Biology subjects

Li, W.

Publications and source records attributed to Li, W..

At least 199 records · Page 11Linked to original sources

bioRxiv2025

A geometric criterion links HIV-1 capsid topography to its biophysical properties and function

Mathematical models of virus capsid structure are pillars of modern virology, aiding the understanding of viral mechanisms and the design of antiviral interventions. Traditionally, the HIV-1 capsid core geometry is represented as a fullerene lattice, akin to the icosahedral models of spherical viruses in Caspar-Klug theory. However, recent studies revealed that many viral capsids deviate from such idealised lattices, with important functional implication. Here we show that this is the case also for the conical HIV-1 core geometries, in which the hexamer and pentamer boundaries form a pseudo-tiling rather than a perfectly aligned fullerene network. We introduce a triangular geometric criterion that quantifies local deviations of an HIV-1 atomic model from its idealised fullerene backbone. Using this criterion, we present that this difference in geometric organisation between idealised (fullerene) and actual (data-derived) capsid model has implications for the capsids biophysical properties. We also discuss the use of the geometric criterion as a predictive tool regarding cofactor binding and implied geometric changes in the capsid surface coupled to the interfacial frustration response. Our results establish a quantitative framework linking capsid geometry, curvature, and biophysical function, offering new perspectives for assembly inhibitor design and lentiviral vector engineering.

bioinformatics↗

bioRxiv2025

Benchmarking Cell-Type-Specific Spatially Variable Gene Detection Methods Using a Realistic and Decomposable Simulation Framework

Identifying spatially variable genes within individual cell types is essential for characterizing spatially organized cell states and microenvironments from spatial transcriptomics data. Several computational methods have been developed for identifying cell-type-specific spatially variable genes (ctSVGs), but their relative performance and practical utility under realistic biological complexity remain largely unknown. To address this gap, we present the first systematic bench-mark study of all five existing ctSVG detection methods--CELINA, STANCE, C-SIDE, CTSV and spVC--using an integrated evaluation framework that combines idealized simulations, Xenium-based realistic simulations, and a decomposition-based diagnostic analysis. We compared the methods in terms of detection accuracy, scalability, and usability. Across realistic datasets generated on various tissue types, all methods experienced sharp declines in detection accuracy and substantial inflation of false discoveries compared to idealized simulations. To explain this failure, we developed a new simulation framework that decomposes the "realness" of the realistic simulation into interpretable biological and technical components, enabling us to attribute method-specific performance losses to specific components, including realistic diversity of cell types, heterogeneous cell layouts, null gene distributions, capture efficiency and realistic intra-cell-type spatial patterns. Together, our results show that no single method dominates across detection accuracy, scalability and usability, and we further clarify why current ctSVG methods fall short in realistic settings. We summarize these tradeoffs into a practical user guide to support method selection and highlight key challenges in developing robust, scalable ctSVG detection tools for real spatial transcriptomics data.

bioinformatics↗

bioRxiv2025

Engineering an Anaerobic Microenvironment to Empower Hydrogenase-Catalyzed Hydrogen Therapy for Diabetic Wound Healing

The inherent oxygen sensitivity of hydrogenases has long restricted their applications to anaerobic systems. Here, we present a hybrid peptide-nanocluster hydrogel that establishes a self-sustaining anaerobic microenvironment to enable hydrogenase-catalyzed hydrogen therapy under aerobic conditions. This system integrates a custom-designed Fmoc-KYF peptide hydrogel with integrated silver nanoclusters (AgNCs), which host an engineered [NiFe]-hydrogenase (3S1C-Hyd-2). Mechanistic studies combining molecular dynamics simulations and spectroscopic analysis revealed that hydrophobic pockets within the peptide network trap oxygen molecules, while photoexcited AgNCs rapidly deplete invasive O2. Our design ensures stable hydrogen evolution, effectively overcoming the oxygen sensitivity that has long restricted hydrogenase applications in biomedical contexts. In vitro, the in-situ-generated hydrogen effectively scavenges reactive oxygen species, suppresses pro-inflammatory cytokine production. In a diabetic mouse model, this light-activated system markedly accelerates wound closure (87% by day 11), reduces oxidative stress, promotes macrophage polarization toward a reparative phenotype, enhances angiogenesis, and upregulates tissue repair pathways, as confirmed by transcriptomic profiling. Our work establishes a new bioengineering paradigm for constructing anaerobic microenvironments through synergistic material-enzyme-light interactions, offering a versatile platform for hydrogenase-enabled therapeutic interventions in oxidative stress-related diseases.

