Biology subjects

Chen, J.

Publications and source records attributed to Chen, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Kintsugi maps nucleus-poor RNA compartments in subcellular spatial transcriptomics

Subcellular spatial transcriptomics captures where RNA is in tissue, but a single location holds too few molecules of any one gene to estimate composition alone. Every current method fixes in advance where to borrow -- a smoothing scale, a cell outline or a factor model -- and the fixed choice shapes what is visible. Kintsugi removes the fixed choice and lets held-out molecules decide, gene by gene, how much to borrow from spatial neighbours and from other genes at the same location. On a lung section measured by both Xenium and Visium HD, the data-chosen allocation placed an epithelial programme where the Xenium molecules were, ahead of smoothing, cell segmentation and a factor model; the result replicated across tissues and against protein. Across a 45-core pulmonary fibrosis cohort, separating composition from captured amount shows that a fibroblastic focus is not a place with more RNA but a place with different RNA: 2.8-fold higher in activated-fibroblast composition while segmented nuclear density is at most 1.08-fold higher.

bioinformatics↗

bioRxiv2026

A patient-centric therapeutic paradigm uncouples prostate cancer suppression from systemic metabolic collapse

The clinical benefits of cancer therapies are often compromised by the tolerable adverse effects that impair systemic organismal health and may evolve into latent life threats. Here, we identified profound abiraterone-induced but androgen-independent metabolic perturbations in prostate cancer patients and developed Lifehug-9892 to balance tumor therapy with systemic metabolic homeostasis. By integrating population cohorts with high-resolution metabolomics, we demonstrate that abiraterone induces profound systemic lipidomic dysregulation, characterized by the massive, pathological accumulation of desmosterol. Abiraterone inhibits but stabilizes DHCR24, leading to a metabolic trap in patients showing elevated levels of both desmosterol and cholesterol. Desmosterol accumulation is highly lipotoxic, potently triggering endothelial cell senescence and necrosis, macrophage foam cell formation, murine atherosclerosis, and hepatic senescence. To mechanistically uncouple and therapeutically rescue this systemic metabolic collapse, Lifehug-9892 was rationally designed to selectively retain on-target CYP17A1 inhibition while completely sparing DHCR24 function. Lifehug-9892 maintains potent tumor-suppressive activity while fully preserving the desmosterol-cholesterol metabolic axis and preventing systemic cardiovascular and hepatic damage. Our study uncovers a critical mechanistic link between drug-induced metabolic dysregulation and organismal health in cancer patients, providing a biochemical framework for developing patient-centric targeted therapies that preserve host homeostasis.

cancer biology↗

bioRxiv2026

Single-Molecule Nanopore Profiling of p53-TAD Conformational Dynamics, Interactions, and Inhibition

Investigating the conformational dynamics of intrinsically disordered proteins (IDPs) is essential to understanding how their structural heterogeneity underlies function and how their dysregulation contributes to diseases. Here, we utilized an MspA nanopore-based approach for studying the conformational dynamics and interactions of IDPs at the single-molecule level. The platform was demonstrated using the intrinsically disordered transactivation domain of tumor suppressor p53 (p53-TAD), one of the important proteins in cancer biology. We showed that MspA can stably capture p53-TAD and resolve up to six distinct current states with frequent interconversions, revealing a rich conformational landscape. The nanopore also detected the effect of a cancer-associated double mutational variant, N29K/N30D. Combining experiments with steered molecular dynamics simulations, we showed that the mutant sampled compact conformational states more frequently than wild type, consistent with previous NMR studies. Importantly, the MspA platform enabled direct monitoring of E3 ligase MDM2 binding to p53-TAD and resolved how this interaction is inhibited by anti-cancer compound epigallocatechin gallate (EGCG). Notably, EGCG stabilizes one of the six states sampled by p53-TAD, providing a mechanistic explanation for its inhibitory effect. Together, these findings demonstrate the promise of the nanopore platform for label-free monitoring of IDP conformational dynamics, modulation, binding and inhibition at single-molecule resolution.

biophysics↗

bioRxiv2026

ARMC1 regulates mitochondrial fatty acid oxidation through theinsertase/scramblase MTCH2

