Biology subjects

Qiu, T.

Publications and source records attributed to Qiu, T..

At least 19 recordsLinked to original sources

bioRxiv2026

Maternal E-cigarette Exposure Augments Murine Abdominal Aortic Aneurysm

Background: Smoking and family history are major risk factors for abdominal aortic aneurysm (AAA). Smoking and nicotine are modulators of DNA methylation, capable of causing heritable epigenetic alterations. Nicotine infusion and e-cigarette (e-cig) vaping augment murine AAA. We investigated the effects of murine maternal e-cig vaping on offspring experimental AAA, and impacts on transgenerational DNA methylation and accessibility. Methods: We performed perinatal e-cig nicotine vaping in two strains of adult female mice (ApoE-/- and C57BL/6J). Mice were mated to control males, and treated through gestation. A parallel group were instead sacrificed after treatment, for DNA analysis. Offspring were aged to adulthood, and AAAs were then induced by elastase (C57BL/6J) or angiotensin-II infusion (ApoE-/-), and ultrasound-tracked for 4 weeks. In a second cohort, parental and offspring aortic tissue and blood DNA underwent RRBS and ATAC-seq analysis respectively. Offspring abdominal aortic anatomy was examined, and stiffness was assessed with ex vivo arterial myography. Results: Maternal e-cig exposure increased offspring AAA growth in both models and genders. AAA incidence was increased in ApoE-/- males, and observed effects were overall more pronounced in males. Maternal vape exposure altered aortic DNA methylation and blood DNA accessibility in mothers and offspring, with differential sites in numerous genes identified, including AAA-related genes and pathways. Pathways were enriched for transcription factors, inflammation/immune-related genes, and angiogenesis genes, with similar changes identified in exposed mothers. Male offspring displayed more differential genes. Significant changes were located in genes known to harbor AAA risk loci in humans, and overlapped with published epigenetic alterations in human smokers. Differences also occurred in offspring aortic structure and stiffness. Conclusions: Maternal e-cig nicotine exposure augments AAA growth in multiple models across generations. These effects are accompanied by broad epigenetic DNA reprogramming of key AAA modulator genes and pathways.

genomics↗

bioRxiv2026

Establishment of Rabbit Formative-like Pluripotent Cells by Bidirectional Modulation of WNT Signaling Pathway

The generation of embryonic stem cells (ESCs) with full developmental capacity and robust chimera-forming potential remains a major bottleneck for most non-rodent mammalian species including rabbits, an important animal both for biomedicine and agriculture. Formative pluripotency is a unique intermediate state bridging the naive and primed pluripotent states, which is defined by distinct molecular signatures, intrinsic competence for primordial germ cell (PGC) specification, and unique developmental adaptability to early embryonic microenvironments. Here, we established a novel culture medium termed KFiC, which could bidirectionally and coordinately modulate the WNT/{beta}-catenin signaling pathway via combined treatment of WNT activator CHIR99021 and inhibitor IWR-1. The KFiC culture system enables efficient derivation and stable long-term self-renewal of rbESCs with consistent formative-like pluripotent characteristics. KFiC-cultured rbESCs (KFiC-rbESCs) form compact, undifferentiated colonies, maintain intact genomic stability, and recapitulate the transcriptional landscape of pre-implantation epiblast cells, accompanied by sustained high expression of the core formative pluripotency marker OTX2. Functionally, KFiC-rbESCs possess efficient PGC differentiation competence and extensively contribute to embryonic development after microinjection into rabbit morulae, displaying their superior developmental plasticity. Notably, the KFiC system can stabilize an intermediate formative-like pluripotent state in mouse, human, and porcine pluripotent stem cells, and KFiC-adapted mouse ESCs retain potent chimera-forming ability. Collectively, this study establishes a reliable culture platform for generating and maintaining formative-like rbESCs. This cross-species compatible system provides a promising foundation for further optimizing naive-level pluripotency in rbESCs and facilitates the generation of genetically engineered rabbit disease models.

developmental biology↗

bioRxiv2026

A direct RNA sequencing workflow for simultaneous profiling of tRNA abundance and modifications in mouse liver

