Biology subjects

Yang, D.

Publications and source records attributed to Yang, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Wetting-mediated extracellular phase separation drives long-range cell adhesion

Cells must efficiently locate and engage for tissue formation and immune coordination, yet classical receptor-ligand binding is limited to nanometre distances and is inherently slow [1-3]. Here, we uncover a previously unrecognised physical principle, liquid-like adhesion by phase separation (LAPS). This process creates dynamic wetting layers on cell surfaces [4, 5], functioning as "liquid bridges" that enable robust, long-range cell capture across tens of micrometres. Remarkably, this wetting-mediated attraction remains effective at nanomolar concentrations--conditions where bulk phase separation would not be expected--and facilitates high-fidelity cell sorting through competitive wetting. By integrating aqueous two-phase systems, endogenous proteins (Galectin-3, CCL5), and fluid-particle-dynamics simulations [6], we demonstrate that extracellular liquid-liquid phase separation not only mediates long-range cell capture but also acts as a physical catalyst for contact-dependent signaling. These findings establish extracellular phase separation as a key physical principle complementing molecular recognition in multicellular systems, offering new opportunities for understanding immune response, tissue morphogenesis, and therapeutic strategies targeting the extracellular environment [7, 8].

biophysics↗

bioRxiv2026

Interorganelle competition for linoleic acid underlies steatotic liver pathology

Lipid droplets (LDs) are traditionally viewed as protective organelles that sequester potentially cytotoxic lipids. However, whether and how LD biogenesis in pathological contexts actively rewires interorganelle lipid homeostasis to drive organelle dysfunction and disease progression remains unexplored. Here, we identify the adipocyte-enriched protein calsyntenin 3{beta} (CLSTN3B) as a critical promoter of metabolic dysfunction-associated steatotic liver disease (MASLD). CLSTN3B, an ER-LD contact protein previously shown to support LD maturation in adipocytes, is robustly induced in mouse hepatocytes by peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) in response to dietary caloric overload. CLSTN3B drives LD biogenesis and neutral lipid storage by stabilizing hemifusion-like ER-LD membrane bridges via its arginine-rich segment. These bridges preferentially recruit cone-shaped linoleoylated phosphatidic acid (PA), diverting linoleic acid (LA) into triacylglycerides (TAGs) rather than mitochondrial cardiolipin (CL), leading to disrupted cristae architecture, deficient ETC supercomplex assembly, elevated electron leak, and oxidative stress. Hepatocyte-specific CLSTN3B deletion impairs LD formation, reduces TAG accumulation, enhances fatty acid oxidation, restores CL maturation, and mitigates oxidative stress, collectively attenuating MASLD progression. Consistently, hepatic CLSTN3B expression correlates with fibrosis severity and progression in human MASLD. These findings position LDs as active regulators of interorganelle lipid partitioning and establish CLSTN3B as a key determinant of mitochondrial vulnerability, providing a general framework for how dysregulated organelle interfaces shape disease.

cell biology↗

bioRxiv2025

A stem cell knockout village reveals lineage rewiring and a non-canonical islet cell fate in monogenic diabetes

Genetics studies have identified a core set of regulators essential for pancreatic {beta} cell development, many of which are mutated in monogenic diabetes. However, how these mutations alter developmental trajectories to produce pathological cell states remains elusive. Here we introduce a knockout village framework that enables longitudinal scRNA-seq profiling of 79 human pluripotent stem cell mutant lines targeting 30 developmental regulators, including 15 diabetes genes, across five islet differentiation stages. We show that loss of lineage regulators impairs {beta} cell formation in a stage-specific manner and rewires developmental trajectories towards competing lineages. Notably, several monogenic diabetes gene mutations drive a shift from {beta} cells to enterochromaffin (EC)-like cells, a recently recognized non-canonical islet cell fate. These EC-like cells exhibit incomplete activation of hormone regulation programs, along with elevated neuron signatures. Leveraging the diversity of cell fate outcomes across mutants, we predicted and experimentally validated ISL1 as a key downstream effector of PDX1 and PAX6 that safeguards {beta} cell identity against an EC-like fate. Together, our findings reveal cell fate rewiring as a widespread, previously underappreciated pathological mechanism in monogenic diabetes and establish a scalable platform for uncovering developmental vulnerabilities in human genetic disorders.

