Biology subjects

Xu, Z.

Publications and source records attributed to Xu, Z..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Pp6-Pfkfb1 axis modulates intracellular bacterial proliferation by orchestrating host-pathogen metabolic crosstalk

Intracellular bacterial pathogens exhibit heterogeneous replication rates within host macrophages, but the mechanisms by which they manipulate host factors for survival remain incompletely understood. Using a fluorescence-dilution reporter system in Salmonella typhimurium (Salmonella)-infected macrophages, we found that Protein Phosphatase 6 (Pp6) was downregulated in macrophages harboring growing bacteria. Conditional knockout of Pp6 elevated host susceptibility to Salmonella-mediated lethality due to compromised antimicrobial defenses. MicroRNA-31 (miR-31) was identified as a negative regulator of Pp6, and its conditional ablation enhanced bacterial clearance. Yeast two-hybrid screening identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (Pfkfb1), a metabolic regulator, as a substrate of Pp6. Pp6 deficiency resulted in significantly elevated expression of Pfkfb1, which was highly expressed in macrophages containing replicating Salmonella. Pfkfb1 deletion restricted bacterial proliferation by promoting nitric oxide (NO) production while concurrently suppressing arginase-1 (Arg-1) expression and impairing arginine metabolism in macrophages. Collectively, these results establish the Pp6-Pfkfb1 axis as a key regulator of host metabolic adaptation and intracellular bacterial survival, offering potential therapeutic targets against multidrug-resistant pathogens. Author summaryIntracellular pathogens secrete effector proteins that intercept and modify host cells to usurp host defenses and establish habitable intracellular niches, yet the host factors they manipulate for survival and virulence are not fully understood. Using a fluorescence-dilution reporter system in Salmonella typhimurium (Salmonella)-infected macrophages, we found Protein Phosphatase 6 (Pp6) was significantly decreased in macrophages harboring replicating Salmonella and its deficiency indulged bacterial growth in macrophages. However, the deletion of microRNA-31 (miR-31), a negative regulator of Pp6, enhanced Salmonella clearance. Furthermore, through yeast two- hybrid screening, we identified 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 (Pfkfb1) is a substrate of Pp6. And we demonstrated Pfkfb1, abundantly expressed in macrophages containing growing bacteria, is crucial for Salmonella proliferation by regulating nitric oxide (NO) levels, arginase-1 (Arg-1) expression and arginine metabolism. Overall, the molecular changes in Pp6-Pfkfb1 axis drive host metabolic adaptations that enable intracellular bacterial survival.

microbiology↗

bioRxiv2025

Cryo-EM Structure of the Erlin1/2 Complex Reveals a Dynamic Scaffold for Membrane Protein Sequestration and Microdomain Assembly

The SPFH (Stomatin, Prohibitin, Flotillin, and HflK/C) family of proteins are key scaffolding components involved in the organization of functional membrane microdomains (FMMs) across various subcellular membranes, including those of the endoplasmic reticulum (ER) and mitochondria, which are characterized by a low content of saturated lipids. Among this protein family, the erlin1/2 complex is specifically located on the ER membrane. Previous studies have shown that the erlin1/2 complex plays an essential role in the ER-associated degradation (ERAD) pathway, mediating the ubiquitin-dependent degradation of various proteins such as inositol 1,4,5-trisphosphate receptors (InsP3Rs), which are important calcium ion transporters on the ER membrane. However, the molecular mechanisms underlying erlin-mediated FMMs organization and its role in ERAD remain poorly understood. In this study, we determined the single-particle cryo-electron microscopy (cryo-EM) structure of the erlin1/2 complex under different detergent conditions. Our findings reveal that the erlin1/2 complex forms a 26-mer cage-like structure, composed of alternating erlin1 and erlin2 subunits. The erlin1/2 complex defines a nanodomain on the ER membrane, which could recruit various types of proteins to both the interior and exterior membrane regions of the cage. By caging cargo proteins, the erlin1/2 complex physically secludes them from their binding partners, leading to a potential halt in their function. Moreover, individual cages can further interact with one another, facilitating the organization of FMMs of different sizes on the ER membrane. These dynamic properties may play a general and critical role in various processes occurring on the ER, including viral replication, positioning the erlin1/2 complex as a promising new target for antiviral drug development.