biochemistry↗

bioRxiv2025

β-Nicotinamide mononucleotide: a novel broad-spectrum CRISPR inhibitor

CRISPR-Cas systems have revolutionized genome editing with their precision and versatility, enabling transformative applications in various fields, especially in the treatment of genetic diseases. However, the clinical translation of this technology is hindered by challenges such as off-target effects and uncontrolled nuclease activity. At the same time, it has the possibility of causing biosecurity risks, underscoring the urgent need for reliable regulatory tools. Existing CRISPR inhibitors, primarily anti-CRISPR protein or exogenously synthesized small molecules, are limited by their specificity or bioavailability and long research period, unable to address the diverse CRISPR nucleases used in research and therapy. Based on the phenomena obtained from various in vitro and cell experiments, combining molecular dynamics simulation and bio - layer interferometry (BLI) analysis, here we report a naturally occurring small-molecule {beta}-nicotinamide mononucleotide (NMN), the first known endogenous metabolite with broad-spectrum inhibitory activity against multiple CRISPR-associated proteins (Cas9, Cas12, and Cas13) through various mechanisms. Our findings establish NMN as a dual-purpose tool, which reduces cell damage caused by gene editing and mitigates risks of unintended genetic modifications in research and clinical settings. This discovery further shortens the distance between basic medicine and translational medicine, providing a new approach for developing endogenous regulatory molecules in genome engineering.

genetics↗

bioRxiv2025

Molecular evolution of CO2-sensing ab1C neurons underlies divergent sensory responses in the Drosophila suzukii species group

Organisms evolve behavioral and morphological traits to adapt to their ecological niches, yet the genetic basis of adaptation remains largely unknown. Drosophila suzukii has evolved a distinctive oviposition preference for ripe fruit, unlike most Drosophila species such as D. melanogaster, which prefer overripe fruit. Carbon dioxide (CO2), a metabolic volatile that increases as fruit ripens and decays, may act as a critical ecological cue shaping these preferences. Here, we focus on D. suzukii and its sister species D. subpulchrella, which shows an intermediate preference, to investigate the genetic basis of CO2 responses. We report a previously unrecognized shift in CO2-guided oviposition: D. suzukii and D. subpulchrella readily lay eggs on CO2-enriched substrates, unlike the strong aversion displayed by D. melanogaster. Electrophysiological recordings revealed a species-specific sensory tuning, characterized by an early spike in CO2-evoked neuronal firing in D. suzukii and D. subpulchrella--a temporal response feature absent in D. melanogaster. To dissect the genetic basis of this shift, we generated transgenic D. melanogaster expressing either the D. suzukii Gr63a coding sequence or the D. subpulchrella Gr63a cis-regulatory element. Remarkably, both manipulations reproduced the early onset firing pattern of CO2 sensitivity, demonstrating that either receptor function or expression can independently drive this sensitivity adaptation. Our findings reveal that evolution can shape ecological adaptation through distinct genetic mechanisms, leading to convergent physiological traits among closely related species. Author SummaryAnimals rely on their senses to locate food sources and identify suitable reproductive sites in their environment. Closely related species can evolve strikingly different preferences as they adapt to new environments. For example, the invasive fruit fly D. suzukii lays its eggs in ripe fruit, unlike most other fruit flies, such as D. melanogaster, which prefer decaying fruit. Because CO2 levels increase as fruit ripens and ferments, changes in how flies detect CO2 may have contributed to these ecological differences. We compared CO2 responses between D. suzukii and its sister species D. subpulchrella, and found that both species respond to CO2 differently from D. melanogaster: both in their oviposition preferences and neural CO2 sensitivity. By introducing either the D. subpulchrella or D. suzukii CO2 receptor gene coding sequences or regulatory regions into D. melanogaster, we found that this altered sensitivity can arise from changes either in the receptors protein-coding region or in the DNA elements that control its expression. Our results show that evolution can act through multiple genetic mechanisms to fine-tune sensory systems, revealing how subtle molecular changes can generate ecological diversity among closely related species.

