolism supports sustained STAT3 activation in CRC, highlighting a potential metabolic vulnerability for therapeutic targeting.

cancer biology↗

bioRxiv2025

Evaluation of Multiplexed Liquid Glycan Array (LiGA) for Serological Detection of Glycan-binding Antibodies

We test the performance of the multiplexed liquid glycan array (LiGA) technology in serological assays. Specifically, we use LiGA to detect ABO blood group antibodies in human serum. This LiGA, which we name ABO-LiGA, contains ABO blood group trisaccharide glycans with an ethylazido aglycone conjugated to groups of ten multi-barcoded M13 particles carrying dibenzocyclooctyne (DBCO) on p8 proteins. ELISA clonal binding assays to anti-A/B antibodies confirmed the functional performance of ABO-clones and aligned with next-generation sequencing (NGS) of the mixed clones. Multiple DNA-barcoded technical replicates in LiGA allow for quantification of reproducibility and robustness as determined by the Z-score using NGS. We then tested ABO-LiGA for specific detection of IgG and IgM anti-A and anti-B IgG and IgM antibodies in human serum samples. Comparison of antibody binding responses in sera from 31 healthy donors to ABO-LiGA with an ABO-Luminex-based method revealed consistent responses to LiGA-ABO but also minor deficiencies of ABO-LiGA such as low robustness of the current assay format and a limited ability to detect low intensity antibody responses. Some results point to undesired interactions of serum antibodies with small-footprint glycans conjugated to phage via the bulky DBCO moiety. This report illuminates the path for future development of LiGA-based serological assays and suggests the need to develop alternative methods for conjugating glycans to phage to avoid liabilities of the hydrophobic DBCO moiety.

biochemistry↗

bioRxiv2025

Plasma Membrane Damage by Environmental Materials Enhances Cell-Cell Fusion and Impairs Immune Functions of Macrophages

Macrophages are the most abundant phagocytes and play an essential role in host defense. Previous studies have shown that many environmental materials can activate macrophages and trigger inflammatory responses. However, whether these exposures alter macrophage function in host defense remains unclear. This study found that many environmental materials (such as carbon nanotubes, tungsten carbide [WC], and detergents) can damage the plasma membranes of macrophages. This damage leads to decreased reactive oxygen species (ROS) production and phagocytosis but elevated cell-cell fusion. In vivo, airway exposure to laundry detergent impaired the recruitment of macrophages and other myeloid cells to the lung and dramatically dampened protective TH1 and TH17 cell responses, leading to increased susceptibility to Candida infection in mice. Overall, our data indicate that exposure to environmental materials compromises macrophage membrane integrity and impairs host defense. These findings may aid in the development of effective preventive and therapeutic strategies.

immunology↗

bioRxiv2025

The TONSL-MMS22L complex and FANCM form an interdependent complex on chromatin to counter replication stress

FANCM is branchpoint DNA translocase essential for cellular response to replication stress. Here, we show that replication stress stimulates FANCM and the TONSL-MMS22L heterodimer bound to histones H3-H4 to form an interdependent complex on chromatin. TONSL-MMS22L recruits FANCM and Fanconi anemia (FA) core complex to stalled and collapsed forks, maintains FANCM on replication-stressed chromatin, promotes FANCD2 monoubiquitination, facilitates both repair and replication traverse of DNA interstrand crosslinks (ICLs), and suppresses sister chromatid exchanges, through its interactions with FANCM and H3-H4. Reciprocally, both DNA translocase activity and phosphorylation of FANCM facilitate recruitment of TONSL-MMS22L and RAD51 to perturbed forks. Moreover, TONSL-MMS22L and FANCM function together to promote activation of the FA pathway, ICL repair, homologous recombination and replication traverse. Cancer patients with tumors with wildtype FANCM and low expression of TONSL-MMS22L have a more favorable prognosis than those with high expression. Thus, FANCM-TONSL-MMS22L acts coordinately as a complex on chromatin that resolves replication stress, and this complex may present a therapeutic target for wildtype FANCM-linked cancer.

