Biology subjects

Zhang, F.

Publications and source records attributed to Zhang, F..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Palbociclib CDK4/6- and Crizotinib MET/ALK/ROS1-inhibitors Synergize to Enhance Senescence and Immune Recognition in Melanoma Cells Independently of BRAF/NRAS Status

"Pro-senescence therapy", which triggers both permanent cell cycle arrest and an immune response, has been proposed as a strategy for cancer treatment, but is still controversial. To assess this strategy in melanoma, we performed a high throughput microscopy-based senescence screen utilizing a panel of melanoma cell lines with different driver mutations and a collection of clinical and experimental drugs. We found that vemurafenib and trametinib, which inhibit BRAFV600E and MEK1/2, respectively, induced senescence in some but not all BRAF-mutant cell lines. In contrast, palbociclib, BKM-120 and crizotinib, which inhibit CDK4/6, PI3K, and MET/ALK/ROS1, respectively, triggered senescence in most cell lines, irrespective of BRAF/NRAS mutation status, and overcame intrinsic and acquired vemurafenib resistance. The combination of palbociclib and crizotinib synergized to further enhance the senescence response in all cell lines irrespective of BRAF/NRAS mutation status, increased the expression of SASP factors, such as IL-1 and {beta}, and HLA class I and other markers for recognition by NK and T cells. Further, this combination caused a significant increase in CD8+ T cells and pro-inflammatory macrophages in the tumor microenvironment and a marked reduction of mouse melanoma tumor growth that was dependent on CD8+ T cells, suggesting increased immune surveillance. Our findings suggest that pro-senescence therapy based on concomitant inhibition of both CDK4/6 and MET/ALK/ROS1 could be developed further as an alternative treatment strategy for melanoma. Significance: Pro-senescence therapy based on combined targeting of CDK4/6 with palbociclib and MET/ALK/ROS1 with crizotinib inhibits melanoma tumor growth through anti-tumor immune response activation, providing an alternative treatment strategy for melanoma.

cancer biology↗

bioRxiv2025

Tissue architecture dynamics underlying immune development and decline in the thymus

The age-associated decline in adaptive immune function, widely observed in vertebrates, has been attributed to thymic involution. To gain insights into the structural and transcriptional changes underlying this phenomenon, we employed high-resolution spatial transcriptomics and T-cell receptor (TCR) sequencing in mice. By analyzing 21 thymus samples spanning mouse lifespan, we uncovered significant alterations in thymic organization, including disrupted T cell development and the emergence of B cell aggregates. We also observed age- related changes in cell-cell interactions, marked by increased antigen-presenting cell presence in thymic medullary regions and a shift from inflammatory to suppressive macrophages, fostering an immunosuppressive niche. Furthermore, aged thymus tissues exhibited an abundance of regions with reduced TCR diversity, accompanied by distinct changes to gene expression profiles. Our study establishes a valuable reference for understanding aging-related alterations in adaptive immunity, revealing mechanisms underlying age-induced immunological decline.

immunology↗

bioRxiv2025

Simulation and experimental study on the strategy of soil auxiliary heating in a solar greenhouse in northeast China

When solar greenhouses in north eastern China experience extreme weather, the internal soil requires varying auxiliary heating to ensure the normal growth of crops. In this study, considering the effects of four kinds of extreme weather on solar greenhouses, four different types of heating requirements were obtained through experiences in a Liaoshen-type solar greenhouse. Four distinct heating strategies were simulated using a soil temperature prediction model. The initial temperatures for these strategies were 13{degrees}C, 11{degrees}C, 13{degrees}C, and 14{degrees}C, respectively, while the target temperature was uniformly set at 15{degrees}C. The heating durations for the respective strategies were 432,000 seconds, 432,000 seconds, 864,000 seconds, and 1,728,000 seconds. To ensure a minimum soil temperature of 15{degrees}C within the solar greenhouse, the temperature of the heating layer located 400 mm underground needed to be maintained at or above 20{degrees}C, 28{degrees}C, 18{degrees}C, and 19{degrees}C, respectively. The simulation results were validated through experimental verification, with maximum and minimum errors of 3.1% and 0.5%, respectively. Several targeted promotional suggestions were also proposed. The model exhibited high accuracy and is capable of developing optimal and precise soil heating strategies for various types of solar greenhouses in north eastern China.

