Biology subjects

Li, W.

Publications and source records attributed to Li, W..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Parallel Emergence and Adaptive Evolution of Multicountry Circulating Mycobacterium abscessus Clones

Mycobacterium abscessus (MAB) is a recently emerged bacterial pathogen causing an increasing number of human infections. Despite increasing recognition that different circulating clones contribute disproportionately to MAB population expansion, the global population dynamics and the evolutionary pressures underlying the emergence and spread of MAB clones remain incompletely understood. We analyzed 11,314 publicly available genomes of MAB isolates sampled from 30 countries and identified 38 recently emerged clones that have spread across multiple countries, including the seven previously described Dominant Circulating Clones (DCCs). There was a significant association between the time since the emergence of each circulating clone and its population size, with older clones generally having larger populations. Among the 26 circulating clones of M. abscessus subsp. abscessus, 12 carried the macrolide-susceptible erm(41) 28C genotype, highlighting clone-level variation in macrolide susceptibility. Genome-wide analyses identified 55 genes that were previously under purifying selection but showed evidence of positive selection during recent clade expansion. Collectively, our findings reveal that the recent global expansion of MAB comprises a broad continuum of newly emerged clones, accompanied by widespread shifts in gene-level selective pressures indicative of ongoing adaptation to new ecological environments.

microbiology↗

bioRxiv2026

Mapping Enteric Neural Circuits by Anterograde Transsynaptic Tracing

The diverse functions of the enteric nervous system (ENS) arise from communication between molecularly distinct neuronal populations organized into complete circuits. While recent single-cell transcriptomic studies have resolved the molecular identity of enteric neuron classes, methods for defining their synaptic connectivity remain limited. Here, we describe the implementation of mWmC, an anterograde monosynaptic tracer based on a fusion of wheat germ agglutinin (WGA) and mCherry, as a non-toxic, single-component viral tool for mapping neuronal circuits within and beyond the ENS. Following adeno-associated virus (AAV)-mediated expression in enteric neurons, mWmC was efficiently expressed and transmitted selectively to postsynaptic neurons, with no detectable transfer to enteric glia, interstitial cells of Cajal, blood vessels or other mesenchymal cell types. The method also identified postsynaptic neurons in the celiac-superior mesenteric ganglia following tracing of intestinofugal enteric neurons, demonstrating its utility for mapping inter-organ circuits. As proof of principle, we applied mWmC to two genetically defined myenteric interneuron populations and identified preferential postsynaptic targets, revealing selective connectivity with distinct enteric neuron classes. Time-course experiments showed that transsynaptic labeling occurred between 4 and 10 days and reached a plateau thereafter, consistent with monosynaptic transfer. Finally, we developed a dual-reporter version of the system that simultaneously distinguishes input and target neurons within the same tissue. Together, mWmC provides a robust approach for defining circuit architecture in the ENS, linking molecular cell atlases with neuronal connectivity and paving the way for deeper insights into the circuit mechanisms underlying gut physiology. Graphical AbstractSchematics illustrating the implementation and applications of the anterograde monosynaptic tracer mWmC for mapping enteric neuronal circuits. Parts of schematics are generated with Biorender. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=36 SRC="FIGDIR/small/741165v2_ufig1.gif" ALT="Figure 1"> View larger version (12K): org.highwire.dtl.DTLVardef@19635bborg.highwire.dtl.DTLVardef@a18ffborg.highwire.dtl.DTLVardef@f3d011org.highwire.dtl.DTLVardef@e1359c_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

MitoDate: a Nextflow pipeline for molecular clock dating and phylogenetic inference using ancient mitogenomes

SummaryAncient DNA studies are increasingly targeting samples that are beyond the limit of radiocarbon dating (>50 thousand years old) and are often difficult or impossible to date using other geochronological methods. In cases where complete mitochondrial genomes (mitogenomes) can be recovered from such samples, Bayesian molecular clock dating approaches are routinely used as an alternative method for estimating their age. However, molecular clock dating of ancient mitogenomes lacks a standardised, reproducible computational framework, and existing approaches rely heavily on graphical interfaces that limit automation and scalability. To address these gaps, we developed MitoDate, an automated Nextflow pipeline for reproducible molecular clock dating of ancient mitochondrial genomes. The workflow standardises Bayesian time-calibrated phylogenetic inference within a portable, containerised framework, reducing manual intervention and improving analytical consistency. Availability and implementationMitoDate is implemented in Nextflow and is freely available at https://github.com/CpgSthlm/MitoDate. The pipeline is distributed with containerised dependencies and detailed documentation, including example datasets and usage guidelines.