Transfer RNA (tRNA) is highly modified and difficult to profile using reverse-transcription-based sequencing. Here, we established a direct RNA sequencing (tRNA-DRS) workflow to simultaneously characterize tRNA abundance and modification signals in mouse liver. The workflow included small-RNA enrichment, deacylation, splint-adapter ligation, barcoding, reverse transcription, and nanopore sequencing on PromethION with modification-aware basecalling. From 1,678,666 raw reads, 1,421,279 (84.67%) reads were retained after 20-200 nt length filtering, and 17,094 uniquely mapped reads (MAPQ [≥] 10) were obtained. These reads covered 244 tRNA genes and represented all 23 tRNA isotypes. tRNA abundance was strongly skewed, with Asp, Gly, Ser, and Lys accounting for 56.6% of uniquely mapped reads. Read-body coverage indicated that most uniquely mapped reads spanned substantial portions of tRNA molecules (mean 71.1%, median 75.9%; 83.3% reads covering [≥]50% of the reference). Modification analysis identified 41,013 candidate sites, of which 711 passed stringent filtering (modification fraction [≥]50%, coverage [≥]5), spanning eight modification types and dominated by pseudouridine and m5C. Filtered sites showed position-specific clustering and isotype-dependent patterns. Together, these results support tRNA-DRS as a practical single-assay framework for simultaneous tRNA expression and epitranscriptomic profiling in mammalian tissue.

molecular biology↗

bioRxiv2026

EvSpark: Lossless Speculative Decoding for Hybrid DNA Foundation Models

Hybrid DNA foundation models combine convolutional, recurrent, and attention layers, making speculative decoding more difficult than truncating a KV cache. We present EvSpark, a speculative decoding system for Evo2 that verifies draft blocks in parallel and restores all three classes of inference state by selecting retained intermediate states, without replay. A compact, hidden-state-conditioned drafter proposes each block in one parallel forward pass. On Evo2 7B, a 48-prompt benchmark with three training seeds yields 2.96x on 43 real-sequence prompts and 3.27x including the five synthetic controls. Acceleration persists at 262k-token context (1.84x - 2.43x on two bacterial genomes) and over 32k generated tokens. Retraining the same drafter architecture for Evo2 20B and 40B yields 2.18x - 2.46x on real sequences and 2.51x - 2.78x on the full suite. Autoregressive drafter comparisons and batch measurements show why low draft latency, rather than acceptance alone, determines the gain. The method preserves the target distribution in exact arithmetic. In bf16, greedy tests find no non-tie divergences across 48 prompts and six checkpoints; sampling tests expose residual numerical sensitivity, especially in repetitive sequences. A cost-efficient 7B drafter requires 1.06 incremental GPU-hours of training, excluding teacher-data collection, and achieves 2.82x on real sequences. In regulatory-DNA design, EvSpark achieves a median complete-workflow speedup of 1.57x over a calibrated batched native baseline.

bioinformatics↗

bioRxiv2026

Effects of Mechanical Loading on Cranial Joint Mesenchymal Stem Cell Proliferation

Sutures are the primary sites of cranial bone growth, allowing the skull to accommodate the growing brain. External mechanical stimulus has been shown to delay suture fusion and induce tissue remodelling. Recent studies suggest that in vivo cyclic bone loading increased proliferation of mesenchymal stem cells (MSC) in the coronal suture. The overall aim of this study was to understand how many loading sessions (exposure-response) and how long after loading (time-course) did MSC proliferation increase in the coronal suture. In the exposure-response analysis, mice underwent 1, 3, or 5 loading sessions between Postnatal day 7 (P7) and P11, and in the time-course analysis, treated mice underwent 10 loading sessions between P7 and P21. Loading sessions were 10 minutes at a frequency of 1 Hz and a force of 10 g (0.1 N). The loading tip was positioned on the posterior aspect of the left frontal bone, dorsal to the coronal suture. The EdU marker shows a statistically significant increase in proliferation after one loading session and a decrease after three loading sessions. The PCNA marker shows a statistically significant increase after three and five loading sessions. The exposure-response analysis showed that when the results of both markers are combined, levels of proliferation cannot be interpreted until at least five loading sessions have been completed, after which a clear increase in proliferation was observed. In the time-course analysis, proliferation was highest immediately after the final treatment session and 24 hours after the final loading session the effects of mechanical bone loading gradually returned to baseline.