evolutionary biology↗

bioRxiv2025

Single-Cell Multi-Omics Dissects Transcript Isoform and Immune Repertoire Dynamics in Human Immunosenescence

Immunosenescence, a major hallmark of systemic aging, refers to the progressive functional decline of the immune system. This decline not only compromises host defense and immunological memory but also fuels chronic inflammation and tissue degeneration (collectively known as inflammaging). While single-cell RNA sequencing (scRNA-seq) has revealed transcriptomic alterations in immune aging, analyses restricted to transcript abundance fail to capture deeper regulatory layers, such as transcript isoform diversity and the remodeling of immune receptor repertoires. To address this, we present the human peripheral immune single-cell multi-omics atlas that integrates gene expression, transcript isoforms diversity, and immune receptor repertoires. By combining single-cell full-length transcriptome sequencing (scCycloneSEQ), short-read scRNA-seq, and single-cell immune receptor sequencing (scTCR/BCR-seq), we systematically profiled peripheral blood mononuclear cells (PBMCs) from healthy young and elderly donors. Our analyses uncovered extensive age-related remodeling of immune cell composition, functional states, and TCR/BCR diversity. Notably, we identified in CD4 effector memory T cells exhibited widespread differential isoform usage (DIU), 3'UTR length variation, and a marked reshaping of cytotoxic T lymphocyte (CTL) clonotypes--all closely associated with aging-related inflammation and cellular senescence. This multi-omics atlas delineates key molecular features of immunosenescence and provides a high-resolution resource for deciphering the regulatory architecture underlying immune aging.

immunology↗

bioRxiv2025

De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of Hydrogenase

[NiFe]-hydrogenases exhibit outstanding catalytic performance for H2 production and oxidation but suffer from extreme O2 sensitivity, limiting their biotechnological potential. The identity and functional roles of gas channels that connect to the buried [NiFe] active site have remained unclear, impeding the rational engineering of O2-tolerant enzyme variants. In this study, we present an artificial intelligence-guided de novo protein binder design strategy, utilizing compact protein binders as selective molecular probes to map hydrophobic O2 diffusion pathways in Escherichia coli hydrogenase-2 (Hyd-2). By integrating RFdiffusion, ProteinMPNN, and AlphaFold, approximately 100,000 candidate binders were computationally screened, leading to the identification of two high-affinity binders, L1 and L2. Structural, biophysical, and electrochemical analyses reveal that L1 specifically occludes the primary O2 ingress channel, thereby enhancing the enzymes oxygen tolerance by more than threefold, whereas L2, which targets a putative secondary channel, exerts a negligible effect, demonstrating the nonfunctionality of this pathway. These results provide the first direct experimental evidence for a hierarchical organization of O2 diffusion channels in [NiFe]-hydrogenases and establish binder-mediated channel occlusion as a generalizable, mutation-free approach for probing gas transport mechanisms and selectivity in metalloenzymes.