bioinformatics↗

bioRxiv2026

Molecular basis for chikungunya virus recognition of a mosquito-specific receptor

Alphaviruses are arthropod-borne viruses that recognize cellular receptors in both vertebrate hosts and mosquito vectors to complete their transmission cycle, yet how they maintain recognition of receptors across evolutionarily divergent host species remains unresolved. Among alphaviruses, chikungunya virus (CHIKV), which is primarily vectored in urban settings by Aedes species mosquitoes, is the most widespread, and causes explosive outbreaks that can involve hundreds of thousands to millions of cases annually. The cell adhesion protein Lachesin is a mosquito-specific cellular receptor for CHIKV and multiple other arthritogenic alphaviruses. The envelope E2-E1 glycoproteins of these alphaviruses broadly recognize Lachesin orthologs from diverse mosquito species, but not other insects or arachnids. Lachesin genetic manipulation to prevent mosquito virus infection without interfering with endogenous receptor function could have a major impact for CHIKV control. Here, we determined high-resolution cryo-electron microscopy (cryo-EM) structures of alphaviruses bound to Aedes albopictus Lachesin. Comparative analysis of Lachesin-bound CHIKV, Semliki Forest virus (SFV), and Middelburg virus (MIDV) revealed that these three genetically divergent viruses use a similar surface to recognize Lachesin domain 1, but with reorganized E2-E1 glycoprotein contact residues. We show that a soluble Ae. albopictus Lachesin receptor decoy protein blocks the E2-E1-mediated entry of CHIKV and other arthritogenic alphaviruses into mammalian cells with greater breadth than a vertebrate receptor MXRA8 decoy and protects against lethal SFV challenge and CHIKV pathogenesis in murine models. Additionally, we identified a naturally occurring single residue Lachesin polymorphism that is found in some Anopheles (malaria vector) mosquitoes, and fully ablates CHIKV E2-E1 recognition, informing strategies for mosquito-targeted genetic interventions that could prevent mosquito vector infection and virus transmission. These findings define distinct determinants of receptor binding in mosquitoes and humans for arthritogenic alphaviruses, with implications for countermeasure development and outbreak preparedness.

microbiology↗

bioRxiv2026

Computational evolutionary approach to generate antimicrobial peptides

As a consequence of the overuse of conventional antibiotics, there is currently an unprecedented increase in antibiotic resistance in newer generations of pathogenic bacteria. This growing problem has led scientists to discover novel medications that could potentially reduce the usage of antibiotics, such as antimicrobial peptides (AMPs). Recent study has demonstrated that pardaxin could bind deeply into the surface of a lipid model membrane and inhibit the growth of pathogenic bacteria, including Staphylococcus aureus and Escherichia coli. In this work, the antibacterial efficacy of pardaxin was extended further by performing selective in silico substitution, driven by deep learning, Evolutionary-Scale Cambrian (ESMC) combined with conventional AMP design principles. Principal component analyses of the ESMC embeddings combined with conventional design models produced a set of single- and multiple-mutant analogues of pardaxin, which were predicted and validated with experimental data to exhibit selective antimicrobial properties against either E. coli or S. aureus, respectively. Atomistic molecular dynamics simulations further supported the notion that alpha-helical stability is a critical predictor of inner membrane activity, strongly correlated with their selective antimicrobial action tested in the lab. Overall, the findings highlighted a promising application of deep evolutionary machine learning techniques for screening a range of novel AMPs for selective antimicrobial agents.

