Biology subjects

Gong, X.

Publications and source records attributed to Gong, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Loss of cilia drives centriole clustering and elimination during mammalian spermatogenesis

Cilia are microtubule-based organelles essential for signaling and motility, and their dysfunction causes ciliopathies often associated with infertility. In male germ cells, two types of cilia are present: zygotene primary cilia and sperm flagella. To define the role of cilia in spermatogenesis, we conditionally ablated the distal appendage protein CEP164, required for basal body docking and ciliogenesis, in male germ cells. CEP164 localized to the mother centriole/basal body throughout spermatogenesis, and its loss led to male infertility accompanied by absence of both zygotene cilia and sperm flagella. Despite defective ciliogenesis, meiotic chromosome pairing and DNA double-strand break repair proceeded normally. However, round spermatids exhibited basal body docking and flagellogenesis defects, and frequently formed supernumerary centriole clusters that were subsequently eliminated via residual bodies. Live-cell imaging revealed that centrioles were highly mobile, and centriole pairs from neighboring cells often associated through intercellular bridges, forming aggregates. These results establish that basal body docking is crucial for retaining centrioles within spermatids, and its disruption leads to centriole clustering and loss. In contrast, zygotene cilia are dispensable for meiotic chromosome pairing and DNA repair during mammalian spermatogenesis.

developmental biology↗

bioRxiv2025

Stimuli-Expressed Protein Qubits for Quantum Quantification of Heavy Metals in Natural Water

Environmental heavy metal pollution poses a severe threat to ecological security and human health, necessitating the development of highly sensitive, specific, and rapid detection technologies. Traditional fluorescent biosensors are often constrained by high background interference and limited sensitivity, while single-target detection systems struggle to meet the demands of complex environmental monitoring. This study constructs a novel magnetically modulated photonic quantum biosensing system based on the CadC-T7 gene circuit, replacing the traditional fluorescent reporter gene EGFP with the magnetically modulated fluorescent protein MagLOV - a quantum biomaterial. To enhance its magnetic modulation performance, the mutant with the highest lock-in amplitude during the directed evolution (R10, MagLOV 2) was selected; Simultaneously, systematic parameter optimization was conducted to determine the optimal magnetic modulation frequency (0.05 Hz), the heavy metal stimulation duration (the 2-hour group exhibited the most significant intra-group variation), and the bacterial concentration at the onset of the heavy metal stimulation (controlled at OD600 = 1 to prevent fluorescence quenching due to culture turbidity). The system demonstrates excellent multi-analyte detection capabilities for lead chloride, lead nitrate, and cadmium chloride across a concentration range of 10-8 to 10-4 M. Compared to conventional steady-state photometric methods based on EGFP and MagLOV 2, the lock-in analysis of MagLOV 2 achieves detection sensitivities enhanced by 1[~]2 orders of magnitude, with detection limits as low as 2.4 nM for cadmium chloride, 4.8 nM for lead nitrate, and 9.9 nM for lead chloride. Langmuir isotherm fitting results demonstrate high quantitative accuracy (R2 > 0.950), with particularly outstanding fitting performance for cadmium chloride (R2 = 0.999) and lead nitrate (R2 = 0.995).

synthetic biology↗

bioRxiv2025

Development of Collagenous Filaments with Tuneable Mechanical Properties Using a 3D Bioprinter and Molecular Crowding

Engineering collagen constructs that replicate the mechanical strength and biological functionality of load-bearing tissues like tendon remains a significant challenge. This study establishes a scalable and accessible biofabrication method that combines the precision of a commercial 3D bioprinter with the physicochemical principles of molecular crowding. Using an acidic collagen solution in combination with a hypertonic polyethylene glycol (PEG) bath, we systematically investigate how modulating pulling speed and nozzle diameter dictates the final filament properties. Our results demonstrate that faster pulling speeds and smaller nozzle diameters produce thinner, more densely packed filaments. High-resolution scanning electron microscopy (SEM) and polarised light microscopy reveal a tuneable transition in surface morphology, from a disordered isotropic state to a highly ordered phase, quantitatively confirmed by a sharp increase in birefringence. Critically, we demonstrate the preservation of collagens native, periodic 66 nm d-banding, an essential motif for cell interaction. This structural refinement translates to a dramatic enhancement of mechanical performance, with the strongest filaments achieving an ultimate tensile strength of 0.64 GPa and a Youngs modulus of 8.9 GPa, values that surpass native tendon. Furthermore, the fabricated filaments are highly biocompatible and bio-instructive, promoting robust alignment and elongation of mesenchymal stem cells. This work provides a direct link between bioprocess parameters and the resulting hierarchical structure, offering a versatile platform for fabricating high performance, biomimetic materials for regenerative medicine.