biophysics↗

bioRxiv2025

Histo-LCM-Hi-C reveals the 3D chromatin conformation of spatially localized rare cells in tissues at high resolution

It is now well established that an understanding of the chromatin structure is essential to delineate the mechanisms underlying genomic processes. However, while methods to obtain this information from cells in vitro are widely available, there is presently a significant lack of techniques that can acquire this data from cells in the tissue. Such a capability is critical to determine the dependence of the local tissue environment on cell functioning. Further, this ability is particularly necessary for cells that are a significant minority of the total tissue population, which are often obscured in data dominated by more abundant tissue cells. Here we have developed Histological Laser Capture Microdissection Hi-C (Histo-LCM-Hi-C) to enable the characterization of chromatin architecture of phenotype-defined, spatially localized cells within intact tissue sections from as few as about 300 cells. We demonstrate the effectiveness of this approach with the generation of the first 3D Hi-C map of the tissue-resident macrophages of the liver, the Kupffer cells (KC), which are a minor cell population in the normal liver. As expected, owing to their relative rarity, these KC maps are significantly different from those obtained from whole liver, revealing distant contacts between putative enhancers and genes involved in key KC functions as well as significant differences with that of in vitro induced bone-marrow derived macrophages. We anticipate that this method will prove to be an indispensable technique in the growing repertoire of methodologies used for the characterization of the genomic properties of cells within their native environment.

genomics↗

bioRxiv2025

Human meibomian gland organoids to study epithelial homeostasis and dysfunction

Meibomian glands (MGs) are holocrine glands that secrete lipids to maintain the homeostasis of ocular surface, and their dysfunction leads to dry eye disease. Herein, we established long-term 3D organoid culture for murine and human MGs, which retained the cell lineages and lipid-producing ability. The organoids mimicked the drug treatment responses and generated functional MGs after orthotopic transplantation. Inspired by organoid cultures, we found FGF10 eye drops could rescue all-trans retinoic acid-induced MG dysfunction in mice. Besides, nicotinamide uniquely hampered the human MG organoid expansion by inhibiting FGF10 signaling. Single-cell atlas and lipidome not only aligned the delineated cell types and featured lipids between human MGs and organoids, but highlighting MAPK signaling inhibition enhanced acinar cell differentiation and functional maturation of MG organoids. In summary, this study established an organoid platform to explore epithelial homeostasis and dysfunction of MGs, facilitating drug development and regenerative medicine for dry eye disease.

cell biology↗

bioRxiv2025

Group 2 Innate lymphoid cells promote allograft survival by constraining and inducing anergy in alloreactive CD4+ T cells

Although solid organ transplant outcomes have dramatically improved over the last several decades, incomplete understanding of the immune interface between the donor organ and the recipients immune system has impaired our ability to induce immune tolerance in most transplant recipients. Since group 2 innate lymphoid cells (ILC2s) reside in all transplanted solid organs, participate in wound healing, and coordinate other immunoregulatory cell populations, we investigated their role in the alloimmune response. Using a mouse heterotopic cardiac transplant model, we show that recipient ILC2s replace donors ILC2s, upregulate MHCII without expressing costimulatory molecules. In addition, recipient derived ILC2s process and present alloantigen, inducing CD4+ T cell anergy via Caspase-3 pathway. When recipient-derived ILC2s are not present, we observed a significant increase in infiltrating donor reactive CD4+ T cells and worsened allograft survival. Additionally, expansion of ILC2s in vivo through IL33 administration prolonged the survival of murine heart allografts. Overall, these data highlight a critical and novel immunoregulatory role of host-derived ILC2s in solid organ transplant, where they induce anergy in alloreactive CD4+ T cells, promoting the induction of alloimmune tolerance.

immunology↗

bioRxiv2025

Unisexual reproduction in the global human fungal pathogen Cryptococcus neoformans