plant biology↗

bioRxiv2025

Inactivating a β1 subunit of SnRK1 promotes broad-spectrum disease resistance in rice

Rice is a staple crop for over half of the worlds population, and its sustainable production is vital to ensure global food security. However, rice is highly susceptible to several devastating fungal diseases1, including blast disease caused by Magnaporthe oryzae, sheath blight by Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by Bipolaris oryzae, bakanae by Fusarium fujikuroi, and head blight by F. graminearum. The mechanisms underlying the susceptibility of rice to these fungal diseases remain unclear. Here, we report that the {beta} subunit of SnRK1, SnRK1{beta}1A, confers broad-spectrum susceptibility to these fungal diseases. Our findings reveal that diverse rice fungal pathogens have convergently evolved an effector, Gas2, which interacts with SnRK1{beta}1A to prevent its ubiquitination-mediated degradation and promotes its nuclear translocation. While SnRK1{beta}1A is expressed at low levels in healthy plants, its expression is markedly induced upon fungal infections, facilitating susceptibility by inhibiting SnRK11, the subunit of SnRK1, whose overexpression has been shown to enhance broad-spectrum resistance in rice2. Notably, rice lines with disrupted SnRK1{beta}1A are resistant to multiple fungal diseases without compromising growth and yield in the field. Together, this study demonstrates that broad-spectrum disease resistance in crops can be achieved by disrupting inducible susceptibility genes whose encoded proteins are targeted by effectors conserved in multiple pathogens.

plant biology↗

bioRxiv2025

Chromosomal-level genome of the Pinus massoniana 'Minlin WY36'

Owing to conifers complex and large genomes, it is challenging to construct a comprehensive reference genome and conduct evolutionary and genomic research. Here, we present the chromosome-level assembly of Pinus massoniana Minlin WY36, a pioneering conifer species used for afforestation, timber production, and oleoresin extraction. The genome size was determined to be 23.41 Gb, with a contig N50 value of 1.15 Mb and a scaffold N50 value of 2.02 Gb. A total of 23.16 Gb of reads (98.93% of the assembled genome) were anchored and oriented onto 12 pseudochromosomes, with chromosome lengths from 1.47 to 2.29 Gb. A total of 32,144 protein-coding genes were predicted, of which 27,173 (84.54%) were functionally annotated. The P. massoniana Minlin WY36 genome consists of 79.41% (18.57 Gb) repetitive sequences, among which long terminal repeat sequences (LTR) were the most abundant. Through comparative genomic analysis, we found that the unique and significantly expanded genes in P. massoniana Minlin WY36 were enriched in the metabolism related to resin synthesis. This study offers valuable insights into conifer evolution and contributes resources for further investigations of conifer adaptation and developmental processes.

genomics↗

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

Preparation of Scutellariae Radix and Corn-Soy Peptides Complex and Its Hepatoprotective Mechanisms