biochemistry↗

bioRxiv2026

Lachesin is a mosquito receptor for multiple arthritogenic alphaviruses

Arthritogenic alphaviruses cause acute febrile illnesses associated with rash and arthritis when they are transmitted to humans through the bite of infected mosquitoes. Among these, chikungunya virus (CHIKV), transmitted primarily through the bite of infected Aedes aegypti and Aedes albopictus mosquitoes, causes explosive outbreaks involving hundreds of thousands to millions of cases, with recent re-emergence in several global regions. While several cellular receptors that mediate alphavirus entry into mammalian cells have been identified, their mosquito counterparts remained unknown, largely due to a lack of functional genomics tools for these invertebrate species. Here, we established a CRISPR-based genetic screening platform in Aedes albopictus cells and used it to identify Lachesin, a conserved invertebrate cell adhesion molecule, as a receptor for CHIKV and multiple related alphaviruses including Semliki Forest virus (SFV), onyong-nyong virus (ONNV), Mayaro virus (MAYV), and Ross River virus (RRV). Lachesin depletion using RNA interference, anti-Lachesin antibody treatment, and soluble forms of Lachesin blocked CHIKV and SFV E2-E1 glycoprotein-mediated infection of mosquito cells. We show that alphavirus E2-E1 glycoproteins bind the first immunoglobulin domain of Lachesin, facilitating attachment and internalization of virus-like particles. Orthologs from divergent mosquito genera, but not from arachnids or other arthropods, also serve as alphavirus receptors, suggesting that cellular receptor binding is not the main obstacle to arthritogenic alphavirus vector host expansion. Our findings enhance understanding of the mechanisms of alphavirus emergence and vector competence and could aid in the development of broadly active, entry-targeted therapeutics against multiple alphaviruses that threaten public health.

microbiology↗

bioRxiv2026

ERK signaling integrates multiple mechanisms to drive cortical evolutionary expansion

A critical first step in human evolutionary divergence from chimpanzees and other primates is the production of greatly increased numbers of cortical pyramidal neurons during development and over evolutionary time. This expansion underpins the enlarged human cerebral cortex and, consequently, higher-order cognition and consciousness. However, the cellular and molecular mechanisms driving this progressive increase in cortical neuron number remain incompletely understood. Here we show that elevated ERK signaling in human cortical radial glia (RGs), relative to mouse RGs, arises from evolutionary changes in the developmental expression of existing shared genes. Using the Emx1-Cre line to overexpress MEK1DD, a constitutively active mutant of rat MAP2K1, we found that enhanced ERK signaling in mouse cortical RGs upregulates cAMP-PKA signaling, along with promoting self-renewal, expanding the RG pool, and accelerating cell cycle progression. Conversely, overexpression of PKA signaling in mouse cortical RGs via in utero electroporation of constitutively active PRKACA mutants (L206R or W196G) reduces ERK activity, prolongs the cell cycle, suppresses SHH-SMO and YAP/TAZ pathway activity, and blocks ependymal gliogenesis. Together, our results demonstrate that ERK and PKA signaling in cortical RGs engage a dynamic balance of synergistic and antagonistic interactions. This interplay couples evolutionarily enhanced ERK and PKA activities to increased cortical RG numbers, prolonged cell cycle progression, and an extended neurogenic period, which collectively culminate in a marked increase in neuronal production. We conclude that heightened ERK pathway activity in cortical RGs serves as a central driver of progressive neocortical expansion across mammalian evolution. Significance StatementThe human brains extraordinary cognitive abilities stem from a dramatic increase in cortical neuron numbers during evolution. This study reveals that enhanced ERK signaling in human cortical radial glia neural stem cells, relative to other primates, is a key driver of this expansion. By manipulating this pathway in mice, we demonstrate that ERK coordinates multiple mechanisms--including self-renewal, cell cycle acceleration, and a dynamic interplay with PKA signaling--to boost neuronal output. These findings identify a core molecular axis underlying mammalian cortical evolution and provide a framework for understanding how the human cortex acquired its unique size and, consequently, its remarkable complexity.

developmental biology↗

bioRxiv2026

A missing PEPC1 exaptation restricts C₄ evolution in palms (Arecaceae)

O_LIC4 and CAM photosynthesis evolved repeatedly across angiosperms, yet the four palm species examined here -- representing three of five Arecaceae subfamilies ([~]2,600 species total) -- all lack both. We hypothesized that this reflects the absence of PEPC1, a phosphoenolpyruvate carboxylase isoform required for C4 carbon fixation initiation and present in commelinids (Poaceae + Bromeliaceae) but whose distribution across monocots is unknown. C_LIO_LIWe surveyed six core C4 enzyme families by HMMER profiling across nine plant genomes -- four palms (Cocos nucifera, Elaeis guineensis, Phoenix dactylifera, Nypa fruticans), two grasses, one bromeliad, one basal monocot, and one fern. We constructed maximum-likelihood PEPC phylogenies and performed codon-based branch-site likelihood ratio tests using PAML. C_LIO_LIAll six enzyme families were present in palms. PEPC1 was detected in all commelinids (rice, maize, pineapple) but absent from all four palm species and outgroups. No palm PEPC sequence fell within the PPC-1 clade. Molecular dating indicates the Arecaceae-commelinid divergence ([~]120 Mya) predates PEPC1 origin ([~]105 Mya). Branch-site tests on the maize C4-PEPC1 branch were marginally significant (2{Delta}l = 3.03, p {approx} 0.082). C_LIO_LIThe absence of PEPC1 represents an ancestral molecular barrier that likely precluded C4 evolution in palms. This identifies a lineage-specific gene duplication as a constraint on photosynthetic pathway evolution in a major tropical plant lineage. C_LI