MTCH2 (mitochondrial carrier homolog 2) is a noncanonical member of the solute carrier family with five transmembrane (TM) helices, localized to the mitochondrial outer membrane. MTCH2's atypical topology creates a membrane-accessible hydrophilic groove, predicted to be necessary for its protein insertase and lipid scramblase activities. MTCH2 is linked to lipid metabolism and obesity and is required for starvation-induced mitochondrial hyperfusion. Here, we show that MTCH2 is a stable component of a complex containing the Armadillo (ARM) repeat-containing protein, ARMC1, and the DnaJ/Hsp40 chaperone protein, DNAJC11. Protein crosslinking, protein structural modeling, and molecular dynamics simulations demonstrate that the ARMC1 alpha-helical C-terminal domain (CTD) inserts into and stably interacts with the MTCH2 hydrophilic groove and blocks its lipid scramblase activity. We observe that starvation-induced mitochondrial fatty acid oxidation (FAO) is negatively regulated by the ARMC1-MTCH2 interaction. In ARMC1-deficient cells, FAO is stimulated compared to wild-type cells and lipid droplet abundance is significantly reduced. The altered lipid phenotype of ARMC1-/- cells is strictly dependent on MTCH2 and is reversed by ARMC1 expression in a manner dependent on its CTD. Beyond this metabolic axis, we also identify a function for ARMC1 in regulating lysosomal distribution and autophagic flux that is independent of its CTD and interaction with MTCH2. Thus, our data support a model in which the MTCH2-ARMC1 interaction functions as a metabolic switch during starvation to regulate the balance between fat storage and fat burning.

cell biology↗

bioRxiv2026

A New Enzyme Family Catalyzing Methyllanthionine Sulfoxide Formation in Anti-phage Lanthipeptides

Lanthipeptides are one of the largest classes of ribosomally synthesized and post-translationally modified peptides (RiPPs). The coi biosynthetic gene cluster (BGC) from Streptomyces coelicolor A3(2) encodes a canonical class I lanthipeptide dehydratase (CoiB) and cyclase (CoiC), a bifunctional enzyme (CoiSA) with an O-methyltransferase (MT) and glutamyl lyase (GL) domain, and a protein of unknown function (CoiH). The product of the coi BGC was recently shown to impart anti-phage activity, but its structure is still unresolved. Previous work investigated the regioselectivity of the GL domains in CoiB and CoiSA and the stereochemistry of the cyclized precursor peptide, but the function of CoiH was not addressed. In this study, co-expression of the peptide CoiA1 with CoiBCSAH resulted in a +16 Da addition on the cyclized peptide compared to when CoiH was omitted. LC-MS/MS analysis indicated that this modification occurred in the first thioether ring. A combination of site-directed mutagenesis, comparison of linear and cyclized peptide substrates, hydrogen peroxide (H2O2) treatment, and collision-induced dissociation (CID) mass spectrometric analysis suggested that the sulfur atom in the first methyllanthionine was oxidized to a sulfoxide group by CoiH. This hypothesis was confirmed by NMR analysis. CoiH represents a previously uncharacterized oxygenase family catalyzing sulfoxide formation. Structure prediction tools suggest a novel enzyme fold without obvious metal or cofactor binding sites, raising the possibility that CoiH is a cofactor independent oxidation enzyme.

biochemistry↗

bioRxiv2026

Kinesin-1 holoenzyme assembly coordinates cargo-adaptor recognition with heavy-chain autoinhibition

Kinesin-1 is a major microtubule-based molecular motor that transports diverse cellular cargoes, yet how assembly of its subunits is coupled to cargo recognition and motor regulation remains poorly understood. Mammalian kinesin-1 functions as a heterotetrameric holoenzyme composed of kinesin heavy chains (KIF5s) and kinesin light chains (KLCs), but the structural principles linking holoenzyme assembly to motor regulation remain unclear. Here, using KIF5C as a model system, we define the molecular mechanisms underlying kinesin-1 holoenzyme assembly and cargo-adaptor regulation. We identify a conserved coiled-coil interface between KIF5C and KLC1 that mediates their 2:2 assembly, with quantitative mutagenesis revealing key hydrophobic determinants of complex formation. We further demonstrate that the mitochondrial adaptor TRAK2 directly engages the KIF5C CC4 cargo-binding platform through a defined 2:2 interaction required for mitochondrial recruitment of KIF5C. Although KLC1 and TRAK2 bind distinct regions of KIF5C, KLC1 modulates TRAK2 association through steric and conformational effects, revealing how holoenzyme composition influences cargo-adaptor accessibility. Mechanistically, we identify a previously unrecognized intramolecular interaction between the KIF5C CC1 and CC4 domains that forms a stalk-mediated autoinhibitory latch. TRAK2 and KLC1 release this inhibitory interaction through distinct mechanisms. Together, our study establishes a molecular framework in which kinesin-1 holoenzyme assembly regulates cargo-adaptor recognition and autoinhibitory remodeling, providing mechanistic insight into how molecular motors coordinate cargo engagement with activation.