Amidst the growing global burden of alcohol-associated liver disease (ALD) and the limited clinical interventions, this study innovatively developed a complex of Scutellariae Radix and corn-soy composite peptides (SR-CP). SR-CP exhibited significantly enhanced bioaccessible antioxidant capacity, demonstrating a 0.84-2.89-fold increase in DPPH, ABTS, {middle dot}OH, O2-{middle dot}, and FRAP value versus individual components post-gastrointestinal digestion. In ethanol-injured BRL-3A hepatocytes, SR-CP (60 g/mL) significantly ameliorated cellular viability by 38.28% (vs. ethanol model), normalized ALT/AST leakage by 19.92%/87.35%, restored SOD/GSH antioxidant reserves to 24.74 {+/-} 1.71 U/mg prot and 55.35 {+/-} 1.64 mol/g prot respectively, while suppressing lipid peroxidation through 65.93% reduction in MDA production (vs. ethanol model). Mechanistic profiling revealed dual regulatory effects: 1) Inhibiting CYP2E1/NADPH-OX ({downarrow} 51.97%/80.52%) to prevent excessive ROS production and activating the AMPK/SIRT1 axis ({uparrow} 30.70%/6.99%); 2) Potentiation of Nrf2 nuclear translocation ({uparrow} 0.48-fold) and HO-1 induction ({uparrow} 1.63-fold) through AMPK-mediated antioxidant signaling. The superior hepatoprotection of SR-CP over single constituents establishes a novel paradigm for functional food development, bridging traditional herbal wisdom with molecular-targeted ALD intervention via the AMPK/Nrf2/HO-1 axis.

pharmacology and toxicology↗

bioRxiv2025

GABA-independent activation of GABAB receptor by mechanical forces

The heterodimeric GABAB receptor, composed of GB1 and GB2 subunits, is a metabotropic G protein-coupled receptor (GPCR) activated by the neurotransmitter GABA. GABA binds to the extracellular domain of GB1 to activate G proteins through GB2. Here we show that GABAB receptors can be activated by mechanical forces, such as traction force and shear stress, in a GABA-independent manner. This GABA-independent mechano-activation of GABAB receptor is mediated by a direct interaction between integrins and the extracellular domain of GB1, indicating that GABAB receptor and integrin form a novel type of mechano-transduction complex. Mechanistically, shear stress promotes the binding of integrin to GB1 and induces an allosteric re-arrangement of GABAB receptor transmembrane domains towards an active conformation, culminating in receptor activation. Furthermore, we demonstrate that shear stress-induced GABAB receptor activation plays a crucial role in astrocyte remodeling. These findings reveal a previously unrecognized function of GABAB receptor in mechano-transduction, uncovering a novel ligand-independent activation mechanism for GPCRs.

neuroscience↗

bioRxiv2025

Multimodal Validation of the Existence of Transitional Cerebellar Progenitors in the Human Fetal Cerebellum

The developing human cerebellum comprises a series of transient progenitor states that are essential for generating diverse neural subtypes, yet the identity and validation of intermediate cell populations bridging stem-like and lineage-committed neuronal precursors remain limited. In our previous single-cell transcriptomic study, we identified a distinct transitional cerebellar progenitor (TCP) population enriched in specific progenitor zones such as the rhombic lip during human fetal cerebellar development. To address the concerns raised in the Matters Arising regarding the existence of the TCP cells, we provide additional multimodal validations of this population. Rigorous reanalysis of our single-cell transcriptomic data, applying stringent quality control measures, validated the quality of TCP cells and their classification as a transcriptionally distinct population. Multiple orthogonal validations of TCP signature genes (SOX11 and HNRNPH1) using RNAscope in situ hybridization, Xenium-based spatial transcriptomics, and immunohistochemistry on additional fetal cerebellar samples across different stages demonstrated the consistent presence of TCPs in the rhombic lip, transitioning from PRTG+ stem-like zones in the ventricular zone at early developmental stages to the subventricular zone overlapping with EOMES+ unipolar brush cell precursors at later stages. TCP-like populations were also independently identified in two fetal cerebellar single-nucleus transcriptomic atlases, and their gene signature was enriched in a cell population associated with aggressive medulloblastomas. Collectively, these multimodal validations confirm the existence of a transitional progenitor population in the human fetal cerebellum, with implications for cerebellar lineage progression and medulloblastoma origin.

developmental biology↗

bioRxiv2025

Source tracking of larval bacterial community of Pacific white shrimp across the developmental cycle: ecological insights for microbial management and pathogen prevention in larviculture