developmental biology↗

bioRxiv2025

Mitochondrial membrane junction-mediated ATP channeling drives activity-dependent glucose metabolism

Neurons and brown adipocytes rely on rapid ATP production from accelerated glucose metabolism to sustain bursts of activity upon stimulation, a process known as activity-dependent glucose metabolism. The first committed step in this pathway, the hexokinase I (HK1)-catalyzed phosphorylation of glucose, consumes ATP, raising the question of how this reaction can be accelerated when cytosolic ATP becomes limiting during stimulation. We identify Cell Cycle Exit and Neuronal Differentiation protein 1 (CEND1), expressed in both cell types, as a critical regulator of this process. Loss of CEND1 impairs activity-dependent glucose utilization, ATP generation, and stimulation-evoked activity both in vitro and in vivo. Mechanistically, CEND1 assembles a complex with HK1, voltage-dependent anion channel 1 (VDAC1), and adenine nucleotide translocase 1 (ANT1) at hemifusion-like membrane junction between the outer/inner mitochondrial membrane, channeling mitochondrially derived ATP directly to HK1. These findings uncover a previously unrecognized mechanism that sustains activity-dependent glucose metabolism, with broad implications for energy homeostasis in specialized cell types.

physiology↗

bioRxiv2025

Serotonin Engages Divergent 5-HT Receptor Pathways for Cell Type-Resolved Modulation of Prefrontal Layer 5 Microcircuits

Background and PurposeSerotonin (5-HT) is a key neuromodulator in the prefrontal cortex (PFC), yet its cell type-specific effects across excitatory and inhibitory microcircuits remain incompletely understood. We aimed to determine how 5-HT shapes intrinsic excitability and synaptic transmission in defined neuronal populations of the medial PFC (mPFC). Experimental ApproachWe performed whole-cell recordings from morphologically and electrophysiologically characterised layer 5 (L5) neurons in rat mPFC. Pyramidal neurons were classified into adaptive-spiking high input resistance (ASH), adaptive-spiking low input resistance (ASL), and regular-spiking (RS) types; interneurons were categorised as non-fast-spiking (nFS), regular-fast-spiking (rFS), and stuttering-fast-spiking (sFS) interneurons. These cell types exhibited distinct membrane properties, firing patterns, and axonal projections. We assessed serotonergic modulation using bath-applied 5-HT and subtype-specific receptor mechanisms. Key Results5-HT produced divergent postsynaptic responses across pyramidal neuron subtypes: ASH and RS neurons depolarised via 5-HT2A receptor (5-HT2AR) activation, whereas ASL neurons exhibited 5-HT1AR-mediated hyperpolarisation. Among interneurons, rFS and sFS cells depolarised through ionotropic 5-HT3ARs, while nFS interneurons were largely unaffected. At the synaptic level, 5-HT suppressed excitatory synaptic transmission between pyramidal neurons via presynaptic 5-HT1BRs, and conversely enhanced GABAergic transmission from FS interneurons via presynaptic 5-HT3ARs. Conclusions & ImplicationsSerotonin exerts bidirectional, cell type-specific serotonergic modulation of local microcircuits that acts to suppress excitation while facilitating inhibition. This balanced and targeted regulation, arising from distinct distributions of somatodendritic and presynaptic 5-HT receptors, provides a mechanistic basis for serotonergic influence on attention, cognitive flexibility, and emotional regulation.

neuroscience↗

bioRxiv2025

A New Fight-or-Flight Pacemaker Mechanism via Ryanodine Receptor Abundance and Superclustering