biochemistry↗

bioRxiv2025

Anxious vision: Trait-like visual cortical hyperactivity in trait anxiety

Sensory processing varies across individuals, often manifesting as distinct traits. Some traits, particularly sensory hypersensitivity, even to basic non-valenced stimuli, are closely linked to emotional traits and implicated in a diversity of psychiatric disorders. Extant theories attribute this sensory-emotion linkage to limbic and prefrontal modulation, but empirical support remains limited. Meanwhile, it is increasingly recognized that sensory cortex supports flexible, value-based processing beyond labeled-line sensory analysis. Assaying early visual cortical activity (using visual evoked potentials/VEPs) across four high-density electroencephalogram (hd-EEG) experiments, involving three independent samples (N = 150) and repeated assessments (up to three waves), we identify a reliable and generalizable pattern of visual cortical hyperactivity related to high trait anxiety. Notably, this effect was specific to the parvocellular (vs. magnocellular) pathway, emerging as early as 46 ms and localized to V1. Underscoring its trait-like stability, the effect was reproducible across different arousal states, neutral and negative stimuli, extended time intervals, and varied experimental paradigms. Moreover, its ecological validity was affirmed by its presence in response to both basic low-level stimuli (Gabor patches) and complex real-world images. Crucially, an excitation-inhibition (E/I) ratio (indexed by the resting-state EEG aperiodic exponent; 1/f slope) predicted parvocellular VEP magnitude in subjects with low but not high trait anxiety, suggesting disrupted E/I modulation in trait anxiety underpins this hyperactivity. We conclude that in trait anxiety, early visual processing deviates from strict "fidelity" to physical-world input or mere "subservience" to top-down modulation, instead adapting to an individuals biological propensity at the earliest processing stage. HighlightsO_LIHyperactivity in primary visual cortex is stable, trait-like C_LIO_LIIt occurs as early as 46 ms post-stimulus, during initial feedforward sweep C_LIO_LIIt covaries with trait anxiety, a key personality factor and risk predisposition for psychiatric disorders C_LIO_LIIt is related to disrupted excitation-inhibition modulation of visual cortex in trait anxiety C_LI

neuroscience↗

bioRxiv2025

Conserved Gαq-PLCβ-PKC signaling mediates trametinib resistance in BRAFV600E melanoma

Oncogenic BRAFV600E mutations drive constitutive MAPK signaling across various cancers; however, resistance to MEK inhibitors such as trametinib undermines clinical benefits, and the mechanisms sustaining MAPK activity under treatment remain unclear. We developed a lin-45(V627E) Caenorhabditis elegans model to mimic oncogenic BRAF signaling and found that these animals tolerate ultra-high doses of trametinib. This survival is driven by an adaptive resistance bypass, mediated by Gq-PLC{beta}-PKC signaling, which sustains MAPK activity despite MEK inhibition. Transcriptomic analyses of patient tumors and resistant melanoma cells reveal upregulation of the Gq subunits and GPCR PAR2 upon acquisition of resistance. Functional inhibition of PAR2 or downstream Gq signaling suppresses ERK reactivation, selectively impairs the viability of resistant cells. Furthermore, combined inhibition of MEK and Gq-PLC{beta}-PKC signaling synergistically suppresses tumor growth and restores trametinib sensitivity in xenograft models. These findings uncover adaptive GPCR-Gq-driven signaling rewiring as an evolutionarily conserved and therapeutically actionable vulnerability in MAPK-driven cancers.

cancer biology↗

bioRxiv2025

Deep learning reveals a microprotein atlas in maize and uncovers novel regulators of seed amino acid metabolism