bioengineering↗

bioRxiv2025

Symmetric brain-liver circuits mediate lateralized regulation of hepatic glucose output

Neural lateralization is well recognized in the control of contralateral somatic movement, yet its relevance to visceral organ regulation remains poorly understood. This study aimed to determine whether the central nervous system exerts lateralized control over hepatic glucose metabolism and to localize the site of peripheral sympathetic crossover to the liver. Pseudorabies virus (PRV) tracing revealed bilateral projections from the lateral paragigantocellular nucleus (LPGi) with preferential innervation of the contralateral hepatic lobes. Unilateral LPGi activation elevated systemic glucose by enhancing glycogenolysis and gluconeogenesis specifically in contralateral lobes, whereas bilateral activation produced additive effects. Following unilateral hepatic denervation, contralateral LPGi activation induced metabolic compensation in the remaining innervated lobes, characterized by increased norepinephrine release, glucose production, and glycogen depletion. Whole-mount tissue clearing and dual viral tracing localized the sympathetic crossover to the porta hepatis. Developmental analysis showed that lobar-specific innervation along the vasculature emerges by postnatal week 2. These findings demonstrate that the brainstem can exert lobe-specific, lateralized control of hepatic glucose metabolism via bilaterally projecting brain - liver sympathetic pathways. This contralateral regulation arises from a peripheral decussation at the porta hepatis, and the compensatory activation observed after denervation reveals an intrinsic neuroadaptive mechanism that helps safeguard systemic glucose homeostasis. HighlightsO_LIBrain-liver sympathetic projections exhibit predominant contralateral innervation C_LIO_LIUnilateral LPGi activation drives glucose production in contralateral hepatic lobes C_LIO_LIUnilateral denervation augments contralateral LPGi-mediated metabolic compensation C_LIO_LISympathetic crossover to the liver localizes at the porta hepatis C_LI

neuroscience↗

bioRxiv2025

Preemptive SOD1 Silencing via Neonatal Intramuscular AAV Therapy Modifies Disease Trajectory in an ALS Mouse Model

Amyotrophic lateral sclerosis (ALS) is a progressive and fatal neurodegenerative disorder with limited therapeutic options. Mutations in the gene encoding superoxide dismutase 1 (SOD1) represent a major genetic cause of familial ALS, driving motor neuron degeneration through toxic gain-of-function mechanisms. Although gene silencing approaches targeting SOD1 show substantial therapeutic potential, their clinical translation remains restricted by suboptimal delivery to the spinal motor neurons and safety concerns linked to conventional viral vectors. This study presents a minimally invasive gene therapy strategy that combines the retrograde transport capability of rAAV2-retro with the safety of an artificial microRNA (miRNA) to achieve pan-spinal SOD1 silencing. A single intramuscular injection of rAAV2-retro-miRNA into neonatal SOD1G93A mice resulted in widespread transduction of spinal motor neurons, significant reduction of mutant SOD1 protein, and multifaceted therapeutic benefits. Treated mice exhibited delayed disease onset, extended lifespan, preserved motor function, reduced neuroinflammation, and protection of neuromuscular junctions and spinal motor neurons. Importantly, the artificial miRNA construct demonstrated a superior safety profile relative to short hairpin RNA (shRNA)-based constructs, which induced marked toxicity and lethality in wild-type mice. These findings establish neonatal intramuscular delivery of rAAV2-retro-miRNA as a safe, efficient, and clinically translatable strategy for preemptive intervention in SOD1-mediated ALS, offering broader applicability to other motor neuron diseases.