plant biology↗

bioRxiv2026

MetaClaw: an auditable AI agent for end-to-end, multi-directional metagenomic and multi-omics analysis

End-to-end omics analysis requires more than selecting tools: a usable agent must bind data correctly, execute long workflows without blocking, preserve provenance and recover the biological conclusions that motivate an analysis. Existing LLM-driven bioinformatics agents automate parts of this process, but their operational dependencies and conclusion-level validity are often unclear. Here we present MetaClaw, an auditable agent that maps a user request to a registered workflow, executes standardized upstream processing on FlowHub, and runs study-specific downstream analyses in network-isolated OpenClaw containers. A YAML registry and an explicit plan-submit-poll-finalise lifecycle record file bindings, parameters, scripts, environments and outputs in per-job bundles. Across the full cohorts of four published studies (769 metagenomic profiles), MetaClaw recovered 4/4 sorghum marker groups, 3/3 RRMS features, 4/5 canonical CRC markers among the top 20 classifier features and 5/5 permafrost marker groups. In 45 model-by-prompt runs, upstream completion was consistent whereas downstream validity depended on the backend and instruction detail; three decoy-tested endpoints showed no significant differences. In 48 ablation sessions, removing the registry, planning loop or manifest caused distinct losses, with registry removal increasing time, tool calls and token cost. MetaClaw therefore connects standardized upstream execution, local analytical flexibility and conclusion-level validation in a rerunnable framework for metagenomic and microbiome multi-omics analysis.

bioinformatics↗

bioRxiv2026

FXR-mediated recruitment of PPP1CB suppresses SMAD2/3 phosphorylation to mitigate pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive and fatal interstitial lung disease with limited treatment options and poorly understood molecular underpinnings. Dysregulated TGF-{beta}/SMAD signaling is a key driver of fibrotic remodeling, promoting persistent myofibroblast activation and excessive extracellular matrix deposition. Here we identify the Farnesoid X receptor (FXR), a bile acid activated nuclear receptor, as a previously unrecognized suppressor of pulmonary fibrosis. FXR expression is significantly reduced in lung tissues from patients with PF and in myofibroblasts derived from BLM-induced mouse models, correlating inversely with fibrosis severity. Genetic ablation of FXR exacerbates BLM-induced pulmonary fibrosis by promoting fibroblast hyperactivation and dysregulation of the TGF-{beta}/SMAD signaling pathway. Mechanistically, we identify PPP1CB as a previously unrecognized FXR-interacting protein in primary myofibroblasts derived from IPF patients. We further show that FXR both increases chromatin accessibility at the PPP1CB locus and assembles a functional complex with PPP1CB, which in turn promotes SMAD2/3 dephosphorylation and suppresses their nuclear translocation. Notably, the clinical-stage FXR agonist TERN101 exhibits potent therapeutic efficacy in a BLM-induced mouse pulmonary fibrosis model. These findings establish FXR as a critical antifibrotic regulator in lung tissue and suggest that pharmacological activation of FXR may offer a promising therapeutic strategy for IPF.

cell biology↗

bioRxiv2026

PEPC Gene Family Evolution Across Arecaceae: Complete Five-Subfamily Evidence for a Two-Lock Model of Irreversible C4 Exclusion