biochemistry↗

bioRxiv2026

A Conserved SIFamide Circuit Functions as the Insect Vagus Nerve

The insect functional homolog of the mammalian vagus nerve has remained elusive. Here, we identify the SIFamide (SIFa) peptidergic circuit as this homolog in Drosophila melanogaster. SIFa neurons project the longest axons from the brain to the hindgut ampulla, forming synapses with peripheral SIFa-receptor (SIFaR) neurons originating in the abdominal ganglion. This circuit is functionally plastic: sexual experience enhances synaptic strength at the hindgut, increasing excretion while reducing mating duration to to favor energy conservation and metabolic recovery. Mechanistically, this shift involves octopaminergic/tyraminergic gating and SIFa-mediated modulation of Adipokinetic Hormone (AKH) from the corpora cardiaca. We further uncover a feedback loop in which SIFaR/Allatostatin-A (AstA) neurons project back to the brain, signaling hindgut physiological status to SIFa neurons via AstA-R1. This hindgut projection is conserved across diverse insect orders. Thus, the SIFa-SIFaR circuit constitutes an evolutionarily conserved "insect vagus nerve" that integrates metabolic state and reproductive history to optimize survival strategies.

neuroscience↗

bioRxiv2026

RADF: Reference-Anchored Dynamic Flow for Spatial Perturbation Profile Completion

Spatial perturbation profiling is becoming an important tool in functional genomics because it reveals how genetic interventions reshape transcription within intact tissue contexts. However, destructive readout and limited screening capacity leave many perturbation-by-location response profiles unmeasured, motivating the task of spatial perturbation profile completion. The task is to infer the held-out response population at query locations from reported profiles of the same perturbation. Existing methods either generate responses de novo or reuse these profiles without spatial adaptation. These strategies make it difficult to preserve empirical population structure while modeling location-specific variation. Our key insight is that the reported population already defines an empirical response distribution for the target perturbation. To exploit this empirical support, we propose Reference-Anchored Dynamic Flow (RADF), which employs a Sinkhorn-balanced decoder to construct a population-valued anchor in which every reference profile has equal total contribution. Additionally, a bounded dynamic relational flow is used to recompute spatial relations from the evolving expression state and query geometry. Across diverse spatial contexts, RADF reduces macro E-distance by 70.6% compared with an existing state-of-the-art spatial method, highlighting the advantage of combining a reference-supported population anchor with bounded, location-dependent refinement. Code will be made publicly available upon acceptance.

bioinformatics↗

bioRxiv2026

Parasitic Vectors in Aquaculture: Neobenedenia girellae and Leeches as Potential Transmission Agents for Trypanosoma carassii spectrum and Pathogenic bacteria

Parasitic infections pose multifaceted threats to farmed fish, extending beyond direct pathogenicity to facilitate infections of bacteria, viruses, and microparasites. This synergistic interaction often leads to co-infections that significantly exacerbate disease outbreaks and mortality, presenting a severe challenge to aquaculture sustainability. Recently, a novel trypanosomiasis caused by the Trypanosoma carassii spectrum has emerged in cage-cultured Larimichthys crocea along the southeast coast of China, resulting in widespread prevalence and high mortality rates. Although this pathogen is hypothesized to originate from freshwater fish, its transmission route in marine environments has remained elusive. In this study, we investigated potential vectors and intermediate hosts of T. carassii spectrum, including leeches and monogenean in natural marine settings, and simulated transmission pathways using an established laboratory model involving T. carassii spectrum, Micropterus salmoides and the leech Poecilobdella manillensis. First, our field surveys in the coast of Ningde, Fujian Province, revealed a nearly 100% co-infection rate of T. carassii spectrum and the monogenean Neobenedenia girellae in diseased juvenile L. crocea. PCR analysis detected T. carassii spectrum traces in some N. girellae specimens, and subsequent experiments confirmed that N. girellae ingests the trypanosome while feeding on host blood. Furthermore, bacterial co-pathogens, such as Vibrio harveyi, were also detected within N. girellae. We also document two fatal leech infestations: Zeylanicobdella arugamensis in hybrid groupers (Epinephelus moara [female] X Epinephelus lanceolatus [male]) in Zhangpu, and Limnotrachelobdella okae in E. lanceolatus and E. fuscoguttatus in Raoping. These leeches tested negative for trypanosomes but carried pathogenic bacteria that co-infected the host fish; nonetheless, they are established vectors for trypanosome transmission. In a laboratory cohabitation model simulating T. carassii spectrum transmission, infected M. salmoides were housed with healthy conspecifics under three conditions: Group A (with the leech P. manillensis), Group B (no leeches), and Group C (no leeches, with physical separation between infected and healthy fish). After 14 days, blood smear microscopy and PCR analysis revealed infection rates in healthy fish of 58.33% in Group A, 40.00% in Group B, and 0% in Group C. Conclusively, T. carassii spectrum can be transmitted via leeches (with higher efficiency) and may also spread through direct contact under high-density aquaculture conditions, whereas N. girellae may act as an incidental vector, further research is warranted to clarify transmission dynamics in natural marine ecosystems. Additionally, our findings highlight the role of ectoparasites, including N. girellae and leeches, as potential reservoirs and vectors for bacterial pathogens of fish. In high-density intensive aquaculture, this vectorial capacity transforms parasites from primary pathogens into key drivers of polymicrobial disease outbreaks.