neuroscience↗

bioRxiv2025

Structure and Function of Lens Suture Examined by 2-photon Fluorescence Microscopic Imaging

We have applied 2-photon fluorescence microscopy (2PFM) to investigate the structures and functions of mouse eye lenses, especially lens sutures, using wildtype (WT) and KLPH-KO suture-cataract lenses in vivo. Dynamic structures of lens sutures have been hypothesized to act as pathways carrying fluid containing ions, nutrients, and other factors as part of microcirculation for maintaining lens homeostasis and transparency. 3D imaging results show both typical "Y" and "double Y" shaped suture structures in WT lenses, diverse suture patterns including "star" shapes with variations appearing at different depths, and misaligned suture planes in KLPH-KO lenses. The variability in suture patterns, quantified using the mean of image stacks similarity indices (SSIM) to the mean projection of the stack, reveals a significant increase (p<0.05) in pattern randomization for KLPH-KO lenses. Both WT and KLPH-KO lenses exhibit voids around sutures and enlarged vacuoles throughout the lens structure in vivo. Pathological features like irregular and larger central voids containing 2~5-{micro}m-diameter amorphous structures that might result from membrane protein remnants/aggregates in the KLPH-KO mouse eye lens were observed. In conclusion, this work provides new morphological markers for characterizing suture cataract and fiber pathological features. Lens sutures are stabilized structures that are impermeable to dyes, and the extracellular spaces of lens peripheral fibers provide efficient diffusion pathways for lens microcirculation.

biophysics↗

bioRxiv2025

Novel Function of Arylalkalamine N-acetyltransfe- rase-1 in Modulating Host Coagulation and Blood Feeding in Aedes aegypti

During blood feeding, mosquitoes introduce substantial quantities of salivary proteins into their hosts to facilitate feeding. Arylalkylamine N-acetyltransferase-1 (aaNAT1) is a salivary protein prominently produced in the salivary glands of Aedes aegypti. Previous research has demonstrated that mosquitoes with AaaaNAT1 mutations fail to efficiently inhibit host blood coagulation; however, the precise regulatory mechanisms remain unknown. This study identified the primary metabolites and proteins interacting with AaaaNAT1 through integrated transcriptomic, proteomic, and metabolomic analyses. Combined with isothermal titration calorimetry (ITC), immunohistochemistry, ELISA, platelet function assays, and coagulation tests, we further established that AaaaNAT1 binds norepinephrine, reducing host platelet aggregation and thereby limiting activation of the host coagulation cascade and fibrinolytic system. Additionally, behavioral investigations showed that AaaaNAT1 knockdown in Aedes aegypti significantly prolonged the time required for female mosquitoes to locate a host and successfully obtain blood, while also markedly reducing blood consumption. This effect may stem from the inability of aaNAT1-depleted mosquitoes to effectively suppress host blood aggregation during feeding, as well as the downregulation of octopamine following AaaaNAT1 knockdown. Therefore, this study reveals a novel role for aaNAT1 distinct from its known functions in pigmentation and immunity, advancing our understanding of aaNAT1s role in insects.

molecular biology↗

bioRxiv2025

Epidermal Stem Cells Control Periderm Injury Repair via Matrix-Driven Specialization of Intercellular Junctions

Epidermal stem cells interact with the extracellular matrix (ECM) to regulate their differentiation and maintain skin architecture. Here, we demonstrate a novel role for basal epidermal stem cells (BECs)-ECM interaction in regulating adhesion molecules expressed by the periderm--the superficial epidermal cells (SECs) of the embryonic bilayered skin. Using the developing zebrafish fin fold, we identify BECs form distinct regions of collagen-versus laminin-enriched basement membranes through integrin-mediated adhesions. Mechanistically, collagen-associated BECs form desmosomes and adherens junctions (AJs) with SECs while laminin-associated BECs display reduced desmosomes but sustain AJs and actomyosin expression with SECs. Notably, we show both in vivo and in a bilayered human keratinocyte model, that laminin, compared to collagen, is sufficient to repress desmosome formation while sustaining AJs specifically at the interlayer cell contacts. In vivo, laminin deficiency enhances desmosome expression across layers and impairs the wound-healing capacity of SECs. This defect was partially rescued by genetic reduction of the desmosome protein Desmoplakin-1a, highlighting the role of ECM-dependent junctional specialization in mediating differences in SEC injury response. Overall, our findings identify that stem cells, through their matrix, establish specialized junctions in the overlying stratified epithelium, which contribute to skin healing properties.