BackgroundC4 photosynthesis has evolved more than sixty times across flowering plants, but never in palms. Over 2,500 palm species have spent more than 100 million years in high-light, water-stressed habitats where C4 physiology would be advantageous, yet none have taken this path. Phosphoenolpyruvate carboxylase (PEPC) is the enzyme that gates entry into the C4 pathway. In every C4 grass, a commelinid-specific paralog called PEPC1 drives the CO2-concentrating mechanism that defines the syndrome. Until this study, one of the five palm subfamilies -- Ceroxyloideae -- had never been examined for PEPC gene content. ResultsWe present a complete PEPC census across 13 palm species spanning all five subfamilies (Calamoideae, Nypoideae, Coryphoideae, Ceroxyloideae, Arecoideae). Ceroxyloideae was characterized for the first time, using deep tBLASTn screening of ten million whole-genome shotgun reads. PEPC1 is absent from every palm species examined. Copy numbers are tightly constrained to 5-7 per genome, in stark contrast with the 6-25 copies found in grasses. A phylogenetic analysis of 337 PEPC sequences places all 55 palm loci at basal positions relative to the PEPC1 clade, consistent with the palm lineage having diverged approximately 120 million years ago -- roughly 15 million years before the PEPC1 duplication that occurred within the commelinids. Birth-death modeling reveals long-term gene family stasis in palms. Codon substitution analyses yield a genome-wide {omega} of 0.0582, indicating pervasive purifying selection and no signature of C4-specific adaptation. Coconut PEPC promoters uniformly lack the mesophyll-specific MESP-1/GT-1/DOF regulatory module that is required for C4-type gene expression. ConclusionsWe propose a Two-Lock Model of irreversible C4 exclusion in palms. The first is a Gene Lock: PEPC1 is phylogenetically absent from all five subfamilies. The second is a Regulatory Lock: the ancestral promoter architecture of palm PEPC genes lacks the cis-elements needed for mesophyll-specific expression. Together, these two locks -- one phylogenetic, one regulatory -- explain why C4 photosynthesis has never arisen in one of the largest C4-absent plant families. The model provides a testable framework for investigating other lineages that have remained closed to the C4 path.

evolutionary biology↗

bioRxiv2026

Internalized Components of Membrane Attack Complexes Disrupt Proteostasis and Acquire Alarmin-Like Properties

Immune effects of membrane attack complexes (MAC) have been widely attributed to their abilities to cause cell death. Here, we show that the MAC component, C9, forms non-cytolytic aggregates with pro-inflammatory effects. Intracellular aggregates of C9 are detected within inflamed tissues of patients in association with endothelial cell (EC) activation but not increased cell death. We identify NUMBL as a Rab35 effector that directly binds surface-bound C9 to promote C9 internalization and entry into the endolysosomal pathway. Within acidified endolysosomes, C9 forms insoluble aggregates that are targeted for degradative aggrephagy in a process that activates NF-{kappa}B. For C9 aggrephagy to occur, ZFYVE21, a Rab5 effector, complexes with RNF34 to bridge C9 aggregates to LC3B+ aggresome membranes. We detect C9 aggregates in vivo, and we show that a ZFYVE21-RNF34 signaling axis is required for C9 aggrephagy and NF-{kappa}B -dependent EC activation in three separate mouse models. Mice with conditional loss of ZFYVE21 in ECs show reduced aggregraphy, resulting in attenuated systemic inflammation and reduced tissue injury following skin transplantation. Our data show that the C9 component of MACs forms intracellular aggregates with alarmin-like properties.

biochemistry↗

bioRxiv2026

Slc25a34-Mediated Mitochondrial-to-Cytoplasmic AMP Transport Activates Brown Adipose Tissue Thermogenesis

Metabolites are emerging as signaling molecules that mediate cellular function, extending beyond their well-established roles in metabolic pathways. Members of the solute carrier (SLC) family mediate metabolite transport across cellular compartments, raising the possibility that these proteins may sense environmental stimuli and regulate cellular biological processes by triggering signaling cascades linked to metabolite transport. This study investigated the response of the SLC25A family, a unique set of inner mitochondrial membrane-localized transporters, to cold as an environmental stimulus in mediating metabolic reprogramming; and whether this reprogramming, driven by the metabolites transported by SLC25A proteins, subsequently promotes the activation of thermogenesis in brown adipocytes. After screening members of the SLC25A family for their responsiveness to cold stimuli and brown adipose tissue (BAT) activation, we found that Slc25a34 was robustly induced under these conditions. We further demonstrated that Slc25a34 mediates the transport of adenosine monophosphate (AMP), derived from de novo glucose synthesis, from mitochondria to the cytosol. This transport potentiates AMP-activated protein kinase (AMPK) signaling and glycolytic flux in brown adipocytes, both of which facilitate BAT thermogenesis during cold exposure. Intriguingly, cold exposure directly promoted the activation of peroxisome proliferator-activated receptor gamma (PPAR{gamma}), which transcriptionally upregulated Slc25a34 expression. More importantly, genetic ablation of Slc25a34 impaired BAT thermogenesis. Thus, our study reveals a novel cold-induced metabolite-sensing pathway, where Slc25a34-mediated AMP transport between mitochondria and the cytosol serves as a critical signal for activating BAT thermogenesis. These findings provide compelling evidence that metabolite transport across cellular compartments acts as a key driver of cellular physiology, thereby offering novel insights into metabolite-based therapeutic strategies for metabolic diseases. HighlightsO_LISlc25a34 is cold-responsive and transcriptionally regulated by PPAR{gamma}. C_LIO_LISlc25a34 functions specifically to mediate the mitochondrial-to-cytosolic transport of AMP in brown adipocytes. C_LIO_LIMitochondrially sequestered de novo synthesized AMP acts as a signaling reservoir, and its Slc25a34-mediated efflux to the cytosol activates AMPK and glycolysis, supporting BAT thermogenesis. C_LI