The sinoatrial node is the primary cardiac pacemaker. Individual sinoatrial node cells (SANCs) generate spontaneous rhythmic action potentials (APs) that initiate each heartbeat. The mechanism of SANC automaticity and its modulation by autonomic nervous system are based on the coupled function of molecules of both the cell membrane (ion channels, exchangers, and pumps) and the sarcoplasmic reticulum (SR), which generates rhythmic local Ca releases (LCRs). While LCRs are generated by ryanodine receptors (RyRs), the molecular-scale RyR network structure remains unknown. Here we performed single-molecule localization of RyRs via direct Stochastic Optical Reconstruction Microscopy (dSTORM) in rabbit SANCs in basal conditions and 5 minutes after {beta}-adrenergic receptor ({beta}AR) stimulation by isoproterenol. RyRs form clusters of various sizes, with a mean density of 67.7{+/-}13.2 RyR/m2. (Mean{+/-}SEM, 6 cells). While the majority of cluster sizes ranged from 3 to 32 RyRs, each cell had a few substantially larger clusters (>76 RyRs), dubbed superclusters. {beta}AR stimulation significantly increased the RyR density to 119.1{+/-}22.6 RyR/m2 (8 cells, p<0.05) and created more superclusters. Our new numerical SANC model showed that superclustering substantially decreased the AP cycle length (APCL) by creating Ca release hotspots that initiated larger LCRs under any condition. Increasing RyR density prolonged APCL in the basal state but shortened APCL during {beta}AR stimulation. With no change in RyR network, {beta}AR stimulation of only SR Ca pump and ion currents shortened APCL on average from 414.9 to 284 ms. When realistic higher RyR density and superclustering were added to the model, APCL further shortened to 231.9 ms. Thus, dynamic nanoscale changes in RyR network provide a new powerful pacemaker mechanism. This mechanism may help explain athletic bradycardia at rest and high exercise heart rates, with its deterioration contributing to the age-related loss of heart rate reserve. Author summaryThe heartbeat begins in the sinoatrial node, the hearts natural pacemaker. During stress or exercise, pacemaker cells accelerate their firing rate via {beta}-adrenergic ("fight-or-flight") stimulation. Although Ca signals are known to drive this acceleration via electrogenic Na/Ca exchanger, how the underlying ryanodine receptor (RyR) Ca release channels are organized at the nanoscale and how this organization changes during stimulation remain unclear. Here, we used super-resolution microscopy (dSTORM) to visualize individual RyRs in rabbit pacemaker cells. We found that RyRs form heterogeneous clusters that include rare, very large "superclusters." {beta}-adrenergic stimulation increased overall RyR density, enlarged clusters, and markedly increased the number of superclusters. To understand how these structural changes affect pacemaker function, we developed a computational sinoatrial node cell model in which each RyR was represented explicitly and arranged according to our imaging data. Numerical model simulations revealed that superclusters act as Ca-release hotspots that fire early during diastolic depolarization and recruit neighboring RyR clusters to fire via Ca-induce-Ca-release mechanism. When combined with {beta}-adrenergic enhancement of Ca cycling and membrane currents, the superclustering and RyR abundance synergistically accelerated action potential firing. Together, our results identified dynamic nanoscale RyR network reorganization as a key structural mechanism in fight-or-flight response.

biophysics↗

bioRxiv2025

HIV Virion Capturing Liposomes for Therapeutic Vaccination

HIV infection currently has no effective cures and requires lifelong antiretroviral treatments. Cures have failed due to HIVs immune evasion and rapid mutation rate. Here we present a first in class HIV therapeutic vaccine, termed nanotrap therapeutic vaccines (NTVs) that are designed to capture circulating HIV virions and facilitate internalization by local antigen presenting cells. NTVs are modified liposomes that display the CD4 mimetic molecule, CJF-III-288, on their surfaces and have the TLR 7/8 agonist R848 loaded into their core. We show that NTVs can 1) bind gp120 and capture pseudoviral particles, 2) facilitate uptake by antigen presenting cells and 3) generate robust anti-HIV CD8 T cell immunity in transient infection mouse models. NTVs have translational potential to generate patient-specific HIV immunity.

bioengineering↗

bioRxiv2025

Gut Microbiota-derived Adenosine Determines the Efficacy of Electroconvulsive Therapy for Depression

