Biology subjects

Han, X.

Publications and source records attributed to Han, X..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

High frequency electrical stimulation entrains fast spiking interneurons and bidirectionally modulates information processing

BackgroundClinical intracranial electrical stimulation often deploys trains of high frequency pulses. While brief bursts of stimulation are known to heterogeneously modulate neuronal spiking, it is unclear how trains of high frequency pulses influence neural dynamics. ObjectiveAs fast spiking interneurons (FSIs) can support rapid firing, we seek to determine how high frequency stimulation modulates FSIs. MethodsWe characterized the real-time effect of one-second-long local stimulation at 40 versus 140 Hz on parvalbumin positive interneurons, known as FSIs, in motor and visual cortices in awake mice using near kilohertz voltage imaging, free of electrical stimulation artifact. ResultsStimulation at 140 Hz, like 40 Hz, heterogeneously modulates individual FSIs membrane voltage in both cortices, leading to complex temporal dynamics. FSIs in both cortices are robustly entrained by 40 Hz stimulation, even though 40 Hz led to prominent membrane hyperpolarization in visual cortex but not motor cortex. Intriguingly, visual cortical FSIs, but not motor cortical ones, were reliably entrained by 140 Hz stimulation. Finally, while stimulation consistently reduced the response amplitude of visual cortical FSIs to visual flickers, response temporal precision is bidirectionally modulated. ConclusionHigh frequency electrical stimulation mediates brain-region specific entrainment of FSIs, and bidirectionally modulates FSI temporal processing of synaptic inputs. Thus, high frequency stimulation can differentially engage inhibitory neurons in different brain regions to modulate network information processing. HighlightsO_LIEvoked membrane potential (Vm) responses are frequency and brain region specific C_LIO_LI140 Hz stimulation entrains the Vm of visual, but not motor, cortical FSIs C_LIO_LI140 Hz, but not 40 Hz, is effective at reducing Vm amplitude to visual flickers C_LIO_LIStimulation bidirectionally modulates Vm response timing to visual inputs C_LIO_LIVisual cortical FSIs are suppressed by 40 Hz stimulation, unlike other conditions C_LI

neuroscience↗

bioRxiv2025

Mitochondrial calcium influx-driven bioenergetics in the dopaminergic system selectively enable drug reward

Drugs of abuse hijack the brains reward system, driving pathological dopamine surges that underlie compulsive behavior and addiction. However, directly targeting dopamine signaling for treatment risks disrupting natural reward processes. Here, we identify a bioenergetic mechanism that selectively promotes addiction-related dopamine release and behaviors. Opioids and methamphetamine, but not natural rewards, induce mitochondrial calcium (Ca2+) influx via the mitochondrial calcium uniporter (MCU) in dopaminergic terminals of the nucleus accumbens. Optogenetic stimulation reveals that this mitochondrial Ca2+ influx occurs exclusively during high-intensity dopaminergic neuronal activation. This Ca2+ influx drives rapid ATP production, compensating for energy deficits caused by neuronal hyperactivity and enabling sustained dopamine release. Genetic deletion or pharmacological inhibition of MCU in dopaminergic neurons selectively reduces drug-induced dopamine release and prevents addictive behaviors while sparing natural reward processing in mice. These findings uncover a distinct mitochondrial bioenergetic mechanism underlying drug reward and propose MCU as a promising therapeutic target for addiction treatment.

neuroscience↗

bioRxiv2025

Transcranial ultrasound stimulation modulates neuronal membrane potentials across broad timescales in the awake mammalian brain