Microproteins represent a vast and functionally important class of genes that remain largely unexplored in plant genomes. Here, we developed DeepMp, a deep learning framework that integrated multi-omics evidence and built the most comprehensive plant microprotein atlas to date, identifying 18,338 high-confidence candidates in maize. The majority of these appear to have originated de novo from regions previously annotated as noncoding, and they show hallmarks of rapid, lineage-specific evolution and pronounced tissue specificity. These novel microproteins were found integrated into core regulatory networks, particularly in organ development and nutrient storage. Focusing on the maize kernel, population-scale analyses linked microprotein expression to natural variation in amino acid content. We functionally validated three grain-filling-specific candidates originating from noncoding regions by CRISPR-Cas9 knockouts, which confirmed their roles as precise modulators of arginine, aspartate, and methionine levels, without pleiotropic effects on kernel morphology. Our study provides a foundational resource and analytical framework, establishes microproteins as a new and functionally important coding layer in maize, and uncovers a previously untapped source of targets for crop improvement.

genomics↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

Class-I myosin responds to change in membrane tension during clathrin-mediated endocytosis in human induced pluripotent stem cells

Clathrin-mediated endocytosis (CME) is an essential cellular process that needs to operate efficiently across a wide range of conditions. Internalization of the endocytic site involves forces generated by membrane-bound proteins and Arp2/3-mediated branched actin filament assembly to bend the plasma membrane (PM) from flat to omega-shaped. In mammalian CME, the requirement for a branched actin filament network varies depending on cell type and differences in membrane tension. However, how the actin network adapts to changes in load in order to ensure robustness of this process over a range of membrane tensions is not understood. Here, we combine live-cell imaging and super-resolution microscopy of genome-edited human induced pluripotent stem cells (hiPSCs) to investigate the role of the mammalian class-I myosin, Myosin1E (Myo1E), in load adaptation. Under normal conditions, sites that recruit Myo1E are rare and exhibit slow CME dynamics. However, as membrane tension increases and CME dynamics are slowed globally, Myo1E is recruited to more sites, likely to assemble more branched actin, resulting in increased force generation to rescue stalled sites and promote internalization. Loss of Myo1E results in increased Arp2/3 complex lifetime at CME sites under normal conditions, and at high membrane tension, these sites fail to recruit as many Arp2/3 molecules. We propose that Myo1E is recruited to CME sites that have stalled due to increased membrane tension, where it helps build a more effective branched actin network by generating force through motor activity and recruiting additional Arp2/3 complexes to rescue stalled sites. SignificanceFor mammalian cells to internalize extracellular cargo via clathrin-mediated endocytosis (CME), specific regions of the plasma membrane (PM) must bend from flat to inwardly curved, a process that requires force-generating proteins. One key component in generating this force during CME is the branched actin network, in which actin filaments polymerize against the plasma membrane. When PM tension increases, more force is required to generate curvature, prompting the assembly of actin and actin associated proteins to aid the process. We demonstrate that the class-I myosin motor, Myosin1E (Myo1E), becomes increasingly crucial as membrane tension rises, presumably to build a more effective branched actin network to facilitate internalization of slowed sites.

cell biology↗

bioRxiv2025

Dissecting the Cellular Genetics of Cardiovascular Disease Through Endothelial and Immune Compartments Profiling