developmental biology↗

bioRxiv2025

X-Linked Cancer-Associated Polypeptide (XCP) from lncRNA1456 Cooperates with PHF8 to Regulate Gene Expression and Cellular Pathways in Breast Cancer

Recent studies have demonstrated that a subset of long "noncoding" RNAs (lncRNAs) produce functional polypeptides and proteins. In this study, we discovered a 132 amino acid protein in human breast cancer cells named XCP (X-linked Cancer-associated Polypeptide), which is encoded by lncRNA1456 (a.k.a. RHOXF1P3), a transcript previously thought to be noncoding. lncRNA1456 is a pancreas- and testis-specific RNA whose gene is located on chromosome X. We found that the expression of lncRNA1456 and XCP are highly upregulated in the luminal A, luminal B, and HER2 molecular subtypes of breast cancer. XCP modulates both estrogen-dependent and estrogen-independent growth of breast cancer cells by regulating cancer pathways, as shown in cell and xenograft models. XCP shares some homology with homeodomain-containing proteins and interacts with the histone demethylase plant homeodomain finger protein 8 (PHF8), which is also encoded by an X-linked gene. Mechanistically, XCP stimulates the histone demethylase activity of PHF8 to regulate gene expression in breast cancer cells. These findings identify XCP as a coregulator of transcription and emphasize the need to interrogate the potential functional roles of open reading frames originating from noncoding RNAs. Statement of SignificangeXCP, a polypeptide encoded by an X-linked lncRNA, regulates gene expression in breast cancer cells. XCP is a chromatin-associated protein that interacts with the histone demethylase PHF8 and modulates its demethylase activity to regulate gene expression. XCP drives cancer-specific phenotypes and serves as a potential biomarker and/or target for therapeutic intervention.

cancer biology↗

bioRxiv2025

Modulation of TTR Gene Expression in the Eye using Modified Duplex RNAs

Small interfering RNAs (siRNAs) are a proven therapeutic approach for controlling gene expression in the liver. Expanding the clinical potential of RNA interference (RNAi) requires developing strategies to enhance delivery to extra-hepatic tissues. In this study we examine inhibiting transthyretin (TRR) gene expression by short interfering RNAs (siRNAs) in the eye. Anti-TTR siRNAs have been developed as successful drugs to treat TTR amyloidosis. When administered systemically, anti-TTR siRNAs alleviate symptoms by blocking TTR expression in the liver. However, TTR amyloidosis also affects the eye, suggesting a need for reducing ocular TTR gene expression. Here, we demonstrate that C5 and 2-O-linked lipid-modified siRNAs formulated in saline can inhibit TTR expression in the eye when administered locally by intravitreal (IVT) injection. Modeling suggests that length and accessibility of the lipid chains contributes to in vivo silencing. GalNAc modified anti-dsRNAs also inhibit TTR expression, albeit less potently. These data support lipid modified siRNAs as an approach to treating the ocular consequences of TTR amyloidosis. Inhibition of TTR expression throughout the eye demonstrates that lipid-siRNA conjugates have the potential to be a versatile platform for ocular drug discovery. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/642595v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@1e9ad27org.highwire.dtl.DTLVardef@67067borg.highwire.dtl.DTLVardef@1da7eadorg.highwire.dtl.DTLVardef@1b2a552_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Unlocking hidden flaws in PPV and ACC: A step towards more reliable identification of protein complex