BackgroundTranscranial ultrasound stimulation (TUS) offers noninvasive neuromodulation with high spatial and temporal precision, but its cellular-level effects in the awake brain remain poorly understood. ObjectiveWe investigated how low-intensity TUS modulates membrane voltage dynamics in single cortical neurons in awake mice. MethodsUsing the genetically encoded voltage indicator SomArchon, we performed high-speed kilohertz voltage imaging in awake head-fixed mice. TUS was delivered with a 0.35 MHz transducer at 10 or 40 Hz pulse repetition frequency with a 20% duty cycle, at intensities below the estimated threshold for auditory brainstem activation. We analyzed changes in membrane potential (Vm), spiking, and coordination across simultaneously recorded neurons. ResultsTUS evoked rapid (<10 ms) Vm depolarizations in 42.8% of neurons, while only 20.5% showed increased spiking, highlighting a direct effect of TUS on modulating synaptic inputs. Many neurons were entrained at both PRFs (20.8% at 10 Hz; 12.7% at 40 Hz) with Vm exhibiting significant phase-locking to individual TUS pulses. Vm entrainment was accompanied by increased temporal coordination across neurons and reset network synchrony. Furthermore, TUS-evoked cellular responses adapted over time, often transitioning from membrane depolarization to hyperpolarization upon repeated exposures, demonstrating prominent response depression. ConclusionBy resolving single-neuron responses, our results demonstrate that TUS directly activates individual cortical neuron with a latency shorter than 10 ms. TUS pulsed at physiologically relevant frequencies of 10 and 40 Hz robustly entrains neural dynamics, alters network coordination and evokes neuronal plasticity. These results highlight the therapeutic potential of designing TUS pulsing patterns to target specific neural circuit dynamics.

neuroscience↗

bioRxiv2025

High-throughput in vivo screening using barcoded mRNA identifies lipid nanoparticles with extrahepatic tropism for cancer immunotherapy

Interest continues to grow in the use of mRNA vaccines for cancer immunotherapy. While effective for immunization against infectious diseases, current clinical lipid nanoparticle (LNP) formulations used for mRNA delivery suffer from off-target accumulation, poor immune transfection, and reactogenicity, limiting their application to cancer immunotherapy. Development of new mRNA LNPs is severely bottlenecked by the LNP discovery process, which is historically low-throughput due to reliance on low-plexity measurements. Here, we develop a next-generation high-throughput in vivo mRNA LNP screening platform based on barcoded mRNA (b-mRNA). Using this b-mRNA screening platform to simultaneously evaluate 122 LNPs, we identify novel LNP formulations capable of potent hepatic and extrahepatic transfection. We employ novel biochemical characterization techniques to analyze nanoparticle protein corona formation with single-particle resolution and gain insight into the influence of protein adsorption on hepatic and splenic transfection. We evaluate a lead LNP candidate for therapeutic cancer vaccination in a syngeneic mouse model of melanoma and demonstrate a significant reduction in tumor burden and increase in survival compared to a clinical mRNA LNP formulation. Together, our results demonstrate the value of advanced LNP screening and characterization techniques for the development of next-generation mRNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

Single-nucleus epigenomic dysregulation unmasks genetic risk-associated neurodegenerative glia states

The accumulation of abnormal tau protein selectively affects distinct brain regions and specific populations of neurons and glial cells in tau-related dementias, such as Alzheimers disease (AD), Picks disease (PiD), and progressive supranuclear palsy (PSP). Although the three disorders share the feature of tau protein pathology, the regulatory circuitry of non-coding genetic variants underlying risk-associated cell states remains to be elucidated. Using paired single-nucleus profiling of chromatin accessibility and gene expression across AD, PiD, and PSP, we define cell-type-specific cis-regulatory elements (CREs) across six cell types and fifty subclasses. Comparing disease-dynamic CREs across three disorders, we find that glia overrepresent disorder-specific gene regulation related to dynamic cellular response to stress. We show that human genetic variants affecting microglial gene regulation converge into distinct and co-regulated modules affecting specific cellular functions. Moreover, polygenic risk modifiers are maximally co-accessible in disorder-specific glial states, modifying distinct pathways such as sphingomyelin regulation in PiD. Our study informs glial regulators linked to polygenic modifiers of primary tauopathy, introducing modifiable pathways governing resilience for therapeutic consideration.

genomics↗

bioRxiv2025

Biological characteristics of rabbit KLF12 and its regulation of proliferation and apoptosis of ovarian granulosa cells