Developmental Biology↗

bioRxiv2026

On-slide Preparation of Caenorhabditis elegans Towards Quantitative, High-Resolution LA-ICP-TOF Mass Spectrometry Imaging

Metal homeostasis is a complex process wherein essential metals serving structural, catalytic and regulatory roles are acquired, trafficked, and exported once they are present in excess. Understanding changes in metal content and localization in heterogenous tissue types is critical to understanding fundamental physiology as well as a growing number of disease states. Laser ablation inductively coupled plasma time-of-flight mass spectrometry (LA-ICP-TOF-MS) imaging is a powerful technique for untargeted quantitation and mapping of metals in biological systems. While the nematode Caenorhabditis elegans (C. elegans) is a well-established model organism for fundamental biological research and metal-based diseases, there have been few reports of mass spectrometry-based imaging of C. elegans, mostly due to challenges preparing samples that maintain the native distribution of the elements. In this study, we developed an embedding, quantitation and imaging workflow that preserves C. elegans using 3D-printed uniform layer media application tools (ULMATs). Multiple embedding media were evaluated, and petrolatum, commercially known as Vaseline, stood out for its performance in preserving C. elegans for imaging applications. Worms were subjected to microscopy and LA-ICP-TOF-MS imaging where we achieved a 2-m spatial resolution by over-sampling laser shots during ablation. Quantitative elemental maps were obtained using a series of gelatin standards that were sectioned at a 40-m thickness to closely mimic the average tissue ablation depth of a Day 1 gravid adult C. elegans. Our results establish a new workflow for comprehensive elemental profiling of C. elegans using LA-ICP-TOF-MS, which holds high potential for future spatial metal biology research with C. elegans. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/698490v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@7c66c5org.highwire.dtl.DTLVardef@13f4934org.highwire.dtl.DTLVardef@1df3215org.highwire.dtl.DTLVardef@512fd2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Identification of Novel Extracellular Vesicles Scaffold Proteins for Versatile Cargo Engineering

Extracellular vesicles (EVs) are promising drug delivery platforms that have been engineered to carry various drug modalities. Key strategies for generating those therapeutic EVs involve the direct fusion of protein of interest (POI) to EVs scaffold proteins with inherently high EVs-sorting ability. In this work, we identified raftlin (RFTN1) and poliovirus receptor (PVR) as novel EVs scaffold proteins for loading EVs lumen and surface cargos respectively. Truncation studies revealed that the N-terminus 15 residues from RFTN1 (RFTN1-N15) were sufficient for EVs engineering, as demonstrated by distinct cargos including gene editing tools, cytosolic enzymes as well as type II transmembrane proteins. On the other hand, PVR efficiently displayed secreted proteins including antibodies and serum albumins on EVs surface. Critically, RFTN1 and PVR-engineered EVs demonstrated consistent and efficient cargo delivery in vivo. In summary, the discovery of RFTN1 and PVR can potentially benefit EVs engineering for both fundamental research and clinical translation in the future.

bioengineering↗

bioRxiv2025

Splitting Hairs: Optimized Sample Preparation Strategy for Mass Spectrometry Imaging of Nematode Caenorhabditis elegans

Caenorhabditis elegans is a powerful model organism for studying development, neurobiology, aging, and toxicology, yet most investigations rely on genetic and phenotypic measurements that do not directly capture their biochemical landscape. Mass spectrometry (MS)-based metabolomics has begun to address this gap by enabling detection of small-molecule metabolites and lipids. However, conventional liquid or gas chromatography-MS approaches require homogenization of whole worms, eliminating spatial information. Mass spectrometry imaging (MSI) offers an avenue for visualizing metabolite distributions in situ, but its application to C. elegans is hindered by the nematodes small size and thick cuticle which make it challenging for structure preservation during cryo-sectioning and ion image interpretation. We develop an integrated sample preparation workflow to overcome these challenges and enable high-resolution MSI of C. elegans adult hermaphrodites. To facilitate anatomical and ion images interpretation, we employed a dual-fluorescent reporter strain expressing GFP in intestinal cells and RFP in neuronal nuclei. We optimized embedding media compositions and freezing strategies to preserve tissue architecture and genetically encoded reporter fluorescence during cryo-sectioning. Additionally, we implemented a simple "sandwiching" method that reproducibly orients worms, allowing consistent longitudinal sectioning. Using this optimized workflow, we achieved matrix-assisted laser desorption/ionization (MALDI) MSI of 10-m spatial resolution and demonstrated tissue-specific distributions of lipids and metabolites in adult hermaphrodites. With structural preservation, consistent orientation, and fluorescence-guided spatial annotation, our approach provides a foundation for investigating metabolic heterogeneity in C. elegans and can be adapted to other microscale biological systems for MSI applications.