The human fungal pathogen Cryptococcus species complex (encompassing C. neoformans, C. deneoformans, and the C. gattii species complexes) exhibit diversity in sexual reproduction, including -a mating, pseudosexual reproduction, as well as unisexual reproduction initiated from a single isolate or between isolates of the same mating type. A central conundrum is that while most Cryptococcus natural populations exhibit significant mating-type bias, genetic and genomic analyses show recombination occurs in nature. The discovery of unisexual reproduction in C. deneoformans provided insight; however, thus far unisexual reproduction has never been directly observed in the predominant global pathogenic species C. neoformans. Here, we provide evidence that mutating the RIC8 gene, which encodes a conserved guanine nucleotide exchange factor (GEF) involved in both chaperoning and activating G proteins, enables unisexual reproduction in C. neoformans. Additionally, we show that genetic variation in the natural population promotes unisexual reproduction, and unisexual reproduction in C. neoformans involves canonical meiotic recombination. Finally, we found that deletion of both GPA2 and GPA3 in the MAT background leads to self-filamentation without sporulation, suggesting that differential modulation of the G proteins, likely involving Ric8, could underlie the switch between different modes of sexual reproduction in Cryptococcus. Our study further highlights that the highly conserved Ric8 GEF can act as an important regulator of cellular development in response to environmental stimuli and could modulate sexual reproduction in nature. We hypothesize that unisexual reproduction occurs much more frequently in nature than currently appreciated, and possibly in other fungi and microbial eukaryotes as well. Significance statementSexual reproduction is a central tenet of the eukaryotic life cycle, essential for the long-term survival of a species by promoting genetic diversity and facilitating natural selection. In eukaryotes such as unicellular basidiomycetous fungi, sexual reproduction leads to hyphal growth and spore production, enabling escape from harsh environments and long-distance dispersal. Here, we report that mutating the RIC8 gene, encoding a conserved guanine nucleotide exchange factor (GEF) involved in activation of G proteins, enables unisexual reproduction in the predominant human fungal pathogen Cryptococcus neoformans that involves canonical meiosis. Our findings suggest that conditions might exist in nature that could induce, and even promote, unisexual reproduction in Cryptococcus, highlighting the complexity and importance of sexual reproduction in this prominent fungal pathogen.