Granulosa cells (GCs), as the largest somatic cell group in follicles, provide nutrients and microenvironment for oocyte growth and maturation. GC proliferation and apoptosis are influenced by several genes, with the Kruppel Like Factor 12 (KLF12) gene contributing to the modulation of several cellular activities. Nevertheless, the precise modulatory function of this gene within the context of ovarian GCs remains unelucidated. We cloned the KLF12 gene of New Zealand female rabbits, and evaluated its expression and localization in the ovaries of female rabbits of different ages by quantitative real-time PCR (qRT-PCR) and fluorescence in situ hybridization (FISH). In order to determine the role of KLF12 in ovarian GCs, we used qRT-PCR, WB, CCK-8 and Annexin V-FITC/PI to detect the effect of KLF12 on GCs proliferation and apoptosis. The coding sequence of KLF12 gene of New Zealand female rabbit was predicted and cloned for the first time in this study. The coding region was 1209 bp, encoding 402 amino acids. KLF12 overexpression has a negative effect on the proliferation and cell cycle progression of rabbit GCs. KLF12 knockdown partially rescues GCs proliferation, accelerates GCs cycle progression, and promotes Estradiol (E2) and Progesterone (P) secretion. In addition, KLF12 was also proved to be a key regulator of PI3K/Akt signaling pathway in GCs. In conclusion, the study provides evidence that KLF12 plays a pivotal role in the maturation and proliferation of ovarian GCs in female rabbits. This work establishes a conceptual foundation for investigating deeper into the possible regulatory mechanisms underlying follicular development and growth. Author summaryGCs are essential for oocyte growth, not only providing necessary nutritional support for oocyte growth and maturation, but also constructing a key microenvironment. In this study, the biological function of KLF12 gene was systematically elucidated in rabbit for the first time. It was found that KLF12 inhibited follicular development by negatively regulating GCs proliferation and cell cycle. Combined with its effect on E2 and P secretion, the important regulatory role of KLF12 in follicular maturation and hormone balance was revealed. These innovative findings not only deepen the understanding of the regulatory network of ovarian development, but also provide a new theoretical basis for the basic research of reproductive biology. More importantly, it provides a potential molecular target for the development of new technologies to improve the reproductive efficiency of livestock. It also provides a valuable reference model for the study of the mechanism of human reproductive dysfunction related diseases.

genetics↗

bioRxiv2025

Prolonged Single Neuron Voltage Imaging in Behaving Mammals

Long-term recording of single-neuron membrane voltage dynamics during behavior is highly desirable. Using ElectraOFF, a fully genetically encoded, photostable, high-performance fluorescence voltage indicator, we achieve routine cellular-resolution imaging over tens of minutes, occasionally up to eighty minutes, in behaving mice with minimal signal loss across neuron types and brain regions. This extended recording capability reveals plasticity changes throughout intracranial electrical neuromodulation, highlighting the novel insights enabled by prolonged voltage imaging.

neuroscience↗

bioRxiv2025

From Structure to Immunogenicity: Decoding Correlated Dynamics atthe Peptide MHC interface to Understand TCR Recognition

The interaction between a class I peptide-major histocompatibility complex (pMHC) and a T cell receptor (TCR) plays a central role in the elicitation of CD8+ T cell immune responses. As a result, considerable effort has been invested in understanding the structural, dynamic, and biophysical parameters that govern this recognition event, including designing altered peptide ligands (APLs) which seek to modulate the downstream signaling outcomes. However, dynamic links between modified peptide positions and distant residues have until yet been ill resolved. Using an integrative approach combining crystallographic ensemble and single models with atomistic molecular dynamics simulations and correlational analysis, we have established an approach that allows us to identify coupled dynamics between spatially distant residues at the pMHC interface. Furthermore, we constructed a network encoding the inter-residue couplings observed throughout the simulations. This computational workflow corroborates well with experimental data and leads to novel insights regarding the differential immunogenicity of the closely related peptides analyzed in this study. Ultimately, we present an intuitive and comprehensive strategy for decoding the linked dynamics at the pMHC interface allowing for mechanistic insights into the biophysical bases governing immunogenicity. One Sentence SummaryThe dynamics at the pMHC interface can be encoded as a biophysically relevant network to yield molecular insights into immunogenicity

immunology↗

bioRxiv2025

Data Heterogeneity Limits the Scaling Effect of Pretraining Neural Data Transformers