cell biology↗

bioRxiv2025

Neither exogenous, nor endogenous: evidence for a distinct role of negative emotion during attentional control

Negative or threatening stimuli capture attention. However, it remains unclear whether this phenomenon is best conceived as bottom-up (i.e. salience-driven) or top-down (i.e. goal- directed) instead. To address this question, we conducted two experiments using a previously validated dot-probe task (DPT) where physical salience (i.e. abrupt luminance change) and negative emotion (i.e. fearful face) competed with one another for attention selection (Experiment 1, n = 40) or negative (but also positive) emotion could be used as an endogenous cue by the participants to guide this process (Experiment 2, n = 39). Eye-tracking was used to ascertain that both cue and target were processed with peripheral vision. In Experiment 1, we found that negative emotion and physical salience both drove spatial attention in a bottom-up manner, yet their effects were under-additive, suggesting that they could mutually inhibit each other. Moreover, the results of Experiment 2 showed that fear, unlike happiness, could bias spatial attention in a top-down manner, yet only when participants were aware of the association created between the emotional cue and targets location at the block level. Combined together, these novel findings suggest that negative value does not influence the priority map independently from physical salience and goal but depending on the specific combination of cues available for attention selection in the environment, it acts either as an exogenous or endogenous cue, thereby revealing an enhanced flexibility for it.

neuroscience↗

bioRxiv2024

Paired CRISPR screens to map gene regulation in cis and trans

Recent massively-parallel approaches to decipher gene regulatory circuits have focused on the discovery of either cis-regulatory elements (CREs) or trans-acting factors. Here, we develop a scalable approach that pairs cis- and trans-regulatory CRISPR screens to systematically dissect how the key immune checkpoint PD-L1 is regulated. In human pancreatic ductal adenocarcinoma (PDAC) cells, we tile the PD-L1 locus using [~]25,000 CRISPR perturbations in constitutive and IFN{gamma}-stimulated conditions. We discover 67 enhancer- or repressor-like CREs and show that distal CREs tend to contact the promoter of PD-L1 and related genes. Next, we measure how loss of all [~]2,000 transcription factors (TFs) in the human genome impacts PD-L1 expression and, using this, we link specific TFs to individual CREs and reveal novel PD-L1 regulatory circuits. For one of these regulatory circuits, we confirm the binding of predicted trans-factors (SRF and BPTF) using CUT&RUN and show that loss of either the CRE or TFs potentiates the anti-cancer activity of primary T cells engineered with a chimeric antigen receptor. Finally, we show that expression of these TFs correlates with PD-L1 expression in vivo in primary PDAC tumors and that somatic mutations in TFs can alter response and overall survival in immune checkpoint blockade-treated patients. Taken together, our approach establishes a generalizable toolkit for decoding the regulatory landscape of any gene or locus in the human genome, yielding insights into gene regulation and clinical impact.

genomics↗

bioRxiv2024

Regulation of Fentanyl Reward in Male and Female Mice by the Circadian Transcription Factor NPAS2

Synthetic opioids like fentanyl are highly potent and prevalent in the illicit drug market, leading to tolerance, dependence, and opioid use disorder (OUD). Chronic opioid use disrupts sleep and circadian rhythms, which persist even during treatment and abstinence, increasing the risk of relapse. The bodys molecular clock, regulated by transcriptional and translational feedback loops, controls various physiological processes, including the expression of endogenous opioids and their receptors. The circadian transcription factor NPAS2, highly expressed in the nucleus accumbens, may have a crucial function in opioid-related behaviors. Our study found sex-specific roles for NPAS2-mediated reward behaviors in male and female mice, including in fentanyl seeking and craving. We also identified specific cell types and transcriptional targets in the nucleus accumbens of both mice and humans by which NPAS2 may mediate the impact of fentanyl on brain physiology and in opioid reward-related behaviors. Ultimately, our findings begin to uncover the mechanisms underlying circadian rhythm dysfunction and opioid addiction.