genetics↗

bioRxiv2025

Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms

BackgroundRespiratory syncytial virus (RSV) poses a significant public health threat, particularly to children and the elderly. Two protein-based vaccines and one mRNA vaccine have been approved, all targeting the prefusion conformation of the fusion (F) glycoprotein. However, it has been reported that the F protein transitions to the post-fusion state during storage, resulting in a reduction of the vaccines immunogenicity. MethodsIn this study, we engineered novel pre-F-based antigens to preserve pre-F-specific immunodominant epitopes while eliminating sub-potent ones. Based on this, we constructed a series of single-chain dimers and selected the one with the highest expression yield and melting temperature (Tm). Next, we created a heterodimer, scDimer AB. Structural and protein characterization analyses were conducted to verify our design. All monomeric and scDimer antigens were used to immunize rodent models. Additionally, we prepared the antigens in mRNA form and immunized BALB/c mice. Finally, we combined both antigen forms, administering intramuscular mRNA priming followed by intranasal protein delivery in mice. In all immunization strategies, viral challenges were performed in animals to evaluate the immunologic protective effects. FindingsThrough rational design, we developed a monomeric and two single-chain dimeric (scDimer) proteins with the expected characteristics, including complete II, V, and O epitopes and a partial III epitope. The scDimers elicited stronger binding and neutralizing antibody responses in rodent models compared to the monomer, and they also boosted T cell responses when combined with appropriate adjuvants. After three doses of scDimer immunization, live RSV was barely detectable in the tissues of infected animals. The copies of RNA encoding N-gene were significantly reduced in the immunized groups compared to the PBS-injected control groups. We also engineered mRNA versions of the antigens and verified their protective efficacy in mice. Notably, there were no significant differences between intranasal boost and intramuscular two doses after RSV challenged, suggesting that intranasal boost provided equivalent protection to intramuscular vaccination and could reduce the risk of vaccine-enhanced disease (VED) potentially. InterpretationThe scDimer-based RSV vaccines effectively protected rodents from RSV infections, highlighting their clinical potential. Our antigen design removed certain suboptimal epitope regions, enhancing the efficiency of antigen presentation and increasing the proportion of the most potent pre-F-specific neutralizing antibodies. This approach provides a novel perspective for future vaccine design. FundingNational Key R&D Program of China, National Science Foundation of China, Young Scientists in Basic Research, Chinese Academy of Sciences, and Special Program of China National Tobacco Corporation. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe licensed respiratory syncytial virus (RSV) vaccines were based on RSV pre-F structure. We conducted a PubMed search for articles published in English from databases inception to March 31, 2025, using the search terms "RSV" (interchanged with "respiratory syncytial virus"), "pre-F" (interchanged with "prefusion F") and "vaccine". Our search revealed that most of the articles focus on combining pre-F with RSV G protein or other proteins to form viral-like particles (VLPs) or nanoparticles. The second-largest category of articles examined the antibodies level elicited by the pre-F antigens in animal model or some special cohorts. Other studies addressed topics such as optimization of injection dosage and immunization strategies, methodologies for detecting pre-F-specific antibodies, and the development of mRNA-LNP vaccines. Notably, only 4 articles described novel designs of RSV pre-F antigens, all of which were trimeric and based exclusively on the RSV A subtype F protein sequence. Added value of this studyTo our knowledge, our design is the first single-chain dimer version of RSV pre-F antigen. The engineered antigens demonstrated high yield, thermostability, and immunogenicity comparable to that of DS-Cav1. Additionally, we developed the first chimeric RSV-antigen covering both subtype A and B, thereby broadening the potential protective spectrum. We further validated the immunogenicity of our designs in mRNA form and as a protein-mRNA combination. This research emphasizes the potential of constructing and combining minimized, stable antigen modules, offering a novel approach for future vaccine development. Implications of all the available evidenceIn this study, we present a novel approach for constructing and combining minimized, stable antigen modules for future vaccine design. The strong immunogenicity of our antigens underscores their potential for clinical application. Furthermore, given the structural similarities between the RSV antigen and those of other Pneumoviruses, such as human metapneumovirus (hMPV), our design strategy could be extended to the development of multivalent vaccines.

immunology↗

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

Novel Role of Copper Transporter CTR1 and Therapeutic Potential of Copper Chelators in Retinal Ischemia-Reperfusion Injury

BackgroundRetinal ischemia contributes to vision loss in ischemic and diabetic retinopathies through oxidative stress, neurovascular injury, and inflammation. Copper (Cu), while essential, can be toxic in excess and is regulated by Cu transporters such as CTR1. However, the role of CTR1 in ischemic retinopathy remains unclear. Methods and ResultsRetinal ischemia-reperfusion (IR) injury was induced by elevating intraocular pressure to 110 mmHg for 40 minutes in the right eye of Ctr1 heterozygous (Ctr1/-) and wild-type (WT) mice. In WT mice, IR triggered rapid CTR1 upregulation and increased retinal Cu levels (measured by ICP-MS). IR injury caused retinal ganglion cell loss, inner retinal thinning, vascular degeneration, and apoptosis, all of which were significantly attenuated in Ctr1/- mice. Ctr1/- mice also exhibited reduced microglial (Iba1) and glial cells (GFAP) activation and preserved visual function, as assessed by electroretinography. Mechanistically, IR-induced reactive oxygen species (O2-) production (DHE staining), upregulation of NADPH oxidase components (NOX2, p47phox), and NF-{kappa}B activation were markedly suppressed in Ctr1/- mice. Treatment with the Cu chelator tetrathiomolybdate (TTM) similarly reduced retinal thinning, neurovascular damage, apoptosis, gliosis, and oxidative stress after IR injury. ConclusionsCTR1 plays a central role in mediating Cu-dependent oxidative stress, neurovascular degeneration, and inflammation following retinal IR injury. Targeting the CTR1- Cu axis may represent a novel therapeutic strategy for ischemic retinopathy.