A key challenge in analyzing neuroscience datasets is the profound variability they exhibit across sessions, animals, and data modalities-i.e., heterogeneity. Several recent studies have demonstrated performance gains from pretraining neural foundation models on multi-session datasets, seemingly overcoming this challenge. However, these studies typically lack finegrained data scaling analyses. It remains unclear how different sources of heterogeneity influence model performance as the amount of pretraining data increases, and whether all sessions contribute equally to downstream performance gains. In this work, we systematically investigate how data heterogeneity impacts the scaling behavior of neural data transformers (NDTs) in neural activity prediction. We found that explicit sources of heterogeneity, such as brain region mismatches among sessions, reduced scaling benefits of neuron-level and region-level activity prediction performances. For tasks that do exhibit consistent scaling, we identified implicit data heterogeneity arising from cross-session variability. Through our proposed session-selection procedure, models pretrained on as few as five selected sessions outperformed those pretrained on the entire dataset of 84 sessions. Our findings challenge the direct applicability of traditional scaling laws to neural data and suggest that prior reports of multi-session scaling benefits may need to be re-examined in the light of data heterogeneity. This work both highlights the importance of incremental data scaling analyses and suggests new avenues toward optimally selecting pretraining data when developing foundation models on large-scale neuroscience datasets.

neuroscience↗

bioRxiv2025

Neural organoids protect engineered heart tissues from glucolipotoxicity by transferring versican in a co-culture system

Metabolic disorders could cause dysregulated glucose and lipid at the systemic level, but how inter-tissue/organ communications contribute to glucolipotoxicity is difficult to dissect in animal models. To solve this problem, myocardium and nerve tissues were modeled by 3D engineered heart tissues (EHTs) and neural organoids (NOs), which were co-cultured in a generalized medium with normal or elevated glucose/fatty acid contents. Morphology, gene expression, cell death and functional assessments detected no apparent alterations of EHTs and NOs in co-culture under normal conditions. By contrast, NOs significantly ameliorated glucolipotoxicity in EHTs. Transcriptomic and protein secretion assays identified the extracellular matrix protein versican as a key molecule that was transferred from NOs into EHTs in the high-glucose/fatty acid condition. Recombinant versican protein treatment was sufficient to reduce glucolipotoxicity in EHTs. Adeno-associated virus-delivered versican overexpression was sufficient to ameliorate cardiac dysfunction in a murine model of diabetic cardiomyopathy. These data provide the proof-of-concept evidence that inter-tissue/organ communications exist in the co-culture of engineered tissues and organoids, which could be systemically studied to explore potential pathological mechanisms and therapeutic strategies for multi-organ diseases in vitro.

cell biology↗

bioRxiv2025

Small non-coding RNAs encapsulating mammalian cells fuel innate immunity

Cell surface RNAs, notably glycoRNAs, have been reported, yet the exact surface RNA compositions in different cell types remain unclear. Here, we introduce a comprehensive suite of methodologies for imaging, profiling, quantifying, and exploring the biological functions of specific surface RNAs. Utilizing these techniques, we have identified diverse non-coding RNAs present on mammalian cell surfaces. We confirm the membrane anchorage and quantify the abundance of several representative RNAs on human primary cells. Notably, we discover a significant prevalence of Y RNAs on the surfaces of human monocytes and B cells. We find that these Y RNAs on human monocyte surfaces enrich extracellular histones, regulating interleukin-6 (IL-6) gene expression and subsequent protein secretion upon histone stimulation via NF-{kappa}B and AP-1 activation. Our study not only presents effective approaches for investigating surface RNAs, but also uncovers a previously unrecognized immune activation pathway mediated by surface Y RNAs on monocytes. In briefA comprehensive profiling of surface RNAs across diverse mammalian blood cell types unveil abundant Y RNAs on the surface of human monocytes. Subsequent investigations uncover functional roles of surface Y RNAs on monocytes as "immune sentinel" to enrich extracellular histones, revealing a previously unknown pathway of innate immune activation. HighlightsNovel methodologies for cell surface RNA mapping, validation and functional interrogation. Sequencing of surface RNAs across various mammalian blood cell types offers detailed maps of surface RNAs. Abundant Y RNAs localize on human monocyte surfaces and capture extracellular histones released by adjacent ruptured cells. Surface Y RNAs enrich extracellular histones to facilitate transcription and secretion of IL-6 through NF-{kappa}B and AP-1 activation.