Health of postlarvae (as products of larviculture) of Pacific white shrimp (Penaeus vannamei) is critical to subsequent culture. Larval microbiota establishment has potential long-term impact on host health, but bacterial sources of larval shrimps remain largely unexplored. We investigated the larviculture cycles of two shrimp strains by utilizing 16S rRNA gene sequencing alongside mainstream microbial source-tracking tools. Our goal was to evaluate the contributions of environmental elements, feeds, and internal succession to larval bacterial community. Regardless of shrimp strains or tools, the mouth opening marked a pivotal shift in bacterial source composition of larvae, with a notable contribution from the rearing water at the beginning of mouth opening, followed by enhanced internal succession, emphasizing the critical role of early microbiota establishment. Notably, the dominance of external sources at zoea II highlights the necessity for ensuring microbial safety due to the prevalence of zoea-II syndrome at this vital stage. Source tracking of specific bacterial groups suggests regulatory timing and routes of Roseobacteraceae (with potential probiotics) and frozen Artemia as a major source of vibrios (with opportunistic pathogens). The determinism-dominated assembly of bacteria, sourced either internally or externally, highlights strong host selection. This process exhibits overall similarities in taxonomic preferences for internal succession, while differences in taxonomic preferences from external sources reflect the influence of the genetic backgrounds of shrimp strains. Our work presents the first systematic assessment on bacterial sources of P. vannamei larvae across the complete developmental cycle, providing new insights that facilitate microbial management and pathogen prevention in larviculture.

microbiology↗

bioRxiv2025

TidyMass2: Advancing LC-MS Untargeted Metabolomics Through Metabolite Origin Inference and Metabolic Feature-based Functional Module Analysis

Untargeted metabolomics provides a direct window into biochemical activities but faces critical challenges in determining metabolite origins and interpreting unannotated metabolic features. Here, we present TidyMass2, an enhanced computational framework for Liquid Chromatography-Mass Spectrometry (LC-MS) untargeted metabolomics that addresses these limitations. TidyMass2 introduces three major innovations compared its predecessor, TidyMass: (1) a comprehensive metabolite origin inference capability that traces metabolites to human, microbial, dietary, pharmaceutical, and environmental sources through integration of 11 metabolite databases containing 532,488 metabolites with source information; (2) a metabolic feature-based functional module analysis approach that bypasses the annotation bottleneck by leveraging metabolic network topology to extract biological insights from unannotated metabolic features; and (3) an intuitive graphical interface that makes advanced metabolomics analyses accessible to researchers without programming expertise. Applied to longitudinal urine metabolomics data from human pregnancy, TidyMass2 identified diverse metabolites originating from human, microbiome, and environment, and uncovered 27 dysregulated metabolic modules. It increased the proportion of biologically interpretable metabolic features from 5.8% to 58.8%, revealing coordinated changes in steroid hormone biosynthesis, carbohydrate metabolism, and amino acid processing. By expanding biological interpretation beyond conventionally MS2 spectra-based annotated metabolites, TidyMass2 enables more comprehensive metabolic phenotyping while upholding strict open-source principles of reproducibility, traceability, and transparency.

bioinformatics↗

bioRxiv2025

DNA repair under heat: DNA Polymerase {lambda} modulates heat stress-induced mutagenesis in plants