As classic evaluation indexes, clustering-wise predictive positive value (PPV) and accuracy (ACC) have been widely used for the detection of protein complexes ([1]). However, we identified a critical error in their calculation, which can lead to inaccurate evaluation results under most conditions. Here, we elaborate on the problem of the original indexes and propose revised indexes PPVM (PPV Modified) and ACCM, which correct the identified error. Experiments demonstrate that revised indexes achieve higher reliability. Based on the new indexes, we reevaluated three state-of-the-art computational methods for protein complex detection on five benchmarks to provide a revised baseline to facilitate comparison of performance for algorithms developed later. The code and data involved in the experimental section of this paper can be found in https://github.com/hyx-1/PPV_M-and-ACC_M.

bioinformatics↗

bioRxiv2025

Convergent evolution of a fungal effector enabling phagosome membrane penetration

The ability of pathogens to evade phagosomal killing is critical for their pathogenicity. Previously, we had identified the HscA effector protein in the clinically important fungal pathogen Aspergillus fumigatus, which redirects conidia-containing phagosomes from the degradative to the non-degradative pathway. Here, we discovered a pathogenic form of this surface protein, determined by a single tyrosine residue (Y) at position 596, which is lacking in most fungi analyzed, that have a leucine (L) instead. Y596 enables HscA to penetrate the phagosomal membrane. In line, the introduction of a single L- to-Y exchange in the orthologous Ssb protein of Saccharomyces cerevisiae enabled the protein to penetrate phagosomal membranes that was reduced by deletion of one of the two Y-encoding SSB genes in the pathogenic fungus Candida glabrata. These data suggest a convergent evolution of HscA/Ssb proteins among human-pathogenic fungi and that a single amino acid exchange determines a virulence factor. HighlightsO_LIHscA with Y596 penetrates host cell membranes and causes phagosomal damage C_LIO_LIMost fungi (96%) have a leucine at the respective position C_LIO_LIAn L-to-Y mutation in Ssb enables S. cerevisiae to damage phagosomes C_LIO_LIRecruitment of ESCRT complex to the phagosomal membrane requires human p11 protein C_LI

microbiology↗

bioRxiv2025

Single-cell spatial transcriptome reveals pathological features of human hippocampus with sclerosis

More than half of epileptic patients ultimately turned to intractable epilepsy. Mesial temporal lobe epilepsy with hippocampal sclerosis (MTLE-HS), the most common type of intractable epilepsies, whose pathological mechanism remains elusive. Here, using 42 human hippocampal samples from surgical donors of MTLE (32 with and 10 without HS) through single-cell resolution Stereo-seq and histologcial experiments, we revealed spatially pathological changes of gene expression and cell type composition with HS systematically. After precise parcellation of hippocampal subregions and differentially expressed gene (DEG) analysis between each region with and without sclerosis, we found Cornu Ammonis (CA) subregions with higher number of DEGs were vulnerable to sclerosis, especially CA1 and CA3. Within CA1, we found that CA1-superficial and proximal areas were more vulnerable than CA1-deep and distal areas in sclerosis. Meanwhile, after analyzing 350,795 segmented cells from Stereo-seq, we found dramatically increasing density of astrocyte accompanied with significantly decreasing density of excitatory neurons in CA1, especially superficial and proximal CA1, and CA3 in sclerosis. In these two vulnerable subregions, proliferative astrocyte (P_astrocyte) and reactive astrocyte (R_astrocyte) were found to be enriched whereas apoptotic subtype of astrocyte (A_astrocyte), related with apoptotic pathway, was mainly located in alveus, which strengthened cell communication with reactive microglia (R_microglia) in HS, revealing the novel pathological feature in our work. The pseudotime analysis indicated that CA excitatory neurons underwent synaptic impairment, energy dysfunction, aging, and finally losing cell identity until death through autophagy or apoptosis. Besides, we also found a resilient subtype, EX_CA2-4.3, highly expressed extracellular matrix related genes including PDYN, and was increasing the interaction of BDNF-NTRK, NFASC-CNTN1 to withstand the damage from sclerosis. Together, our study provided a reference of human hippocampus with and without HS caused by MTLE, and highlighted the potential pathological mechanism on molecular and cellular level of MTLE-HS.