zoology↗

bioRxiv2026

Logic-Gated Fluorogenic RNA Reporters for Multiplexed Live-Cell Imaging

Multiplexed imaging of biomolecular networks in living cells is limited by the small number of spectral separable fluorophores and the need to monitor dynamic processes in real time. Here, we present logicFRIES, a fluorogenic RNA (FR)-based platform that enables eight-plex live-cell imaging through programmable, logic-gated activation coupled with sequential fluorescence imaging. By integrating small-molecule-binding RNA aptamers into dye-activating fluorogenic RNAs, we engineered trigger-responsive FR reporters. This design implements an AND-gated mechanism in which fluorescence activation requires both a cognate trigger molecule and its corresponding fluorogenic dye, thereby expanding multiplexing capacity without adding new fluorophores. Using three membrane-permeable triggers, tetracycline, ASP2905, and guanine, we generated three distinct trigger-defined activation states for each engineered Broccoli and Pepper FR. Combined with orthogonal Corn/DFHO and DNB/TMR-DN reporter pairs, logicFRIES supports eight-plex imaging through sequential trigger/dye addition, imaging, and wash-based stripping cycles. We demonstrate robust, specific, and reversible fluorescence switching of these multiplexed FR reporters in living HEK293T and SKBR3 cells. Overall, logicFRIES extends live-cell imaging beyond conventional spectral limitations and provides a modular foundation for potentially developing multiplexed sensors targeting endogenous RNAs, proteins, and small molecules in complex cellular systems.

molecular biology↗

bioRxiv2026

Shared phylogeographic structuring and recurrent hybridization underlie the diversification of Microhyla frog complexes in the Indochinese biodiversity hotspot

Comparative phylogeography provides a powerful framework to identify the historical processes shaping biodiversity hotspots by testing whether co-distributed species exhibit shared patterns of diversification. Southeast Asia harbors exceptional biodiversity, yet the extent to which common paleogeographic and climatic drivers have structured diversification across taxa remains poorly understood. Here, we investigated the evolutionary history of five widespread Microhyla species complexes distributed across the Indochinese Peninsula and adjacent regions using dense mitochondrial sampling (1,388 individuals) combined with genome-scale ddRAD sequencing (280 individuals). Across all complexes, both approaches recovered multiple lineages and remarkably congruent phylogeographic breaks and contact/intergradation zones associated with major Indochinese regions, including Myanmar, the Tenasserim-Malay Peninsula, southern Vietnam, and northern Vietnam-southern China, supporting the hypothesis that Indochina functions as a mosaic of stable biogeographic units. However, lineage divergence varied substantially among complexes, suggesting that common biogeographic drivers interacted with species-specific demographic histories. Phylogenomic analyses and cyto-nuclear discordance further revealed historical introgression in every complex, indicating that diversification involved both long-term allopatric isolation and reticulate evolution. These findings portray the Indochinese biodiversity hotspot as a dynamic evolutionary system where cycles of fragmentation and reconnection have repeatedly reshaped lineage boundaries. Moreover, the complex phylogeographic structure recovered exemplifies the urgent need for taxonomic revisions, for which genome-scale data provide an essential framework to validate mitochondrial hypotheses and assess admixture patterns for species delimitation. Finally, regions such as the southern Annamites and Tenasserim Hills emerged as recurrent hotspots of genetic diversity across independent lineages, highlighting their importance for conserving not only species/lineage richness but also the evolutionary processes and adaptive potential that sustain biodiversity.