biochemistry↗

bioRxiv2025

Derivation, Characterizations, and Applications of Rabbit Haploid Embryonic Stem Cells

Haploid embryonic stem cells (haESCs), which contain a single set of chromosomes, provide powerful systems for investigating gene function and creating gene-edited animal models. haESCs have been derived from several mammalian species including human, mouse and rats, yet not from rabbits. Here, we report the derivation of parthenogenetic haESCs of rabbit (rbPhESCs) using an optimized culture medium. These cells maintain a stable haploid karyotype during long-term culture and own pluripotency features comparable to diploid embryonic stem cells derived from rabbit fertilized embryos. By integrating gene trapping cassette into ROSA26 locus, rbPhESCs offer an ideal platform for high-throughput functional genomic screening, as shown in haESCs from other mammals. Consistent with their parthenogenetic origin, rbPhESCs durably preserve maternal-specific imprinting patterns even after extended culture in serum-containing conditions, providing a valuable platform for generating disease models deficient in maternally expressed imprinted genes. Therefore, our findings expand the repertoire of mammalian haESCs and establish rbPhESCs as a valuable platform for genetic studies and biotechnological applications in rabbits.

cell biology↗

bioRxiv2025

Design and Development of DNA Damage Chemical Inducers of Proximity (DD-CIP) for Targeted Cancer Therapy

Many chemotherapies are effective against cancers that display high levels of genome instability by disrupting or overwhelming the DNA damage response to induce cell death. PARP inhibitors (PARPi) exploit this vulnerability by stalling DNA repair particularly in homologous recombination (HR)-deficient cancer cells. Although PARPi are now used to treat BRCA1/2-mutated cancers such as ovarian and breast cancers, they are still limited to a narrow range of clinical indications and are susceptible to acquired resistance. Here, we introduce "DNA Damage Chemical Inducers of Proximity" (DD-CIPs), bivalent molecules that rewire the mechanism of action of conventional PARPi. The DD-CIPs function through chemical induced proximity between PARP1/2 and the chromatin remodeling protein, BRD4. From a candidate library of DD-CIPs, we identified DD-CIP1 which induces the DNA damage response (DDR) and apoptosis to a range of cancer lines at two-digit nanomolar concentrations. Further optimization yielded DD-CIP2, which induces tumor cell death at nanomolar concentrations across diverse blood and solid cancer cells, including cancer types that are insensitive to PARPi. Using small-cell lung cancer (SCLC) as a model, we found that DD-CIP2 triggers DDR, cell cycle arrest, and apoptosis in vitro, leading to anti-tumor efficacy without substantial toxicity in preclinical SCLC xenograft models at well tolerated doses. Our findings demonstrate that DD-CIPs may provide an opportunity to address the limitations of traditional PARPi and establish chemical induced proximity as a strategy for modulating the DDR in cancer.

cancer biology↗

bioRxiv2025

Isomer-specific distribution of perfluorooctane sulfonate (PFOS) in hepatic zonation in mouse

Per- and polyfluoroalkyl substances (PFAS) are a class of emerging contaminants that are widely distributed and persistent in the environment, accumulated in biological organisms and associated with adverse health outcomes. Evidence has shown a wide existence of branched PFAS isomers from source to applications. Notably, linear and branched isomeric PFAS structures are associated with differential toxicity outcomes and health effects. Herein, we investigated distribution of perfluorooctane sulfonate (PFOS) isomers in mouse liver tissue after exposure using matrix-assisted laser desorption/ionization-trapped ion mobility spectrometry-mass spectrometry imaging (MALDI-TIMS-MSI). Mice were treated with vehicle control or commercially sourced PFOS, a mixture of linear and branched isomers, at concentrations to achieve doses of 0.1 and 1 mg/kg/day for 84 days. Liver tissues were collected, followed by sample preparation and MALDI-TIMS-MSI analysis. Using a TIMS ramp time of 150 ms, we successfully separated linear and branched isomers on-tissue. Coupling with post-MALDI immunofluorescence imaging of canonical zonation markers, we discovered hepatic zonation-specific distribution for linear isomer but more homogenous distribution of branched PFOS. Dual-polarity MSI was performed on the same tissue for hepatic metabolites and lipids, and results showed concomitant alteration of liver lipid zonation upon PFOS exposure. With MALDI-TIMS-MSI, our results for the first time demonstrated on-tissue differentiation of PFOS isomers. Multi-modal imaging revealed isomer-specific PFOS distribution and spatial lipidomic changes, both mapped to canonical hepatic zonation markers, to reveal zone-selective PFOS toxicokinetics/toxicodynamics. Together our results demonstrate the critical need for further investigating isomer-specific PFAS toxicity.