neuroscience↗

bioRxiv2024

Multi-stage-mixing to create a core-then-shell structure improves DNA-loaded lipid nanoparticles transfection by orders of magnitude

As they became the dominant gene therapy platform, lipid nanoparticles (LNPs) experienced nearly all their innovation in varying the structure of individual molecules in LNPs. This ignored control of the spatial arrangement of molecules, which is suboptimal because supramolecular structure determines function in biology. To control LNPs supramolecular structure, we introduce multi-stage-mixing (MSM) to successively add different molecules to LNPs. We first utilize MSM to create a core-then-shell (CTS) synthesis. CTS-LNPs display a clear core-shell structure, vastly lower frequency of LNPs containing no detectable mRNA, and improved mRNA-LNP expression. With DNA-loaded LNPs, which for decades lagged behind mRNA-LNPs due to low expression, CTS improved DNA-LNPs protein expression by 2-3 orders of magnitude, bringing it within range of mRNA-LNPs. These results show that supramolecular arrangement is critical to LNP performance and can be controlled by mixing methodology. Further, MSM/CTS have finally made DNA-LNPs into a practical platform for long-term gene expression.

bioengineering↗

bioRxiv2024

Mild neonatal hypoxia disrupts adult hippocampal learning and memory and is associated with CK2-mediated dysregulation of synaptic calcium-activated potassium channel KCNN2

ObjectiveAlthough nearly half of preterm survivors display persistent neurobehavioral dysfunction including memory impairment without overt gray matter injury, the underlying mechanisms of neuronal or glial dysfunction, and their relationship to commonly observed cerebral white matter injury are unclear. We developed a mouse model to test the hypothesis that mild hypoxia during preterm equivalence is sufficient to persistently disrupt hippocampal neuronal maturation related to adult cellular mechanisms of learning and memory. Methods: Neonatal (P2) mice were exposed to mild hypoxia (8%O2) for 30 min and evaluated for acute injury responses or survived until adulthood for assessment of learning and memory and hippocampal neurodevelopment. ResultsNeonatal mild hypoxia resulted in clinically relevant oxygen desaturation and tachycardia without bradycardia and was not accompanied by cerebral gray or white matter injury. Neonatal hypoxia exposure was sufficient to cause hippocampal learning and memory deficits and abnormal maturation of CA1 neurons that persisted into adulthood. This was accompanied by reduced hippocampal CA3-CA1 synaptic strength and LTP and reduced synaptic activity of calcium-sensitive SK2 channels, key regulators of spike timing dependent neuroplasticity, including LTP. Structural illumination microscopy revealed reduced synaptic density, but intact SK2 localization at the synapse. Persistent loss of SK2 activity was mediated by altered casein kinase 2 (CK2) signaling. InterpretationClinically relevant mild hypoxic exposure in the neonatal mouse is sufficient to produce morphometric and functional disturbances in hippocampal neuronal maturation independently of white matter injury. Additionally, we describe a novel persistent mechanism of potassium channel dysregulation after neonatal hypoxia. Collectively our findings suggest an unexplored explanation for the broad spectrum of neurobehavioral, cognitive and learning disabilities that paradoxically persist into adulthood without overt gray matter injury after preterm birth.

neuroscience↗

bioRxiv2024

Expansion of mammary intraepithelial lymphocytes and intestinal inputs shape T cell dynamics in lactogenesis

Pregnancy brings about profound changes in the mammary gland to prepare for lactation, yet immunocyte changes that accompany this rapid remodeling are incompletely understood. We comprehensively analyzed mammary T cells, revealing a marked increase in CD4+ and CD8+ T effector cells, including an expansion of TCR{beta}+CD8+ cells, in pregnancy and lactation. T cells were localized in the mammary epithelium, resembling intraepithelial lymphocytes (IELs) typically found in mucosal tissues. Similarity to mucosal tissues was substantiated by demonstrating partial dependence on microbial cues, T cell migration from the intestine to the mammary gland in late pregnancy, and shared TCR clonotypes between intestinal and mammary tissues, including intriguing public TCR families. Putative counterparts of mammary IELs were found in human breast and milk. Mammary T cells are thus poised to manage the transition from a non-mucosal tissue to a mucosal barrier during lactogenesis.