cell biology↗

bioRxiv2026

Effect of CSFV on Differential Genes of Histone Lactylation at H3K18 in the PI3K-AKT Signaling Pathway

Classical swine fever (CSF) is a highly contagious disease caused by Classical swine fever virus (CSFV), posing a serious threat to the global swine industry. This study aimed to investigate the effect of CSFV on differential genes of histone lactylation at the H3K18 site in the PI3K-AKT signaling pathway. The site with the most significant change in histone lactylation antibody level was screened by Western blot. Omics analysis was performed using CUT&Tag technology to identify differential genes in the PI3K-AKT pathway between the CSFV-infected group and the mock group, followed by validation using RT-qPCR. Functional analysis of significantly differential proteins was conducted, and the protein expression level of THBS4 was detected by Western blot. The results showed that after CSFV infection of 3D4/21 cells, the H3K18la site exhibited the most significant difference in antibody level. A total of 8,859 differential genes at the H3K18la site were identified by CUT&Tag analysis, including 6,349 up-regulated genes and 2,510 down-regulated genes. Further focusing on the PI3K-AKT signaling pathway, 10 differential genes were identified, comprising 6 up-regulated genes and 4 down-regulated genes. Compared with the control group, the mRNA expression levels of CD19, LAMA1, PDGFRA, BDNF, ANGPT4, and THBS4 were up-regulated in the CSFV-infected group, while FOXO3 and NRTN were down-regulated. Western blot results showed that the protein expression level of THBS4 increased after CSFV infection. These findings lay an important foundation for understanding the molecular mechanisms regulating viral replication and immune evasion, and have significant scientific implications and potential application value.

microbiology↗

bioRxiv2026

eRNAformer enables genome-wide de novo mapping of enhancer-derived RNA loci

Enhancer-derived RNAs (eRNAs) are critical regulators of gene transcription, yet their genome-wide annotation remains challenging. Here, we present eRNAformer, a multi-modal deep learning framework that integrates convolutional neural networks with transformers, specifically designed to capture long-range genetic features associated with bidirectional transcription. This approach enables de novo mapping of eRNA loci using DNA sequence and aggregated conventional RNA-seq data. When evaluated on ENCODE datasets, eRNAformer demonstrated high sensitivity and specificity in discriminating known eRNA loci from non-eRNA loci. Notably, the newly identified eRNA loci were enriched with evolutionarily constrained variants and genetic risk factors for complex diseases, and exhibit potential relevance for cancer therapy. Applied to GEO datasets, eRNAformer identified a range from 14,219 to 56,451 eRNA loci across multiple hematologic malignancies, facilitating the construction of a comprehensive eRNA database for blood cancers. We further identified and experimentally validated FOXO1e, a cluster of eRNAs located approximately 120 kb upstream of FOXO1, a known oncogene that drives t(8;21) acute myeloid leukemia (AML) preleukemic program. Together, these findings establish eRNAformer as a powerful tool for genome-wide eRNA annotation, provide a valuable resource for eRNA studies in hematologic cancers, and underscore the functional importance of eRNAs in AML pathogenesis.

bioinformatics↗

bioRxiv2026

CellTosg2Sequence: A Unified Text-Omics-Signaling-Graph Large Language Model for Single-Cell Analysis