Mutation rates can increase substantially under environmental stress, known as stress-induced mutagenesis. Specifically, heat stress has been shown to elevate mutation rates, thereby enhancing genetic variability and facilitating adaptation. However, the underlying mechanisms remain elusive in eukaryotes. Here, we investigated how heat stress affects DNA repair and induces mutations both locally and globally through CRISPR-Cas9 targeted DNA breaks and whole genome sequencing analyses in Arabidopsis thaliana. Heat stress was found to enhance CRISPR editing efficiency across all chromatin contexts, with particularly significant increases, up to 29.9-fold, in heterochromatic regions. Moreover, heat stress consistently shifts mutation outcomes toward 1-bp insertions regardless of chromatin states. We identified a heat-inducible, error-prone DNA polymerase, Pol{lambda}, as the key mediator of mutation profile changes. When extending our investigation from targeted mutations to genome-wide effects, we found that increases in global mutation rates under heat stress are also dependent on Pol{lambda}. Single-cell transcriptomic analysis further demonstrated that Pol{lambda} expression is tightly regulated and cell-type specific, with the highest expression levels in central zone meristematic cells. Together, these findings provide practical applications for improving editing efficiency in heterochromatic regions and fundamental insights into heat-induced mutagenesis, establishing Pol{lambda} as a crucial mediator of stress-induced genetic variation in plants.

plant biology↗

bioRxiv2025

Fluctuating selection breaks Hamilton's rule for the evolution of altruism

Altruistic behaviours, those that benefit recipients at a cost to donors, have long posed a puzzle in evolutionary biology and sociobiology. Established theories, such as kin selection, group selection, and reciprocal altruism, explain altruism via assortment mechanisms that depend on preferential interactions among altruists to ensure a higher average payoff than selfish individuals. Hamiltons rule defines the minimum level of such assortative interactions required for altruism to evolve. However, in populations with limited growth, increased competition can erode the selective advantage of altruism and thus require more stringent Hamiltons rule. Here, we propose a fundamentally different mechanism: fluctuating selection driven by increased competition due to added social benefits of altruism in populations with limited carrying capacity. Under fluctuating selection, altruists can invade a selfish population without the need of assortment mechanisms and outcompete selfish individuals through a transient phase, even when the cost of altruism exceeds its direct benefit. Classical invasion analysis, which compares the long-term growth rates of rare altruistic mutants and resident selfish individuals, fails in our model because both strategies exhibit zero long-term growth. Instead, we show that altruism can invade when its short-term, time-averaging growth rate exceeds that of selfish individuals, which necessitates a prolonged transient phase. This invasion is enabled by payoff-regulated density dependence, which captures the dynamic interplay between payoff and density on fitness under fluctuating selection. Our findings challenge the necessity of Hamiltons rule and show that genuine altruism, with less average payoff than selfish individuals, even extremely self-sacrificial, can emerge under natural selection. This suggests that altruism may arise not from preferential interaction, but as an adaptive response to population fluctuations in constrained environments, providing an alternative paradigm for understanding the evolution of altruistic behaviour.

evolutionary biology↗

bioRxiv2025

Lysosomal cathepsin D regulates bone turnover through distinct mode of actions of the autophagy pathways in osteoblasts and osteoclasts

Insufficiency in nutrient availability, oxidative stress and autophagy failure are fundamental factors for the decline of bone mass and strength with aging. Accumulating evidence indicates that these factors affect normal autophagosomal or lysosomal activities which are the major force in clearance of aggregated or damaged proteins. Cathepsin D (CtsD), the principal lysosomal aspartate protease and a main endopeptidase, exists in the skeleton during development or homeostasis. However, the molecular and cellular mechanisms of CtsD mediated autophagosome or lysosome function in the skeletal homeostasis remain unclear. In the present study, we showed that deletion of CtsD dramatically decreased bone mass in the 3-week old mutant mice compared with their control littermates as indicated by decreased bone volume (BV), bone volume / total volume (BV/TV), bone surface (BS), trabecular number, trabecular thickness and increase trabecular separation in the microCT analysis. Histomorphometry analysis revealed that the phenotype was characterized by decreased osteoblast numbers, osteoblast surface/bone surface and mineral apposition rate, increased osteoclast numbers, osteoclast surface/bone surface and erosion surface/bone surface. At molecular level, siRNA medicated inactivation of CtsD in MC3T3E1 cells attenuated osteoblastic differentiation and downregulated LC3B expression, which was accompanied by decreased levels of P62, p-Akt and p-GSK3beta in osteoblasts. Intriguingly, inactivation of CtsD in RAW264.7 cells increased osteoclast differentiation with decreased LC3B expression but upregulated P62 level. This was accompanied by alterations in the formation of autophagosome and differential transcription profiles associated with the autophagy pathway during the differentiation of osteoblasts and osteoclasts. The results suggest that CtsD mediated autophagy pathway plays important roles in regulation of bone mass and homeostasis through distinct mode of actions in osteoblasts and osteoclasts, and CtsD may serve as a potential therapeutic target for the maintenance of bone mass.