neuroscience↗

bioRxiv2024

Comparative transcriptomic rhythms in the mouse and human prefrontal cortex

Alterations in multiple subregions of the human prefrontal cortex (PFC) have been heavily implicated in psychiatric diseases. Moreover, emerging evidence suggests that circadian rhythms in gene expression are present across the brain, including in the PFC, and that these rhythms are altered in disease. However, investigation into the potential circadian mechanisms underlying these diseases in animal models must contend with the fact that the human PFC is highly evolved and specialized relative to that of rodents. Here, we use RNA sequencing to lay the groundwork for translational studies of molecular rhythms through a sex-specific, cross species comparison of transcriptomic rhythms between the mouse medial PFC (mPFC) and two subregions of the human PFC, the anterior cingulate cortex (ACC) and the dorsolateral PFC (DLPFC). We find that while circadian rhythm signaling is conserved across species and subregions, there is a phase shift in the expression of core clock genes between the mouse mPFC and human PFC subregions that differs by sex. Furthermore, we find that the identity of rhythmic transcripts is largely unique between the mouse mPFC and human PFC subregions, with the most overlap (20%, 236 transcripts) between the mouse mPFC and the human ACC in females. Nevertheless, we find that basic biological processes are enriched for rhythmic transcripts across species, with key differences between regions and sexes. Together, this work highlights both the evolutionary conservation of transcriptomic rhythms and the advancement of the human PFC, underscoring the importance of considering cross-species differences when using animal models.

neuroscience↗

bioRxiv2024

Design of diverse, functional mitochondrial targeting sequences across eukaryotic organisms using variational autoencoder

Mitochondria play a key role in energy production and cellular metabolism, making them a promising target for metabolic engineering and disease treatment. However, despite the known influence of passenger proteins on localization efficiency, only a few protein-localization tags have been characterized for mitochondrial targeting. To address this limitation, we exploited Variational Autoencoder (VAE), an unsupervised deep learning framework, to design novel mitochondrial targeting sequences (MTSs). In silico analysis revealed that a high fraction of generated peptides are functional and possess features important for mitochondrial targeting. Additionally, we devised a sampling scheme to indirectly address biases arising from the differences in mitochondrial protein import machinery and characterized artificial MTSs in four eukaryotic organisms. These sequences displayed significant diversity, sharing less than 60% sequence identity with MTSs in the UniProt database. Moreover, we trained a separate VAE and employed latent space interpolation to design dual targeting sequences capable of targeting both mitochondria and chloroplasts, shedding light on their evolutionary origins. As a proof-of-concept, we demonstrate the application of these artificial MTSs in increasing titers of 3-hydroxypropionic acid through pathway compartmentalization and improving 5-aminolevulinate synthase delivery by 1.62-fold and 4.76-fold, respectively. Overall, our work not only demonstrates the potential of generative artificial intelligence in designing novel, functional mitochondrial targeting sequences but also highlights their utility in engineering mitochondria for both fundamental research and practical applications in biology.

synthetic biology↗

bioRxiv2024

Comprehensive evaluation and practical guideline of gating methods for high-dimensional cytometry data: manual gating, unsupervised clustering, and auto-gating

Cytometry is an advanced technique for simultaneously identifying and quantifying many cell surface and intracellular proteins at a single-cell resolution. Analyzing high-dimensional cytometry data involves identifying and quantifying cell populations based on their marker expressions. This study provided a quantitative review and comparison of various ways to phenotype cellular populations within the cytometry data, including manual gating, unsupervised clustering, and supervised auto-gating. Six datasets from diverse species and sample types were included in the study, and manual gating with two hierarchical layers was used as the truth for evaluation. For manual gating, results from five researchers were compared to illustrate the gating consistency among different raters. For unsupervised clustering, 22 tools were quantitatively compared in terms of accuracy with the truth and computing cost. While no method outperformed all others, several tools, including PAC-MAN, CCAST, FlowSOM, flowClust, and DEPECHE, generally demonstrated strong performance. For supervised auto-gating methods, four algorithms were evaluated, where DeepCyTOF and CyTOF Linear Classifier performed the best. We further provided practical recommendations on prioritizing gating methods based on different application scenarios. This study offers comprehensive insights for biologists to understand diverse gating methods and choose the best-suited ones for their applications.

bioinformatics↗