pharmacology and toxicology↗

bioRxiv2025

Development of Degraders and 2-pyridinecarboxyaldehyde (2-PCA) as a recruitment Ligand for FBXO22

Targeted protein degradation (TPD) is a promising therapeutic strategy that requires the discovery of small molecules that induce proximity between E3 ubiquitin ligases and proteins of interest. FBXO22 is an E3 ligase that is overexpressed in many cancers and implicated in tumorigenesis. While FBXO22 was previously identified as capable of recognizing ligands bearing a primary amine degron, further investigation and development of recruitment ligands is required to enable its broader utility for TPD. Here, we describe the discovery of chemical probes that can either selectively degrade FBXO22 or recruit this ligase for TPD applications. First, we describe AHPC(Me)-C6-NH2 as a potent and selective FBXO22 degrader (DC50 = 77 nM, Dmax = 99%) that is suitable for interrogating the effects of FBXO22 loss of function. Further, we discovered that the simple hexane-1,6-diamine acts as a minimal FBXO22 self-degrader, whereas shorter C4 (putrescine) to C5 (cadaverine) analogs, found in mammalian cells, do not induce degradation. Finally, we found that 2-pyridinecarboxaldehyde (2-PCA) functions as a novel electrophilic degron capable of forming a reversible thioketal with cysteine 326 for recruiting FBXO22. Conjugating 2-PCA to various ligands successfully induced FBXO22-dependent degradation of BRD4 and CDK12. Collectively, these chemical probes will facilitate the study of FBXO22 biology and broaden its applicability in TPD.

biochemistry↗

bioRxiv2025

FEDRANN: effective overlap graph construction based on dimensionality reduction and approximate nearest neighbors

Overlap detection is a key step in de novo genome assembly pipelines based on the Overlap-Layout-Consensus (OLC) paradigm. However, existing methods for overlap detection either rely on heuristic seed-and-extension strategies or locality-sensitive hashing (LSH), both of which struggle to handle repetitive genomic regions and the computational burden of large-scale datasets. Here, we present FEDRANN, a novel strategy for overlap graph construction that integrates feature extraction, dimensionality reduction (DR), and approximate nearest neighbor (ANN) search. We find the pipeline combining inverse document frequency (IDF) transformation, sparse random projection (SRP), and NNDescent enables accurate detection of overlaps across diverse datasets. We developed an efficient open-source implementation of this pipeline named Fedrann (https://github.com/jzhang-dev/fedrann). Through systematic benchmarking on real long-read sequencing data, we demonstrate that Fedrann produces overlap graphs comparable to or better than those generated by existing state-of-the-art tools, including MECAT2, minimap2, and wtdbg2, while maintaining competitive runtime. Despite being implemented primarily in Python, Fedrann achieves performance on par with tools written in compiled languages, owing to matrix-based representations and C-accelerated numerical libraries. Our results suggest that DR and ANN techniques offer a promising new direction for scalable and accurate overlap detection in long-read assembly and broader sequence similarity search tasks.

bioinformatics↗

bioRxiv2025

Revealing Spatial Heterogeneity across the Gut Tissue-Lumen Interface through MALDI Mass Spectrometry Imaging

AbstractMetabolites play critical roles in modulating gut-microbe interactions and are closely related to health and disease consequences. One critical aspect of the gut-microbe interactions is spatial heterogeneity, particularly at the interface space between gut tissue and luminal contents, where a unique microhabitat of diverse microbial functions encounters the host tissues. Exploring the spatial heterogeneity of this interface enables insights into these gut-microbe interactions. Previous studies commonly investigated metabolome through tissue homogenization and bulk analysis, but these methods result in the loss of spatial information. In this project, we use high-resolution matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI) approaches to reveal the chemical spatial heterogeneity of colon tissue, luminal contents, and the tissue-lumen interface across multiple colonic regions. We applied a swiping technique to aid the preservation of luminal content integrity and used two MALDI matrices to cover a wide range of metabolites. The MALDI-MSI analyses revealed distinct patterns of metabolite spatial localization across the gut tissue-lumen interfaces, amongst which the interface-enriched features are of particular interest due to their possibly connection to the gut-microbe interactions. Overall, the rich spatial heterogeneity of metabolomic profiles across the gut tissue-lumen interfaces highlight the molecular participants in host-microbe interactions, providing new opportunities for examining host-microbiome-metabolome dynamics.