molecular biology↗

bioRxiv2025

Two telomere-to-telomere, gap-free genome assemblies and comparisons revealed the conserved key genes associated with sugar accumulation in Rubus genus

For the first time, we assembled two highly continuous, completely gap-free reference genomes of the Rubus subgenus: Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP), which are widely distributed in southern China with similar phenotypic traits (Figures 1A, 1B, and Figure S1), yet ripe fruits display distinct sugar accumulation levels (Table S1), making them ideal candidates for investigating the mechanisms underlying sugar accumulation in the Rubus genus. The XMM (213.53 Mb, 28,204 genes) and DHP (218.26 Mb, 28,569 genes) genomes exhibit close evolutionary relationships, diverging approximately 3.21 Mya. Comparative genomics identified extensive synteny, interspecific structural variations (translocations, inversions, segmental duplications), and presence/absence variation (PAV). Using Hi-C interaction heatmaps and Sanger sequencing, we validated interspecific structural inversions. Additionally, we identified a sugar transporter gene (MFS1), which is present in XMM but absent in DHP. Combined analysis of the gene family expansion/contraction and transcriptome identified two conserved key genes (RhSTP13 and RhSTP7) associated with sugar accumulation in Rubus genus and displayed distinct roles through transient expression assay. To facilitate functional genomics study, we also established a comprehensive Rubus database, RubusDB, a freely accessible repository consolidating all genomic, transcriptomic and phenotypic data of Rubus genus. These findings provide a foundational framework for elucidating the genetic basis of sugar accumulation, genome diversification, and trait improvement in Rubus species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=170 SRC="FIGDIR/small/646780v2_fig1.gif" ALT="Figure 1"> View larger version (72K): org.highwire.dtl.DTLVardef@1baca20org.highwire.dtl.DTLVardef@2c01eaorg.highwire.dtl.DTLVardef@131dc00org.highwire.dtl.DTLVardef@62a04f_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFIGURE 1.C_FLOATNO Phenotypic characterization, de novo genome assemblies, variation, and evolution of Rubus hirsutus Thunb. Penglei (XMM) and Rubus eustephanos Focke ex Diels Dahongpao (DHP). (A) Illustration of XMM whole plants, stem, flower bud and flower, respectively. (B) Illustration of DHP whole plants, stem, flower bud and flower, respectively. (C) The chromosome karyotype analysis of XMM. Bar = 10 {micro}m. (D) Circular diagram of XMM and DHP reference genomes. (a) Chromosomes are represented by centromeres (dark red) and telomeres (blue); (b) CEN18 density; (c) CEN17 density; (d) Gene density; (e) TE density; (f) PAV density; (g) SNP density; (h) Collinear lines at the center of diagram highlight homoeologous chromosomes relationships and non-homoeologous regions. (E) Genomic alignments between XMM and DHP. Inversions, duplications and translocations are marked with orange, blue and green ribbons, respectively. (F) Identification of large inversions in chromosome 7 between XMM and DHP. The three heatmaps show the chromatin interaction matrix, including mapping Hi-C data of DHP against DHP genome (left), mapping Hi-C data of DHP against XMM genome (middle) and mapping Hi-C data of XMM against XMM genome (right). The lower panel illustrates gene alignments between XMM and DHP. (G) Synteny, structural rearrangements, monomer, and identity distribution in the 16-20 Mbp region of chromosome 6 between XMM and DHP. (H) Local genome synteny of chromosome 5, with a structural variation that is present only in XMM. The PAV region includes a gene related to sugar transporter (MFS1, XMM05G025540). (I) Gene-level matchings of MFS genes in the PAVs region between XMM and DHP. (J) Phylogenetic relationships and divergence times between raspberries and other Rosaceae species. The black numbers close to the divergence nodes indicate the divergence times and the red bars represent the 95% confidence intervals. The red and black numbers indicate expanded and contracted ortholog groups at the corresponding node. Scale bar corresponds to 10 Mya. C_FIG

genomics↗

bioRxiv2025

Boosting Antitumour Efficacy and Immunity by Boron Neutron Capture Therapy with Size-Controlled Nanoparticles