Electroconvulsive therapy (ECT) is a final procedure for major depressive disorders (MDD). However, the effectiveness of ECT in treating MDD patients varies. Here we identified gut microbiota as a potential restraining factor of ECT efficacy. By using a 5-day electroconvulsive shock (ECS) in depression mouse model of chronic restraint stress (CRS), it was observed that the antidepressant effect of ECS was suppressed after antibiotics (ABX)-induced microbiota dysbiosis, which also resulted in elevated c-Fos expression of CRH neurons in paraventricular nucleus of hypothalamus (PVN) and increased serum corticosterone levels after ECS. Metabolomic analysis revealed the critical involvement of microbiota associated purine metabolism, and the supplement of gut microbiota-derived adenosine was able to recover the antidepressant effect of ECS in ABX-treated CRS mouse model. Based on the neural tracing from colon to brain and the immunofluorescence staining, it was surmised a gut-brain axis originated from Adora1-expressing cells in colon mediate this biological process. Furthermore, adenosine supplement alleviated the further deterioration of post-ECS memory loss and impairment of synaptic plasticity induced by ABX-treatment as well. Our findings suggest a potential role of microbial adenosine metabolism in ECT efficacy determination and side effect protection, highlights potential application of adenosine supplement in antidepressant therapies of those depression patients with microbiota dysbiosis.

systems biology↗

bioRxiv2025

KIF5A binds RNA to orchestrate synaptic mRNA localization and stress granules in ALS

Neuronal health depends on the precise transport and local translation of mRNAs to maintain synaptic function across highly polarized cellular architecture. While kinesin motor proteins are known to mediate mRNA transport, the specificity and direct involvement of individual kinesins as RNA-binding proteins (RBPs) remain unclear. Here, we demonstrate that KIF5A, a neuron-specific kinesin implicated in amyotrophic lateral sclerosis (ALS), functions as an RBP. We show that KIF5A directly binds mRNAs encoding synaptic ribosomal proteins and is required for their synaptic localization and for maintaining normal synaptic composition and function. Additionally, we show ALS-linked KIF5A mutations confer gain-of-function properties, enhancing mRNA binding, increasing synaptic ribosomal protein accumulation, inducing neuronal hyperexcitability, and impairing stress responses. These findings reveal a previously unrecognized mechanism by which mutant KIF5A disrupts synaptic homeostasis. Our work positions a kinesin motor protein as an RBP with critical roles in mRNA transport, local translation, and stress response. HighlightsO_LIKIF5A interacts with mRNA encoding synaptic ribosomal proteins C_LIO_LIKIF5A is required for normal synaptic composition and function C_LIO_LIKIF5A binds to G3BP1 and G3BP1 stress granule associated proteins C_LIO_LIKIF5A mutant ALS patient-derived motor neurons have abnormal synaptic function and stress response C_LI

neuroscience↗

bioRxiv2025

CFDP1 is required for histone variant H2A.Z deposition by the human SRCAP chromatin remodeling complex

Craniofacial Developmental Protein 1 (CFDP1) is a member of the evolutionarily conserved family of Bucentaur (BCNT) proteins and was originally classified as a protein required for cell survival and differentiation during tooth development. Yeast Swc5, a BCNT family member, is an essential subunit of the yeast SWR1C chromatin remodeling complex that catalyzes the deposition of histone variant H2A.Z. Direct connections between CFDP1, H2A.Z deposition, and the mammalian SWR1 homolog, Snf2-Related CREBBP Activator Protein (SRCAP), have not been identified. Here, we perform detailed biochemical reconstitution and characterization of the human SRCAP complex (SRCAP-C). We find that CFDP1 weakly interacts with SRCAP-C in a salt concentration-dependent manner. SRCAP-C purified under a high-salt condition does not co-purify with CFDP1 and is inactive in H2A.Z dimer exchange reaction, but the addition of exogeneous CFDP1 restores the H2A.Z deposition activity of SRCAP-C, demonstrating that CFDP1 is required for H2A.Z dimer exchange by SRCAP-C. We show that CFDP1 stimulates the basal ATPase activity of reconstituted SRCAP-C, suggesting a requirement for CFDP1 in regulating intrinsic catalytic ATPase activity. Consistent with this idea, CFDP1 deficiency in human induced pluripotent stem cells (hiPSCs) leads to a genome-wide reduction of H2A.Z, H3K27me3, and H3K4me3 deposition, accompanied by the upregulation of developmental genes normally marked by these modifications. Taken together, our results provide mechanistic insights into how CFDP1 regulates histone variant H2A.Z deposition by SRCAP-C. Given mutations in the SRCAP gene cause Floating-Harbor syndrome (FHS), a rare, dominant developmental disorder, our study provides an additional link between craniofacial defects and SRCAP-mediated H2A.Z deposition.