In single-cell (sc)-based scientific discovery, text-formatted biomedical prior knowledge and signaling graphs are essential for annotating and interpreting numeric sc-omics data and for generating novel testable hypotheses. A major limitation of existing single-cell large language models (scLLMs) is that they rely on numeric expression data with gene names as the only textual signal, while comprehensive biomedical priors -- cellular localization, gene function, disease associations, and signaling interaction patterns -- remain absent from the model input. We introduce CellTosg2Sequence, a textual-prior- and signaling-graph-augmented cell-omics-sentence language model. A lightweight heterogeneous graph encoder maps a curated 62,507-node biomedical knowledge graph (KG) into compact virtual tokens that are prepended to each cell sentence, allowing the language model to condition on biological structure with minimal sequence-length overhead. We train CellTosg2Sequence with a three-stage objective: Stage I anchors the KG channel under autoregressive language-model pretraining, leveraging Qwen2.5-32Bs own language reasoning for rapid KG alignment; Stage II aligns labels via supervised fine-tuning with KG-anchored InfoNCE; Stage III applies Group Relative Policy Optimization (GRPO) with an ontology-hierarchy reward, enabling free-generation cell-type prediction that generalizes beyond the closed training vocabulary. Across multiple benchmarks and ablation experiments, CellTosg2Sequence outperforms strong baselines. All results are achieved with lightweight LoRA training and a single unified checkpoint. Data ethicsThis work uses publicly available single-cell datasets from the Human Cell Atlas (https://www.humancellatlas.org) and the Tahoe-100M consortium. All HCA constituent studies were collected under appropriate donor consent and institutional oversight as described in their original publications; we perform computational re-analysis only and introduce no new human subjects data. HCA data access follows the HCA Data Portal terms of use. No new patient data are collected in this study; no additional IRB approval is required for this secondary computational analysis.

bioinformatics↗

bioRxiv2026

From hotspot dependence to distributed robustness in resistance-aware lead optimization

Drug resistance remains a recurrent failure mode in targeted anticancer and antiviral therapy, and resistance evidence often enters only after compound selection. ResistAgent is an evidence-constrained framework that converts mutational liabilities into design-time objectives through site- and combo-aware resistance mapping, deterministic mechanism diagnosis and robust counter-design. In EGFR-Erlotinib and HIV-RT-Rilpivirine, the framework separated residue-level liabilities from observed HIV combination liabilities and linked prioritized mutations to anchor loss, pocket rearrangement, electrostatic shifts and contact redistribution. Same-budget paired searches showed that robust objectives changed lower-tail mutant-panel behavior and interaction-dependence profiles while prioritizing robustness over average-affinity behavior. Under predefined liability panels, robust-objective trajectories shifted support away from mutable hotspot contacts toward more distributed interaction networks. Supplementary physical summaries and ranking-first benchmarks support the validation envelope of this resistance-aware design strategy.

bioinformatics↗

bioRxiv2026

Fibulin-2 transduces a matrix-to-metabolism signal in kidney fibrosis

Fibrotic extracellular matrix (ECM) is not merely a structural scaffold but an instructive signaling interface that shapes epithelial cell state. However, the molecular cues by which matrix remodeling controls tubular metabolism during kidney fibrosis remain poorly defined. Here, we identify Fibulin-2 (FBLN2) as a fibroblast-derived matrix cue that transduces fibrotic ECM remodeling into tubular mitochondrial metabolic reprogramming. Using fibroblast-selective deletion of Smoothened (Smo) across distinct fibroblast subpopulations, we found that loss of fibroblast Smo preserved kidney function and attenuated fibrosis in mouse models of chronic kidney injury. Multi-omics profiling revealed coordinated remodeling of the fibrotic matrisome, highlighted by suppression of FBLN2, an ECM glycoprotein genetically linked to kidney function in humans. Mechanistically, FBLN2 engaged EGFR in tubular epithelial cells and activated EGFR-AKT signaling in a non-canonical ligand-like manner. This signaling axis suppressed acetyl-CoA acetyltransferase 1 (ACAT1), a mitochondrial regulator of fatty acid oxidation and amino acid metabolism. Disruption of fibroblast Smo-FBLN2 signaling restored ACAT1-dependent oxidative metabolism and reduced tubular fibrotic activation. Spatial lipidomics revealed compartment-specific lipid remodeling associated with altered mitochondrial fatty acid metabolism, including acylcarnitine and phospholipid changes linked to reduced fibrotic injury. Together, these findings define a Fibulin-2-EGFR-ACAT1 matrix-to-metabolism signaling axis that couples fibrotic ECM remodeling to tubular mitochondrial metabolism during kidney fibrosis.

cell biology↗