BackgroundNon-communicable diseases such as coronary artery disease, atrial fibrillation, type 2 diabetes, hypertension, and others share endothelial dysfunction as one of their underlying features. The endothelium, as the interface between blood and vasculature, shapes disease onset and progression through its response to environmental cues. However, while the genetic component of these diseases has been captured by genome wide association studies (GWAS), which also highlighted a shared immune component, it remains unclear which of these disease loci exerts their effects through endothelial cells. This study identifies, and quantifies, the genetic determinants of endothelial cells molecular traits and their overlap to the common genetic variation component of these diseases. MethodsWe generated genotype, RNA-sequencing, H3K27ac ChIP-sequencing, ATAC-sequencing, and endothelial cells barrier stimuli response measurements for 100 samples of human umbilical vein endothelial cells. These were used to identify quantitative trait loci (QTL) for gene expression, transcriptional isoform usage, splice junction usage, chromatin activity and barrier response. We applied statistical colocalisation to identify the overlap between data layers, and to explain molecular QTLs contribution to GWAS disease loci. ResultsWe used molecular QTLs to identify the regulatory features of 8,214 genes, representing 36% of all expressed genes in endothelial cells. We also identified the molecular mechanisms underlying 815 loci across 16 disease GWAS. These represent between 29% and 40% of all loci for each disease, compared to the previous average of 23%. This is due to the choice of a cell type often underrepresented in tissue level data, and the inclusion of isoform, splicing and chromatin activity datasets. Furthermore, we compared the endothelial cells molecular QTLs with similar datasets in monocytes, neutrophils and CD4 T lymphocytes to shed light on the interplay between the endothelial and the immune compartments in these diseases. We identified loci acting through both the endothelial and the immune compartment, mostly with the same directionality of effect, and endothelial specific ones. ConclusionsThis work expands the knowledge of the mechanisms and genes underlying the effect of common genetic variation on non-communicable diseases having endothelial dysfunction as a shared feature. It also illustrates the interplay between endothelial cells and immune cell types in these diseases, highlighting shared and unique pathways.

genomics↗

bioRxiv2025

Inflammatory Agonists Modulate the Host Response to Type 2 ECM scaffold Immune Environment and Long-Term Remodeling After Severe Traumatic Injury

The immune system is a vital regulator of tissue repair after trauma and the response to implantable scaffolds for regenerative medicine. Decellularized extracellular matrix (ECM) scaffolds promote tissue integration and remodeling following traumatic injury in part due initiating a pro-reparative Type-2 immune response. However, exogenous soluble inflammatory immune signals can be introduced during scaffold implantation, including microbial products in contaminated surgical fields or during immunotherapy to treat autoimmunity and cancer. It remains largely unknown how such immune mediators modulate the ECM scaffold immune environment and subsequent scaffold remodeling. In the present study, we co-delivered 3 distinct inflammatory immune adjuvants (cyclic di-AMP [CDA], monophosphoryl lipid A [MPLA], and granulocyte colony stimulating factor [GM-CSF]) with small intestinal submucosa (SIS) ECM in a murine volumetric muscle loss injury model, evaluating acute (1 week) and long-term (8-week) immune environments and scaffold remodeling. High parameter spectral cytometry, histologic analysis, and PCR revealed differential potentiation of the ECM scaffold microenvironment. Type 2 immune programs including IL-4, eosinophils, CD4 T cells, and CD206/CD86 macrophage ratios were induced in all ECM groups but attenuated by varying amounts with the CDA and MPLA co-delivery. By 8-weeks, inflammation had largely subsided, and histologically ECM with GM-CSF or MPLA showed the greatest degradation and remodeling into adipose tissue. These findings suggest that early pro-inflammatory compound delivery does not abrogate the ECM immune environment but does attenuate some programs while inducing others. These have long-term effects on scaffold remodeling and should be a consideration for surgical reconstruction in patients receiving immune stimulatory therapies.

immunology↗

bioRxiv2025

Dual apical methyltransferases orchestrate motility initiation in apicomplexan parasites

Apicomplexan parasites such as Toxoplasma gondii initiate motility through rapid, spatially confined cytoskeletal activation at their apical end. While calcium-, lipid-, and kinase-based signalling pathways have been partially elucidated, how these cues are translated into mechanical force remains unclear. Here, we uncover a dual methyltransferase mechanism that orchestrates this process. We identify PCKMT, a preconoidal ring-associated lysine methyltransferase, as an essential upstream regulator of motility. PCKMT anchors the actin nucleator Formin-1 (FRM1) at the conoid, enabling conoid protrusion and F-actin assembly. Loss of PCKMT abolishes FRM1 recruitment, blocks conoid extrusion, and arrests invasion and egress despite preserved conoid structure. In contrast, the apical methyltransferase AKMT, previously linked to motility through recruitment of the glideosome-associated connector (GAC), acts downstream, disengaging from the conoid upon activation and likely promoting GAC-dependent force transmission. PCKMT depletion prevents AKMT translocation, revealing that actin assembly and lysine methylation are mechanistically coupled. Together, these findings define a two-step methylation checkpoint that coordinates actin nucleation with force propagation, uncovering methylation as a central regulatory axis for motility initiation in apicomplexan parasites.