Boron neutron capture therapy (BNCT) is emerging cancer radiotherapy requiring 10B sensitizer. Although boronophenylalanine (BPA)-BNCT is approved clinically in Japan, the low tumour selectivity and retentivity result in the long-time infusion of high doses. Based on our finding of the size-controllable mechanochemical synthesis of boron-10 carbide nanoparticles (10B4C NPs), the 50 nm size NPs grafted with poly(glycerol), {superscript 1}BC(50)-PG, is found to show superior tumour selectivity and retentivity to enhance the eradication efficacy at much lower dosage (5 mg [10B] / kg (mouse)). The dosage is further reduced by twice neutron irradiation or combination with an immune checkpoint inhibitor (ICI). Antitumour immunity is found to be boosted by {superscript 1}BC(50)-PG-BNCT to induce abscopal effect to treat remote or metastatic tumours and long-term memory to prevent cancer recurrence. Additionally, minimal side effects and gradual NP excretion are observed for one year. The 10B4C(50)-PG is concluded to be a promising 10B carrier for clinical application of BNCT due to the prominent antitumour efficacy and immune-activation with minimal toxicity.

cancer biology↗

bioRxiv2025

Evolutionary Trade-off Between Stomatal Defense and Gas Exchange in Brassicaceae

Stomatal opening is crucial for gas exchange, but it unavoidably offers invasion by pathogens. In response, plants close stomata to prevent pathogen entry, while the bacterial pathogen Pseudomonas syringae pv. tomato DC3000 (Pto) produces coronatine (COR), a jasmonate (JA) mimic, to counteract this plant response. Here, we demonstrate that by COR, Pto exploits CYP707A1 activation in Arabidopsis thaliana, encoding an enzyme that degrades abscisic acid, essential for stomatal closure. Notably, COR-induction of CYP707A1 is absent in other Brassicaceae species, such as Capsella rubella and Eutrema salsugineum, rendering them resistant to Pto invasion. In contrast, in A. thaliana, CYP707A1 enables rapid stomatal opening at dawn in a JA-dependent manner, enhancing gas exchange and chlorophyll content, unlike C. rubella and E. salsugineum. Promoter-swap experiments confirm that the regulatory region of CYP707A1 underlies these evolutionary diversifications. Together, our study presents a mechanism underlying an evolutionary trade-off between stomatal defense and gas exchange.

plant biology↗

bioRxiv2025

SAXS reveals the molecular basis underlying pH-driven G3BP1 conformational dynamics: implications for stress granule formation

G3BP1 is the central node and molecular switch in stress granule (SG) assembly. However, structural insights into full-length G3BP1 remain elusive owing to its extensive intrinsically disordered regions (IDRs). Using size-exclusion chromatography-coupled small-angle X-ray scattering (SEC-SAXS), we have characterized the solution architecture and conformational dynamics of full-length G3BP1. Under physiological conditions, G3BP1 adopts an elongated, head-to-head antiparallel homodimeric conformation, whereas acidification induces a pronounced conformational compaction. Subsequent biophysical studies reveal that this compact state enables robust RNA-mediated and, notably, homotypic phase separation in vitro. Deletion of the RGG region abolishes this acidity-induced compaction and markedly impairs phase separation, establishing a causal link between the RGG-dependent conformational switch and phase separation propensity. By moving beyond hypothetical models to experimental solution-state data, our work fills a longstanding void in the field and provides critical insights into the structural plasticity that underlies G3BP1 function, offering a missing structural link essential for deciphering the molecular mechanism of SG formation. We propose that stress-associated physicochemical changes, specifically localized acidification coupled with mRNA accumulation, trigger this reversible structural reconfiguration of G3BP1, thereby facilitating phase separation.