zoology↗

bioRxiv2026

Amyloid-Tau PET Fusion Reveals Covarying Network Territories Linked to Disease Stage, Cognition, and APOE4 in Alzheimers Disease

BackgroundAmyloid-beta (A{beta}) and Tau are defining pathologies of Alzheimers disease, but their relationship varies substantially across the brain. Amyloid deposition is spatially widespread, whereas Tau shows greater regional heterogeneity and closer relationships with disease severity. Consequently, understanding the disease requires more than measuring the two pathologies independently or summarizing them within predefined regions. A major unresolved question is how Amyloid and Tau covary across the whole brain, where their spatial patterns converge or diverge, and whether their local combination carries distinct information about disease stage and cognition. MethodsWe analyzed paired florbetapir Amyloid PET and flortaucipir Tau PET from the Alzheimers Disease Neuroimaging Initiative (ADNI), comprising 378 paired imaging sessions from 320 participants spanning cognitively normal (CN), mild cognitive impairment (MCI), and Alzheimers Dementia (AD). High-order joint independent component analysis was used to identify fine-grained, data-driven patterns of Amyloid-Tau covariance across individuals. The resulting Amyloid and Tau maps were characterized by their spatial similarity and correspondence with rsfMRI-derived intrinsic functional networks. We then used the same data-driven spatial regions to quantify, for each participant, the relative extent of Amyloid abnormality alone, Tau abnormality alone, and spatially overlapping Amyloid-Tau abnormality. ResultsNinety-six non-artifactual Amyloid-Tau components were identified, of which 73 showed appreciable spatial correspondence between their paired Amyloid and Tau maps, while 17 were Tau-localized and 6 Amyloid-localized. Amyloid component maps more frequently corresponded with rsfMRI-derived intrinsic network organization than Tau maps. Expression of the joint components differed across diagnosis groups, demonstrating spatially heterogeneous disease-stage patterns. Within the same data-driven regions, isolated Amyloid, isolated Tau, and overlapping Amyloid-Tau abnormality showed markedly different disease-stage profiles: Amyloid-only abnormality was more prominent in the earlier CN-to-MCI contrast, Tau-only abnormality in contrasts involving AD, whereas spatially overlapping Amyloid-Tau abnormality showed the broadest differences across disease stages and the largest mean CN-to-AD expansion. Overlapping abnormality was also associated with cognition across the greatest number of components and showed the strongest overall association with ADAS13. APOE4-related diagnosis-stage differences were considerably more widespread for pathology measures containing Amyloid than for Tau-only abnormality.

neuroscience↗

bioRxiv2026

Brain State Dynamics and Developmental Differences in Reading Comprehension

Reading comprehension is a complex cognitive task that involves dynamic interactions between the brain and external information. Previous studies on reading development primarily focused on localized or static brain activities. However, it remains an enigma how brain state dynamics evolve with development underlying reading comprehension. This study aims to address this issue by combining functional magnetic resonance imaging (fMRI) with Hidden Markov Model (HMM) to explore brain state dynamics. A total of 35 typically developing children and 31 adults were scanned while reading a story. Our results demonstrated a tripartite brain state organization, characterized respectively by high activities in the visual (State #1), language (State #2), and default mode network (DMN, State #3) regions. Children exhibited significantly longer dwell time in the DMN state (State #3) compared to adults, along with a higher probability of transitioning from the language state (State #2) to the DMN state (State #3). In addition, adults exhibited greater flexibility in state transitions during reading comprehension. Finally, the alignment between the dynamic states of children and the average states of adults was a significant positive predictor of their reading comprehension performance. This study provides a novel, intuitive perspective on how brain state dynamics evolve during the development of reading comprehension.