molecular biology↗

bioRxiv2025

Human Dicer1 hotspot mutation induces both loss and gain of miRNA function

The core miRNA biogenesis enzyme Dicer1 sustains recurrent mutations in cancer that compromise its RNase IIIb domain, which cleaves 5p arms of pre-miRNA hairpins. However, the lack of knockin models has limited fuller understanding. Here, we generated Dicer1-KO and Dicer1-S1344L (homozygous and hemizygous) human ESCs; the latter is a non-catalytic mutation in RNase IIIa that impairs RNase IIIb activity. Dicer1 knockouts lack canonical miRNAs, while S1344L induces two trends: ablation of miRNA-5p strands, and selective changes in miRNA-3p strands. Curiously, we recognized directional upregulation of miRNA-3p passenger strands, indicating a broad strand switch. We used multiple in vitro assays to show 3p arm-nicked pre-miRNAs preferentially load miRNA-3p species into Argonaute, compared to corresponding duplexes. Moreover, activity assays, RNA-seq data, and Argonaute-mRNA profiling, confirm that these confer increased repression capacity. These data expand the molecular consequences of Dicer1 hotspot mutations in cancer.

biochemistry↗

bioRxiv2025

Lysine-R2HGylation identified as a post-translational modification in R2HG-elevated cancers

R-2-Hydroxyglutarate (R2HG), an oncometabolite predominantly produced by mutated isocitrate dehydrogenase 1/2 (IDH1/2) in various cancers, is known to drive cancer progression through noncovalent inhibition of -ketoglutarate (KG)-dependent enzymes. In this work, we propose an alternative mechanism wherein R2HG contributes to cancer development via covalent modification of biologically critical lysines, a process termed lysine-R2HGylation (KR2HG). We designed and synthesized R2HG-mimicking probes, demonstrating their effectiveness in facilitating KR2HG target profiling and site mapping. We identified KR2HG as a previously unrecognized post-translational modification, confirmed its C5-linkage on GSTP1(K209), and demonstrated that SIRT5 functions as a deacylase for GSTP1-KR2HG in vitro. Furthermore, we found that R2HG slightly but significantly inhibits the enzymatic activity of GSTP1 through KR2HG and dramatically suppresses monocyte differentiation via this catalytically important lysine modification. Our findings provide an alternative perspective on the role of R2HG in leukemia progression and offer a practical tool for the clinical investigation of R2HG-elevated cancers.

molecular biology↗

bioRxiv2025

Internal desynchrony of the circadian clock system in middle-aged mice under social jet lag-like conditions

Social jet lag (SJL) refers to the discrepancy in sleep patterns between weekdays and weekends, leading to a misalignment between the internal clock and social time. In this study, we investigated the effects of weekly shifts in light-dark (LD) conditions: two days per week with 6-h delayed LD cycles (simulating Saturday and Sunday), followed by a 6-h advance on Monday. Core body temperature rhythms rapidly entrained to the delayed LD cycles on weekends, and these delayed rhythms persisted even after the LD cycle was advanced on Monday. In contrast, plasma corticosterone rhythms on Mondays were aligned with the LD cycle but exhibited reduced amplitude. In the livers of SJL mice on Monday, the expression rhythms of Per1, Per2, and Hsp70 were delayed by 3-5 h compared to that in the controls, whereas Rev-erb expression rhythms remained comparable to those of the controls. The expression of lipid and glucose metabolism-related genes in the liver showed either delayed rhythms or no significant changes. To determine whether the dissociation of gene expression rhythms resulted from gene-specific responses to circadian body temperature and hormonal signals, we conducted ex vivo culture experiments using mouse liver slices. High-temperature stimulation induced Per2 and Hsp70 expression, while dexamethasone induced Per1 expression. High temperature and dexamethasone affected distinct sets of metabolic genes, whereas insulin induced only minor changes. Moreover, these responses were strongly influenced by the age and light exposure of the mice. We also examined the effect of weekly housing by providing environmental enrichment (EE), which had minimal impact on circadian parameters but promoted anti-aging effects on bone density and behavior. Overall, our findings indicate that weekly shifts in LD cycles induce internal desynchronization within the hepatic molecular clock and metabolic pathways by uncoupling core body temperature rhythms, hormonal rhythms, and gene-specific responses to stimuli.