cell biology↗

bioRxiv2025

Natural diversity of telomere length distributions across 100 yeast strains

Telomeres gradually shorten at each cell division and telomerase counteracts this shortening by elongating telomere sequences. This dynamic balance between elongation and shortening results in a steady-state telomere length (TL) distribution. We developed a method for detecting telomeric sequences in Saccharomyces cerevisiae genomes from raw Oxford Nanopore Technologies (ONT) sequencing reads, providing a comprehensive view of TL distributions both genome-wide and at individual chromosome extremities. We analyzed the TL distribution in 100 S. cerevisiae strains, representing the genetic and ecological diversity of the species. Our analysis revealed a large diversity in TL distributions within the species, largely driven by inter-extremity differences, ploidy level, and subtelomere structure. Polyploid strains displayed significantly longer telomeres than diploid and haploid strains, and experiments with artificially generated polyploids in two independent genetic backgrounds confirmed that higher ploidy levels lead to telomere elongation. Furthermore, we found that the subtelomeric Y element exerts two distinct and opposing effects: (i) the presence of Y elements at a chromosome extremity is associated with shorter telomeres in cis, but (ii) the overall Y element content in a strain correlates with longer telomeres. Interestingly, the length of the shortest telomeres remained relatively constant across strains, suggesting a selective constraint at the species level. This study reveals the diversity of TL in S. cerevisiae and highlights key factors shaping TL distributions both genome-wide and at individual chromosome extremities.

genomics↗

bioRxiv2025

Organism-wide cellular dynamics and epigenomic remodeling in mammalian aging

To investigate organism-wide cellular alterations and epigenomic dynamics during aging, we constructed a single-cell chromatin accessibility atlas spanning 21 mouse tissues across three age groups and both sexes. We found that around one quarter of 536 organ-specific cell types and 1,828 finer-grained subtypes exhibited significant age-related population shifts. Cellular states from broadly distributed lineages displayed synchronized dynamics with age, indicating systemic signals that coordinate these changes. Molecular analyses identified both intrinsic regulators (chromatin peaks, transcription factor activity) and extrinsic factors (cytokine programs) underlying these shifts. Moreover, [~]40% of aging-associated population dynamics were sex-dependent, with tens of thousands of peaks altered exclusively in one sex. Together, these findings present a comprehensive framework for how aging reshapes the chromatin landscape and cellular composition across diverse tissues.

genomics↗

bioRxiv2025

EnrichSci: Transcript-guided Targeted Cell Enrichment for Scalable Single-Cell RNA Sequencing

Large-scale single-cell atlas efforts have revealed many aging-or disease-associated cell types, yet these populations are often underrepresented in heterogeneous tissues, limiting detailed molecular and dynamic analyses. To address this, we developed EnrichSci--a highly scalable, microfluidics-free platform that combines Hybridization Chain Reaction RNA FISH with combinatorial indexing to profile single -nucleus transcriptomes of targeted cell types with full gene-body coverage. When applied to profile oligodendrocytes in the aging mouse brain, EnrichSci uncovered aging-associated molecular dynamics across distinct oligodendrocyte subtypes, revealing both shared and subtype-specific gene expression changes. Additionally, we identified aging-associated exon-level signatures that are missed by conventional gene-level analyses, highlighting post-transcriptional regulation as a critical dimension of cell-state dynamics in aging. By coupling transcript-guided enrichment with a scalable sequencing workflow, EnrichSci provides a versatile approach to decode dynamic regulatory landscapes in diverse cell types from complex tissues.

genomics↗

bioRxiv2025

Uncovering Convergent Cell State Dynamics Across Divergent Genetic Perturbations Through Single-Cell High-Content CRISPR Screening