biochemistry↗

bioRxiv2025

Cholinergic synaptic plasticity shapes resilience and vulnerability to tau

Synaptic dysfunction is a hallmark of Alzheimers disease (AD). Yet due to their plasticity, synapses may also adapt to early AD pathology. Here, we demonstrate that cholinergic neurons mount a presynaptic response to tau pathology in the living human brain. Using multi-tracer positron emission tomography in cognitively normal older adults at risk for AD, we observe that cholinergic neurons increase presynaptic vesicular acetylcholine transporter (VAChT) protein levels when colocalized to tau, but not amyloid. Notably, stronger VAChT responses were associated with cognitive resilience over a decade. Whole-brain single-nucleus RNA sequencing in human and mouse tissue reveal that cholinergic neurons are enriched for a plasticity gene-network anchored to the microtubule-associated protein tau (MAPT) gene. In mice, forebrain-specific deletion of VAChT impairs cortical plasticity and hippocampal structural integrity. Overall, our findings identify cholinergic synaptic plasticity, and its failure, as a fundamental mechanism of resilience and vulnerability to tau in presymptomatic AD.

neuroscience↗

bioRxiv2025

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

bioRxiv2025

Dynamics of biofilm-forming Bacillus subtilis in Caenorhabditis elegans gut

Biofilm-forming Bacillus subtilis strain NCIB3610 has been reported to show biofilm-mediated beneficial effects when fed to Caenorhabditis elegans, including enhanced stress resistance, extended lifespan, and protection against neurotoxic agents. However, biofilm-forming B. subtilis presents multiple cell types, and thus a thorough characterization of B. subtilis cell dynamics in the C. elegans gut in vivo is necessary to understand mechanisms of the biofilm-mediated beneficial effects. In this study, we utilized an isogenic NCIB3610 strain expressing a biofilm reporter PtapA-mKate2 to monitor matrix-producing components in C. elegans gut. Interestingly, our results revealed that in live C. elegans gut, no B. subtilis biofilms were formed but only free spores and diffused fluorescence, which were likely from dietary matrix-producing cells crushed by the pharynx. Additional data showed that spores can geminate into motile cells but not matrix-producing cells in living C. elegans gut. Biofilm formation was found in gut after C. elegans death, indicating that mechanistically, life-dependent functions of the worm inhibit the formation of matrix-producing cells in gut. These findings resolved a key piece of puzzle in understanding the fundamental mechanisms of C. elegans-B. subtilis interaction and highlighted the importance of characterizing cell dynamics in vivo in host-microbe interaction research.

physiology↗

bioRxiv2025

Investigating the genomic landscape of mouse models of breast cancer metastasis

Metastasis remains a major cause of cancer mortality. AbstractThis study, expanding upon previous findings in the MMTV-PyMT model, investigated four independent mouse models, representing luminal (MMTV-PyMT, MMTV-Myc), HER2-amplified (MMTV-Her2) and triple negative (C3(1)TAg) breast cancer subtypes. Consistent with previous results, limited evidence for metastasis-associated somatic point mutations was found for all models. We also found that oncogenic drivers significantly influenced the number and size of metastasis-specific copy number variations (MSCNVs), but common driver-independent MSCNVs were rare. Furthermore, analyzing a cohort with varying genetic backgrounds while maintaining a constant oncogenic driver (PyMT) revealed that genetic background profoundly impacts MSCNVs. Transcriptome analysis demonstrated that oncogenic drivers strongly shaped metastasis-specific gene expression (MSGE), with each driver exhibiting distinct expression profiles. In contrast, MSGE in the PyMT-F1 cohort was more variable across strains. Despite the diversity of MSCNV and MSGE, functional analysis revealed that both mechanisms converge on the modulation of key cellular processes, including immune responses, metabolism, and extracellular matrix interactions. These findings emphasize the complex interplay between oncogenic drivers and genetic background in shaping the genomic and transcriptional landscapes of metastatic lesions.

cancer biology↗