neuroscience↗

bioRxiv2026

Integrin diversity enables dynamic adhesion control in a homeostatic epithelium

Homeostatic epithelia must balance stem cell maintenance, progenitor differentiation, and clearance of damaged cells while preserving barrier integrity. We investigated how integrin- ECM adhesion is regulated in the Drosophila midgut, a homeostatic epithelium with basal stem cells. The midgut expresses two beta integrins: ubiquitous {beta}Mys and endoderm-specific {beta}{nu}. ISCs and enteroblasts express only {beta}Mys, which pairs with Mew to mediate enteroblast attachment to the basement membrane. In contrast, enterocytes express both {beta}Mys and {beta}{nu}; Mew/{beta}{nu} supports ECM adhesion, while {beta}Mys pairs with Scab and localises to the basal labyrinth. Enterocytes lacking Mew or {beta}{nu} detach and are apically extruded, but this phenotype is rescued when the corresponding integrin is removed from the entire epithelium. Thus, enterocytes compete for basement membrane adhesion, with less adhesive cells being eliminated by their neighbours. In {beta}{nu} homozygotes, enteroblasts expand basally and adopt a migratory-like morphology. We propose that integrin-mediated competition for ECM adhesion is a general phenomenon that functions in the midgut to promote enterocyte extrusion, which stimulates the migration of nearby enteroblasts to maintain gut homeostasis.

developmental biology↗

bioRxiv2026

PASTRI: Resolving Stage-Specific Cell-State Dynamics from Annotated Cell Lineage Trees

Cellular transitions between phenotypic states are fundamental to development and disease, yet quantitative analysis of their dynamics remains challenging. Here we present PASTRI (Phylogenetic Adjacency-based State Transition Rate Inference), a computational framework that infers transition rates from cell lineages/phylogenies annotated with terminal phenotypic states, such as single-cell transcriptomes. We validate PASTRI using simulated lineages and the Caenorhabditis elegans embryonic lineage. Importantly, by leveraging cell pairs at varying phylogenetic distances, PASTRI accurately resolves stage-specific transition rates, circumventing the issue of developmental changes in dynamics. Applied to three cell phylogeny datasets from our lineage-tracing experiments spanning diverse developmental/disease models and tracing systems, PASTRI uncovers rate-limiting steps in the activation of hepatic stellate cells and the differentiation of primordial lung progenitors, as well as attractor states that support cancer cell proliferation. PASTRI thus opens up a venue for dissecting cell state transition dynamics from annotated cell lineage/phylogeny.

bioinformatics↗

bioRxiv2026

Mapping the brain basis of appraisals and discrete emotions

The Component Process Model of Emotion conceptualizes any emotional episode (e.g., the discrete emotions of sadness, anger, fear, or interest) as being driven by the multiple appraisal components. However, both the specificity of the neural mechanisms underlying appraisal processes and the way these appraisal networks relate to the neural circuits underlying discrete emotions remain unclear. Here we investigated the neural correlates of appraisal processes and compared them with those of discrete emotions. Participants (n = 97) were scanned with functional magnetic resonance imaging (fMRI) while watching short movie clips with varying emotional contents. Intensity for 12 appraisals and 12 basic and epistemic emotions evoked by the movie clips were rated by independent participants (n = 444). The neural responses were modelled with convolved ratings of appraisals and discrete emotions. The results indicated that appraisals and discrete emotions are supported by a shared set of distributed brain regions that extend beyond typically reported emotion-related areas, encompassing perceptual, action-related, and higher-order cognitive systems. Activations were more consistent for and better explained by appraisals versus discrete emotions. Within this network, epistemic emotions elicited less consistent activations than basic emotions, particularly in limbic regions. Our results highlight the functional organization of appraisals and discrete emotions under dynamic and complex conditions and indicate that appraisal theories better explain neural responses than discrete emotion models.

neuroscience↗

bioRxiv2026

Tumor-tropic E. coli engineered as living T and NK cell engagers

Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

bioengineering↗

bioRxiv2026

Cross-Species Comparison of Topologically Associating Domains (TADs) in Cereals Reveals Their Role in Genome Stability During Evolution

Topologically associating domains (TADs) are essential structural and functional modules of the genome that play a crucial role in regulating gene expression. In this study, we systematically investigated the conservation and evolution of TADs in five closely related crops, including maize, sorghum, coix, foxtail millet and broomcorn millet. Our results show that 74% of TAD boundaries are conserved between two inbred maize lines, B73 and Mo17, and that approximately 50% or more of TAD boundaries are conserved across different crop species. TAD number remains relatively stable in the face of changes in genome size. However, the length of TADs varies depending on genome size. Furthermore, we found that large-scale transposable element expansion leads to TAD expansion, while chromosomal inversions lead to TAD fusion and the formation of new TAD boundaries. Frequent chromatin interactions between subgenome chromosomes occur after whole-genome duplication. Moreover, we also found that crossovers are enriched at TAD boundaries in maize, indicating the importance of TADs as a fundamental unit during species evolution. Overall, our study provides insights into the conservation and evolution of TADs in crop genomes and their roles in genome organization and function.

plant biology↗