High-throughput genomic studies have uncovered associations between diverse genetic alterations and disease phenotypes; however, elucidating how perturbations in functionally disparate genes give rise to convergent cellular states remains challenging. Here, we present PerturbFate, a high-throughput, cost-effective, combinatorial-indexing single-cell platform that enables systematic interrogation of massively parallel CRISPR perturbations across the full spectrum of gene regulation, from chromatin remodeling and nascent transcription to steady-state transcriptomic phenotypes. Using PerturbFate, we profiled over 300,000 cultured melanoma cells to characterize multi-modal phenotypic and gene regulatory responses to perturbations in more than 140 Vemurafenib resistance-associated genes. We uncovered a shared dedifferentiated cell state marked by convergent transcription factor (TF) activity signatures across diverse genetic perturbations. Combined inhibition of cooperative TF hubs effectively reversed cellular adaptation to Vemurafenib treatment. We further dissected phenotypic responses to perturbations in Mediator Complex components, linking module-specific biochemical properties to convergent gene activations. Together, we reveal common regulatory nodes that drive similar phenotypic outcomes across distinct genetic perturbations. We also delineate how perturbations in functionally unrelated genes reshape cell state. PerturbFate thus establishes a versatile platform for identifying key molecular regulators by anchoring multi-modal regulatory dynamics to disease-relevant phenotypes.

genomics↗

bioRxiv2025

Unique Gluing Effect of ASXL1 K351 Monoubiquitination Stimulates PR-DUB-Mediated Nucleosomal H2AK119Ub Deubiquitination

Protein ubiquitination plays a critical role in regulating fundamental biological processes through both proteolytic and nonproteolytic mechanisms. While classically known for its role in targeting proteins for degradation, ubiquitination can also modulate enzymatic activity. However, all of the known mechanisms of such modulation involve spatially constrained mechanisms that take place near the enzyme-substrate interfaces. Here, we report an unprecedented regulatory paradigm mediated by ubiquitination that is located distal to the enzyme-substrate interface but can still activate the polycomb repressive deubiquitinase (PR-DUB) complex. Using cryo-electron microscopy, molecular dynamics (MD) simulations, hydrogen-deuterium exchange mass spectrometry (HDX-MS), and kinetics assays, we determined that the ASXL1 K351 monoubiquitination promotes PR-DUB-mediated nucleosomal H2AK119Ub deubiquitination by stabilizing the catalytic pocket of PR-DUB, causing significant increase in maximal catalytic velocity (Vmax) but almost no change in the substrate binding affinity (Km). Structural analysis revealed that the ubiquitin moiety at ASXL1 K351 bridges the BAP1 and ASXL1 subunits, acting as an intramolecular "glue" that constrains the conformational dynamics of these subunits without altering the nucleosome binding interface. Further MD and HDX-MS results demonstrated the monoubiquitination of ASXL1 K351 enables PR-DUB to effectively maintain a spatial arrangement of the catalytic conformation that closely aligns with substrate cleavage. This study expands our understanding of the mechanisms of ubiquitin function to include intramolecular fastening with a molecular gluing effect and provides a deeper mechanistic understanding of PR-DUB activation in nucleosomal H2AK119Ub removal.

biochemistry↗

bioRxiv2025

Niche Macrophages Recycle Iron to Tumor Cells and Foster Erythroblast Mimicry to Promote Bone Metastasis and Anemia

Bone marrow is both a primary site for blood cell production and a fertile niche for metastatic cancer cell growth, notably in breast cancer. Although anemia is common among patients with bone metastasis, the mechanistic link between metastatic colonization and disrupted erythropoiesis remains poorly understood. Using in vivo niche labeling and single-cell RNA sequencing, we identified a specialized population of VCAM1+CD163+CCR3+ macrophages enriched in the bone metastatic niche. These macrophages, typically essential for erythropoiesis in healthy bone marrow, are co- opted by tumor cells to support their growth through iron acquisition. The hijacking of these macrophages by tumor cells reduces iron availability for erythroblasts, impairing erythropoiesis and contributing to anemia. With increased iron supply, tumor cells further adapt by mimicking erythroblasts, producing hemoglobin under GATA1 regulation in response to hypoxic stress. Notably, macrophages with similar iron- regulating features were found in human bone metastases across multiple cancer types, and elevated HBB expression in breast cancer correlates with increased risk of bone metastasis. These findings establish iron-recycling macrophages as essential regulators within the metastatic bone niche, revealing novel insights into the interplay between immune modulation, metal metabolism and tumor cell plasticity in driving metastatic progression and anemia.