immunology↗

bioRxiv2024

Integrated Analysis of Single-Cell and Bulk RNA-Seq Data reveals that Ferroptosis-Related Genes Mediated the Tumor Microenvironment predicts Prognosis, and guides Drug Selection in Triple-Negative Breast Cancer

BackgroundTriple-negative breast cancer (TNBC) is aggressive, lacking methods to predict recurrence and drug sensitivity. Ferroptotic heterogeneity varies in TNBC subtypes. However, the tumor microenvironment (TME) mediated by ferroptosis genes is unclear. Our study aims to integrate single-cell and bulk RNA sequencing (RNA-seq) data to reveal the ferroptosis-mediated TME in TNBC, predicting prognosis and guiding treatment. MethodsThe single-cell and bulk RNA-seq data of TNBC were sourced from the Gene Expression Omnibus (GEO) database. Using these data, a machine learning algorithm was employed to integrate and analyze the characteristics of the TME mediated by ferroptosis-related genes in TNBC. Prediction models for TNBC survival prognosis and drug treatment response were established and then validated in an independent set. ResultsAt the individual cell level, T cells were categorized into three distinct subpopulations, and local macrophages into two subpopulations. The infiltration degree of these different cell subpopulations was closely associated with prognosis and treatment outcomes. Based on this, the risk score model we developed effectively predicted recurrence-free survival in TNBC patients, with independently validated pooled predicted 3-, 4-, and 5-year Area Under the Curves (AUCs) of 0.65, 0.67, and 0.71, respectively. Additionally, we found that patients in the high-risk group may be more responsive to 27 drugs. ConclusionsWe have uncovered the tumor immune cell clusters in TNBC mediated by ferroptosis. A risk score model was constructed to identify high-risk TNBC patients, which can assist physicians in disease monitoring and precision therapy. The genes identified hold significant potential as therapeutic targets for TNBC patients. FundingThis project is funded by the National Natural Science Foundation of China (81974268, 82472000, 82304151), the Talent Incentive Program of Cancer Hospital Chinese, Academy of Medical Sciences (801032247), the Cooperation Fund of CHCAMS (CFA202202023), and the open project of Beijing Key Laboratory of Tumor Invasion and Metastasis Mechanism, Capital Medical University(2023ZLKF03). Impact StatementIntegrating single-cell and bulk RNA-seq data elucidates the role of ferroptosis in TNBC, offering a prognostic model and personalized therapeutic insights.

cancer biology↗

bioRxiv2024

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

Asgard archaea were pivotal in the origin of complex cellular life. Hodarchaeales (Asgardarchaeota class Heimdallarchaeia) were recently shown to be the closest relatives of eukaryotes. However, limited sampling of these archaea constrains our understanding of their ecology and evolution1-3, including their anticipated role in eukaryogenesis. Here, we nearly double the number of Asgardarchaeota metagenome-assembled genomes (MAGs) to 869, including 136 new Heimdallarchaeia (49 Hodarchaeales) and several novel lineages. Examining global distribution revealed Hodarcheales are primarily found in coastal marine sediments. Detailed analysis of their metabolic capabilities revealed guilds of Heimdallarchaeia are distinct from other Asgardarchaeota. These archaea encode hallmarks of aerobic eukaryotes, including electron transport chain complexes (III and IV), biosynthesis of heme, and response to reactive oxygen species (ROS). The predicted structural architecture of Heimdallarchaeia membrane-bound hydrogenases includes additional Complex-I-like subunits potentially increasing the proton motive force and ATP synthesis. Heimdallarchaeia genomes encode CoxD, which regulates the electron transport chain (ETC) in eukaryotes. Thus, key hallmarks for aerobic respiration may have been present in the Asgard-eukaryotic ancestor. Moreover, we found that Heimdallarchaeia is present in a variety of oxic marine environments. This expanded diversity reveals these Archaea likely conferred energetic advantages during early stages of eukaryogenesis, fueling cellular complexity.

microbiology↗