physiology↗

bioRxiv2025

PD-1 signaling is essential for the early accumulation of HBV-specific CD8+ T cells during HBV infection

Background & AimsProgrammed cell death Protein 1(PD-1) is one of the key inhibitory receptors that regulates CD8 T cell exhaustion during chronic viral infection. However, the role of PD-1 in modulating effector T cell differentiation and function during early phase of hepatitis B virus (HBV) infection remains poorly defined. MethodsUsing adoptive transfer of wild-type or PD-1 KO HBV-specific TCR transgenic (C93-TCRtg) CD8 T cells, flow cytometry, and transcriptome sequencing, we systematically profiled early PD-1 dynamics in splenic and intrahepatic T cells and evaluated how PD-1 deficiency shapes anti-HBV T cell responses in acute self-resolving (AR) and chronic (CH) HBV mouse models. ResultsAcute HBV infection induced sustained PD-1 upregulation on intrahepatic/splenic CD8 T cells, which predominantly exhibited an effector phenotype. PD-1 cells displayed enhanced proliferation, cytotoxicity, and effector cytokine production compared to PD-1- counterparts. Adoptive transfer of PD-1 KO C93-TCRtg CD8 T cells resulted in significantly impaired early expansion in both spleen and liver during acute infection, accompanied by reduced granzyme B expression while maintaining IFN-{gamma}, TNF-, or IL-2 production. Transcriptomic analysis revealed that PD-1 deficiency was associated with the upregulation of apoptosis gene signatures. In chronic HBV infection, PD-1 KO cells failed to expand long-term and exhibited exacerbated exhaustion evidenced by a loss of IFN-{gamma} production. ConclusionsPD-1 is essential for the early expansion and survival of HBV-specific CD8 T cells during acute infection and does not suppress their effector cytokine function. Its absence impairs proliferation and promotes exhaustion of HBV-specific CD8 T cell in chronic infections. Impact and implicationsOur study redefines PD-1s role in acute HBV infection. Rather than merely constraining effector function, PD-1 is essential for the early expansion and survival of HBV-specific CD8+ T cells, acting as a safeguard against activation-induced apoptosis. The context-dependent functions position PD-1 as a critical rheostat calibrating the magnitude and quality of the antiviral CD8+ T cell response, with significant implications for immunotherapeutic strategies targeting this pathway in hepatitis B.

immunology↗

bioRxiv2025

RhoV Promotes Proliferation, Migration, and MAPK Activation in Pancreatic Ductal Adenocarcinoma

Background and AimsPancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy characterized by diagnosis at advanced stages, limited therapeutic options, and frequent resistance to therapies. Although oncogenic KRAS mutations are central drivers of PDAC, alternative pathways indisputably contribute to its tumorigenesis and progression. RhoV, a member of the Rho family of small GTPases, has been implicated in tumor development in other cancer types, such as breast cancer and lung adenocarcinoma; however, its role in PDAC remains unclear. MethodsIn this study, we investigated the expression and functional impact of RhoV on PDAC. Analysis of publicly available datasets and immunohistochemical profiling of 114 PDAC patient specimens were used to evaluate the expression of RhoV in PDAC and its prognostic impact. Overexpression and CRISPR-Cas9-mediated knockout of RhoV were established in three pancreatic cancer cell lines. Functional analyses, such as cell proliferation, migration, invasion, colony formation, spheroid growth, and mouse xenograft, were used to evaluate the role of RhoV in PDAC cells. ResultsRhoV overexpression was associated with reduced overall and recurrence-free survival in public datasets and our own patient cohort. Functional assays demonstrated that RhoV overexpression promoted PDAC cell proliferation, colony formation, and spheroid growth, whereas knockout of RhoV suppressed these changes. Moreover, RhoV enhanced PDAC cell migration and invasion in vitro, accompanied by downregulation of E-cadherin and upregulation of N-cadherin and vimentin, indicating induction of epithelial-mesenchymal transition. Mechanistically, RhoV overexpression activated key MAPK pathway components, including phosphorylation of ERK, JNK, and p38. In vivo, xenograft models confirmed that RhoV drives tumor growth and increases tumor burden. ConclusionThese results establish RhoV as a novel oncogenic factor in PDAC progression and highlight its potential as a biomarker and therapeutic target, warranting further investigation into combinatorial targeting strategies to overcome KRAS inhibitor resistance.