cell biology↗

bioRxiv2025

Structural and Functional Studies of Rabbit SAMD9 Reveal a Distinct tRNase Module That Underlies the Antiviral Activity

Human SAMD9 and SAMD9L (collectively SAMD9/9L) are large cytoplasmic proteins with antiviral and antiproliferative activities, recently shown to regulate protein synthesis by specifically cleaving phenylalanine tRNA (tRNAPhe). The enzymatic activity of human SAMD9 (hSAMD9) resides within its N-terminal tRNase domain, which depends on three essential basic residues for tRNA binding and biological activity. While these residues are highly conserved across mammalian SAMD9/9L, lagomorph SAMD9 orthologs uniquely harbor a charge-reversal acidic residue at one of three sites, a change known to inactivate hSAMD9/9L. Here, we show that despite this variation, rabbit SAMD9 (rSAMD9) potently restricts vaccinia virus replication and specifically reduces tRNAPhe levels, mirroring hSAMD9. However, unlike hSAMD9, rSAMD9s minimal tRNase module extends beyond the homologous tRNase domain (amino acid 158-389) to include the SIR2 region. Additional basic residues, one unique to rSAMD9, were also found to be important for its antiviral activity. The crystal structure of rSAMD9158-389 closely resembles hSAMD9156-385, though with difference in loop conformations. These findings demonstrate that lagomorph SAMD9 preserves core tRNA-targeting and antiviral functions despite a key residue variation and the need for an extended tRNase module. AUTHOR SUMMARYSterile Alpha Motif Domain-containing 9 (SAMD9) and its paralog SAMD9-like (SAMD9L) are antiviral factors and tumor suppressors. Gain of function (GoF) mutations of SAMD9/9L, however, cause a spectrum of human diseases with immunological or/and neurological presentations. We recently identified the effector domain of SAMD9/9L as a previously unrecognized tRNase, a function critical for both their normal physiological roles and the pathogenic effects of by patient-derived mutations. We also identified three basic residues within the tRNase domain that are highly conserved across mammalian SAMD9/9L as key to its enzymatic and biological activities. However, lagomorph SAMD9 orthologs uniquely harbor a negatively charged acidic residue at one of three sites. Through extensive structural and functional analyses, here we demonstrate that rabbit SAMD9 (rSAMD9) retains both tRNA- cleaving and antiviral activities, despite notable differences in its tRNase module- including a unique basic residue specific to rSAMD9 and a larger domain architecture extending beyond the conserved tRNase core. These data highlight both the evolutionary conservation of tRNase activity in mammalian SAMD9/9L and the flexibility of the tRNase module within the protein family.

biochemistry↗

bioRxiv2025

Self-contrastive learning enables interference-resilient and generalizable fluorescence microscopy signal detection without interference modeling

Every weak signal in fluorescence microscopy may contain critical biological information. However, the inter-ference resilience required to detect such signals has traditionally relied on task-specific interference modeling, which limits generalizability. Here, we present a self-contrastive learning-based signal detection solution that achieves interference resilience without the need for interference modeling, thereby offering high generalizability. The method, DEep PAttern Fitting (DEPAF), is a module that contrasts asynchronously generated data views from asymmetric model paths to extract signals from interference, while incorporating highly parallel signal recognition and localization in the process. Benchmarking shows that DEPAF substantially improves signal detection performance across diverse imaging modalities and dimensions, especially under challenging conditions such as low SNRs and ultra-high signal densities. It is also compatible with, and consistently enhances the performance of various imaging techniques, such as super-resolution imaging, spatial transcriptomic imaging, and two-photon calcium imaging. Notably, DEPAF relies only on image patches with signal patterns and one tunable hyperparameter to adapt to new tasks, making it accessible to users without domain-specific expertise and lowering the barrier to broader adoption. DEPAF is expected to advance the signal-centric fluorescence microscopy techniques and inspire further advancements, especially in the era of image-based multi-omics.