cancer biology↗

bioRxiv2025

The ISW1 and CHD1 chromatin remodelers suppress global nucleosome dynamics in living yeast cells

The budding yeast genome is globally accessible to DNA methyltransferases in living cells, unlike in isolated nuclei, where it is mostly inaccessible. Here, we assess the roles of the RSC, ISW1 and CHD1 ATP-dependent chromatin remodelers in generating nucleosome dynamics in vivo. We compare DNA methylation rates in wild type cells and chromatin remodeler mutants by normalizing nuclear methylation rates to the non-nucleosomal mitochondrial DNA methylation rate in each strain. Depletion of subunits of the RSC, ISW1 or CHD1 ATP-dependent chromatin remodelers has little effect on normalized methylation rate. A decaying sine wave model used to fit nucleosome phasing data shows that nucleosome dynamics decrease with distance from the promoter in an Isw1/Chd1-dependent manner. Depletion of both Isw1 and Chd1 increases the methylation rate, suggesting that these remodelers act together to suppress nucleosome dynamics. Furthermore, the TFIIIB and TFIIIC transcription factors exhibit differential dynamics at tRNA genes. Our analysis provides insight into nucleosome and transcription factor dynamics in vivo. TeaserThe budding yeast ISW1 and CHD1 ATP-dependent remodelers organize chromatin on genes, slowing nucleosome dynamics in living cells.

genomics↗

bioRxiv2025

Kinocilia of Vestibular Hair Cells: Bridging Structural and Functional Traits of Primary and Motile Cilia

Vestibular hair cells (HCs) convert gravitational and head motion cues into neural signals through mechanotransduction, mediated by the hair bundle--a mechanically integrated organelle composed of stereocilia and a kinocilium. The kinocilium, a specialized form of primary cilium, remains incompletely defined in structure, molecular composition, and function. To elucidate its characteristics, we conducted single-cell RNA sequencing of adult vestibular and cochlear HCs, uncovering a selective enrichment of primary and motile cilia-associated genes in vestibular HCs, particularly those related to the axonemal repeat complex. This enrichment of orthologous axonemal-related genes was conserved in zebrafish and human vestibular HCs, indicating a shared molecular architecture. Immunostaining validated the expression of key motile cilia markers in vestibular kinocilia. Moreover, live imaging of bullfrog and mouse HCs from crista ampullaris revealed spontaneous kinociliary motion. Together, these findings define the kinocilium as a unique organelle with molecular features of primary and motile cilia and suggest its previously unknown role as an active, force-generating element within the hair bundle.

neuroscience↗

bioRxiv2025

HIF-1α/STOML2 mediated PINK1-dependent mitophagy activation against hypoxia-induced neuronal injury

Hypoxia contributes to brain disorders by causing neuronal injury. However, in the early stage of stress, neurons initiate a series of compensatory pathways to resist cell damage, but the underlying mechanisms have not been fully elucidated. In this study, we found that hypoxia transiently activates PTEN-induced kinase 1 (PINK1)-dependent mitophagy in the early stage before cell damage and neurological dysfunction. PINK1 overexpression protects neurons and it knockdown exacerbates neuronal damage, highlighting the key role of PINK1-dependent mitophagy in hypoxic adaptation. Mechanistically, hypoxia promotes HIF-1 nuclear translocation, inducing transcription of stomatin like 2 (STOML2). STOML2 relocates to the mitochondrial membrane, aiding phosphoglycerate mutase 5 (PGAM5) cleavage, which triggers PINK1-dependent mitophagy. Silencing HIF-1, STOML2, or PGAM5 inhibits PINK1-dependent mitophagy and worsens neurological function under hypoxia. Notably, intermittent hypoxia, a hypoxic conditioning strategy for improving hypoxic tolerance, enhances PINK1-dependent mitophagy by activating HIF-1/STOML2 axis, and protects neurons against hypoxia. In conclusion, our study reveals a new "self-protection" mechanism of neurons against hypoxic stress and discovers that intermittent hypoxia is a potential therapeutic strategy against hypoxia-induced injury.

neuroscience↗