cancer biology↗

bioRxiv2025

Editing-independent effects of Adar in Drosophila melanogaster

Vertebrate ADAR RNA editing enzymes prevent cellular dsRNA from aberrantly activating antiviral dsRNA sensors. ADARs inhibit antiviral sensor activation by deaminating selected adenosines to inosines in dsRNA and by engaging in inhibitory protein interactions with sensors on dsRNA. ADARs interact with Dicers and, in the Drosophila Adar5G1 null mutant Dicer 2 acts as the antiviral dsRNA sensor mediating aberrant innate immune induction. We overexpressed active Adar isoforms or a catalytically-inactive Adar E374A protein from UAS-Adar constructs under the control of a temperature-regulated Act5Cts-GAL4 driver. Overexpression of the edited AdarG isoform or AdarEA cause larval lethality with aberrant innate immune induction. Some escaper pupae are formed with head eversion defects. AdarS overexpression is also lethal with no progeny pupae. Ecdysone signaling gene and innate immune gene expression are aberrantly elevated in the AdarG overexpressing pupae. RNAi knockdown of Ecdysone Receptor A (EcR A) or increasing expression of HP1 partially rescue AdarG overexpression defects and normalize gene expression in progeny flies, indicating that aberrant epigenetic silencing is also involved. The structure of an ADAR2 dimer on dsRNA shows the the glycine in AdarG is suitably positioned for Adar contacts with other proteins on dsRNA.

developmental biology↗

bioRxiv2025

Genome Sequencing of Rice Landraces from the Yuanyang Terraces Uncovers Ancient and Diverse Lineages of Indica Rice

High-yielding elite rice cultivars exhibit limited genetic variability, raising concerns about our capacity to sustain productivity in the face of changing biotic and abiotic threats. Meeting the challenges that lie ahead largely depends on our ability to make use of novel sources of genetic variation and re-engineer agrosystems. Here, we report on the evolutionary history and population genetic structure of 353 accessions representing 91 landraces from Chinas centuries-old Yuanyang terraces of rice paddies (YYT). We found that the indica YYT landrace population is genetically structured and exhibits high standard variation. Analysis of natural selection reveals that innate immunity genes have a marked difference in coevolutionary dynamics between modern and traditional rice, characterized by a stronger influence of directional selection, which reduces diversity, in modern varieties. Our study highlights the importance of preserving landraces and the need for targeted efforts to integrate the standing variation in landraces into new varieties.

evolutionary biology↗

bioRxiv2025

Efficient Search of Ultra-Large Synthesis On-Demand Libraries with Chemical Language Models

Ultra-large building block catalogs provide inexpensive access to billions of synthesis-on-demand molecules, but the combinatorial scale renders conventional virtual screening impractical. We present Vector Virtual Screen (VVS), a score-function-agnostic machine learning framework for efficient navigation of combinatorial libraries and rapid identification of promising molecules for experimental validation. VVS comprises four key innovations: (i) the Embedding Decomposer, which factors molecules into building blocks in latent space; (ii) ChemRank, a correlation-based loss that improves retrieval precision; (iii) BBKNN, an algorithm for nearest-neighbor search directly in building block space; and (iv) a multi-scale hill-climbing algorithm for gradient-based navigation of molecular embedding vector databases. Across diverse scoring functions, VVS consistently outperforms existing methods in retrieving high-scoring molecules while evaluating only a fraction of the library, achieving orders-of-magnitude runtime improvements. By turning ultra-large libraries into tractable search spaces, VVS enables virtual screening to keep pace with the rapid expansion of chemical space and adapt seamlessly to future advances in scoring functions.

bioinformatics↗