microbiology↗

bioRxiv2025

Timing of immune checkpoint blockade shapes anti-tumor immunity via a clock-dependent chemokine axis

Circadian clocks regulate immunity, yet how they shape the tumor immune microenvironment and influence cancer immunotherapy remains unclear. Here, we show that tumor immune infiltration and immune checkpoint inhibitor efficacy vary by time of day in mice, driven by intrinsic clocks in dendritic cells and CD8+ T cells. Time-of-day modulates the abundance, spatial organization, and cytokine-chemokine production of tumor-infiltrating immune cells. Mechanistically, dendritic cell clocks control expression of Cx3cl1, driving recruitment of CX3CR1+CD8+ T cells and thereby reshaping the tumor immune microenvironment to enhance immunotherapy efficacy. Disruption of this axis abolishes time-of-day-dependent differences in treatment response. These findings identify a circadian mechanism of immune cell recruitment to tumors and provide mechanistic insight into clinical observations linking treatment timing to immunotherapy outcomes. One sentence summaryTime of day determines cancer immunotherapy efficacy through a circadian clock-dependent chemokine axis.

immunology↗

bioRxiv2025

Time-Series RNA Sequencing Reveals Temperature-Specific and Temperature-Compensated Circadian Genes in Drosophila

Circadian rhythms align the physiology and behavior of living organisms with the 24-hour day. As a defining property of circadian rhythms, temperature compensation preserves the 24-hour rhythmic periodicity despite environmental temperature changes. While the molecular clockwork that drives genome-wide oscillations in gene expression is well characterized, how circadian gene expression contributes to the maintenance of rhythmic outputs under thermal variation and to produce temperature compensation remains uninvestigated. We profiled circadian gene expression in the ectothermic animal Drosophila melanogaster using time-series RNA-seq of head tissues under constant darkness at 18{degrees}C, 25{degrees}C, and 29{degrees}C. Locomotion assays confirmed that behavioral rhythms were temperature compensated under these conditions. Analyses of the time-series RNA-seq samples revealed hundreds of oscillating genes at each temperature, yet the majority were temperature specific. Only 14 genes, including the core clock components period (per) and vrille (vri), oscillated across all three constant darkness conditions at different temperatures. Even among these, the phase, amplitude, and expression levels of these oscillating genes often shifted with temperature. Thus, temperature-compensated oscillating genes are rare and largely confined to core clock genes, while most oscillating genes are temperature-specific. Our results suggested a potential architecture: a robust, temperature-compensated core set of oscillating genes, and a flexible, temperature-responsive output layer. The latter likely establishes temperature-specific oscillating gene expression programs that enable the animal to achieve temperature compensation at behavioral and physiological levels.

molecular biology↗

bioRxiv2025

cfOncoXpress: Tumor gene expression prediction from cell-free DNA whole-genome sequences

Cell-free DNA (cfDNA) fragments in the plasma capture cellular nucleosomal profiles since nucleosome-protected regions escape enzymatic degradation while nucleosome-depleted regions can not. We developed cfOncoXpress, a machine learning framework that uses fragmentation patterns to predict oncogene expression from cfDNA WGS. cfOncoXpress incorporates gene copy number aberrations inferred from cfDNA, including those associated with extrachromosomal DNA. Its application in prostate and breast cancers shows it can predict tumor subtype based on expression of signature genes and activated pathways. cfOncoXpress shows superior performance relative to other state-of-the-art methods and can be used to predict tumor gene expression when tissue biopsies are infeasible.

genomics↗