molecular biology↗

bioRxiv2025

Development of DARPin T cell engagers for specific targeting of tumor-associated HLA/peptide complexes

The compromise between affinity and specificity in TCR-dependent targeting of HLA-restricted tumor-associated antigens presents a significant challenge in developing efficacious immunotherapies. As such, T cell engagers which circumvent these limitations are of particular interest. We have established a process to generate bispecific Designed Ankyrin Repeat Proteins (DARPins) that simultaneously target HLA-I molecules in complex with tumor-associated peptides and CD3{varepsilon}. High-affinity HLA-A*0201/NY-ESO1157-165-specific DARPins were isolated after only four rounds of in-vitro selection from naive DARPin libraries. Combining HLA-A*0201/NY-ESO1157-165-specific DARPins with a CD3{varepsilon}-specific DARPin created potent T cell engagers which elicited CD8+ T cell activation towards tumor targets with high peptide specificity, as confirmed by X-scanning mutagenesis and functional killing assays. The cryo-EM structure of a ternary DARPin/HLA-A*0201/NY-ESO1157-165 complex revealed a rigid and concave DARPin surface that binds to the entire length of the peptide-binding cleft, contacting both -helices and the peptide. The present results unveil promising immuno-oncotherapeutic approaches with the possibility of rapidly developing DARPins with high affinity and specificity to HLA/peptide targets that can be readily combined with a new generation of anti-CD3{varepsilon}-specific DARPins.

synthetic biology↗

bioRxiv2025

Unveiling novel signaling roles for human KDELR3 and KDELR1KDELRs Control AGR2 Biogenesis

KDEL receptors (KDELRs) prevent the secretion of soluble chaperones and enzymes meant to reside in the endoplasmic reticulum. While a single KDELR exists in yeast (ERD2), three variants are present in mammals, displaying high sequence similarity (73-83%). However, the phylogenetic conservation of the differences and the diverse tissue distribution of the three KDELRs suggest functional specialization. Here we show that, while all three receptors can prevent the secretion of KDEL-bearing clients, KDELR1 and KDELR3 regulate the production of AGR2, a key assistant of mucin folding, in opposite ways. AGR2 transcripts increase dramatically upon silencing KDELR3 but decrease when KDELR1 is downregulated. Silencing ERp44, but not other ER residents, phenocopies KDELR3 knockdown, suggesting that AGR2 regulation depends on ERp44-KDELR3 interactions. Our findings identify a novel regulatory circuit that controls the molecular composition of the early secretory pathway based on specific interactions between KDELRs and ER residents.

cell biology↗

bioRxiv2025

Genome-wide analysis reveals the genetic basis of key agronomic traits and modern wheat breeding in Henan Province

Despite the continuous improvement of wheat cultivars in Henan Province, the largest Chinese wheat-producing area, there have been no reports of studies on their breeding advances in the past decades. This study aims to elucidate their genetic basis and breeding advances. A total of 351 landraces and 265 cultivars in Henan Province were employed in selective sweep studies and genome-wide association studies. All the wheat accessions were planted in five locations in Henan Province in 2016-2017, 2017-2018 and 2018-2019. Candidate genes were identified through differential expression, GO annotation, gene homology, and haplotype analyses. Breeding advances were summarized based on four breeding periods (1950s, 1960s-1970s, 1980s-1990s, and post-2000s) of all 265 cultivars. The results demonstrated that 263 known genes with selection signals were found to be associated with important traits. Around the detected quantitative trait loci, 51 genes had been previously reported, while 252 genes were identified as candidate genes. Of the 303 genes and loci identified, 80 genes and 50 loci contributed to the improvement of 12 traits like plant height, and 12 key candidate genes was verified by qRT-PCR, while superior haplotypes of 24 genes explained cultivar climate adaptation. The superior haplotypes of 164 genes are available for future breeding. Transmission of superior haplotypes in four varietal pedigrees revealed pyramiding of superior haplotypes in elite cultivars. The analysis of post-2000 cultivars suggests a broader range of germplasm resources should be considered in parental selection than only recent accessions. This study provides a genetic basis and guide for wheat improvement.

genetics↗