bioinformatics↗

bioRxiv2025

Demethylating agents drive PARP inhibitor resistance in ovarian carcinomas with BRCA1 gene silencing

DNA methyltransferase 1 inhibitor (DNMT1i) therapy is a promising option for increasing immune response as part of combination cancer therapy. High-grade serous ovarian carcinoma (HGSOC) is a highly aggressive cancer with poor survival outcomes, where DNMT1i therapy is being increasingly explored. HGSOC with epigenetically silenced BRCA1 has been shown to respond to PARP inhibitor (PARPi) treatment - a core targeted therapy for HGSOC. However, loss of silencing of even a single BRCA1 allele causes PARPi and platinum chemotherapy resistance. We tested whether BRCA1 silencing was robust to DNMT1i therapy, or would be reversed, thus driving PARPi resistance. We previously generated two homozygously silenced BRCA1 HGSOC cell lines: WEHI-CS62 and an OVCAR8 derivative. DNMT1i treatment caused sustained BRCA1 promoter methylation loss, gene re-expression and PARPi resistance in both of these silenced BRCA1 lines, but not in mutated BRCA1/2 or RAD51C lines. Methylation arrays confirmed transient global CpG methylation losses following DNMT1i. CRISPR deletion of the re-expressed BRCA1 copy in WEHI-CS62 restored silencing and PARPi sensitivity. Furthermore, DNMT1i treatment of a silenced BRCA1 PDX caused heterogeneous BRCA1 promoter methylation loss. In summary, DNMT1 inhibitors caused sustained reduction of BRCA1 promoter methylation in HGSOC cells. This resulted in BRCA1 re-expression and PARP inhibitor resistance, presenting a significant risk for up to 17% of HGSOC patients with BRCA1 gene silencing who could benefit from PARP inhibitor therapy. We conclude that DNA demethylation therapy should be avoided for HGSOC patients with epigenetically silenced BRCA1.

cancer biology↗

bioRxiv2025

Predicting Rhizosphere Competence Related Catabolic Gene Clusters in plant-associated bacteria with RhizoSMASH

Plants release a substantial fraction of their photosynthesized carbon into the rhizosphere as root exudates, a mix of chemically diverse compounds that drive microbiome assembly. Deciphering how plants modulate the composition and activities of rhizosphere microbiota through root exudates is challenging, as no dedicated computational methods exist to systematically identify microbial root exudate catabolic pathways. Here we used and integrated published information on catabolic genes in bacterial taxa that contribute to their rhizosphere competence. We developed the RhizoSMASH algorithm for genome-synteny-based annotation of rhizosphere-competence-related catabolic gene clusters (rCGCs) in bacteria by means of a set of 58 knowledge-based logic detection rules carefully curated through sequence similarity network analysis. Our analysis revealed large heterogeneity of rCGC prevalence both across and within plant-associated bacterial taxa, indicating extensive niche specialization. Furthermore, we validated that the presence or absence of rCGCs in bacterial genomes reflects their catabolic capacity and is predictive for their rhizosphere competence by aligning rhizoSMASH results with paired genome/metabolome datasets of rhizobacterial taxa. RhizoSMASH provides an extensible framework for studying rhizosphere bacterial catabolism, allowing targeted selection of beneficial bacterial taxa for microbiome-assisted breeding approaches for sustainable agriculture.

bioinformatics↗