Biology subjects

Zhang, J.

Publications and source records attributed to Zhang, J..

At least 127 records · Page 7Linked to original sources

bioRxiv2026

NC4touch: An open-source networked touchscreen apparatus for rodent behavioral testing

In recent years, rodent touchscreen-based paradigms have gained popularity for their flexible task design, automated data collection and improved standardization. These devices minimize experimenter intervention and contribute to more replicable and reliable research. However, the high costs and proprietary hardware / software associated with commercially available systems present a financial barrier for smaller labs or researchers with limited resources. To address this issue, we developed "NC4Touch", an open-source scalable, modular rodent testing apparatus. It features three independent touchscreens and a feeding port for easy use in a wide array of tests comparable to those available with standard operant chambers, with the added benefit that visual stimuli can be highly customized. The system includes a user-friendly graphical interface that offers real-time control, task customization, video recording, and data management. We demonstrate its effectiveness in a visual discrimination task using both rats and mice. Several devices can be operated in parallel from the same computer and user interface, allowing high- throughput data collection. We provide detailed assembly instructions for the hardware and well- documented and easily-configurable software. We hope that the affordable open-source nature of NC4Touch will expand the scope of behavioral testing, allowing researchers to overcome traditional financial barriers and create a more collaborative community. Significance StatementTouchscreen-based testing is a powerful tool for assessing cognition in rodent models, however commercial systems remain cost-prohibitive for many researchers. NC4Touch is a rodent touchscreen apparatus that provides an open-source, customizable, and affordable alternative that enables high-throughput, cognitive testing in both mice and rats. By lowering financial barriers and promoting hackability, this system enables greater accessibility and collaboration in research.

animal behavior and cognition↗

bioRxiv2026

HER2 mutation-derived neoantigens in NSCLC as actionable targets for TCR therapy

HER2 mutations are oncogenic drivers in 1-6% of non-small cell lung cancers (NSCLC), but therapeutic resistance limits the durability of current HER2-targeted treatments. Here, we identify T-cell receptors (TCRs) targeting recurrent HER2 hotspot mutations as a potential immunotherapeutic strategy for HER2-mutant NSCLC. Using neoepitope prediction and antigen-specific T-cell enrichment, we isolated HLA-A*02:01restricted TCRs recognizing HER2 A775insYVMA, S310F, and G776delinsVC mutations, collectively covering approximately 60% of HER2-mutant NSCLC. These TCRs selectively recognized mutant HER2 epitopes without detectable wild-type reactivity and some displayed cross-recognition of related hotspot variants, expanding the spectrum of targetable tumors. The G776delinsVC-specific TCR also exhibited co-receptorindependent activity showcased by its ability to activate CD4+ T cells. Importantly, timelapse single-cell flow cytometry analyses demonstrated that TCR-engineered T cells repeatedly reacquired activated polyfunctional states following serial antigen stimulation, while serial tumor rechallenge assays confirmed sustained cytotoxic activity across multiple rounds of tumor killing. These findings identify recurrent HER2 mutations as shared immunotherapeutic targets and provide a foundation for the development of TCR-based therapies for HER2-mutant NSCLC.

immunology↗

bioRxiv2026

Lysine methyltransferase SET7 links cardiometabolic risk to endothelial dysfunction by dysregulating mRNA splicing and eNOS-CaM interaction

BACKGROUNDLysine methyltransferase SET7 activates gene expression through mono- methylation of histone H3 at lysine 4 (H3K4me1) and modulates protein function via mono- methylation of non-histone proteins (Kme1). However, its role and molecular targets in endothelial dysfunction associated with cardiometabolic disorders remain unknown. METHODSEndothelial-specific Setd7 knockout (Setd7EC-KO) mice were generated and endothelial function assessed in WT and Setd7EC-KO mice after high-fat diet (HFD). Human aortic endothelial cells (HAECs) were used to investigate SET7 expression and function under metabolic stress. SET7-dependent histone and non-histone targets were identified by proteomic and ChIP analyses. Insights from these datasets guided the design of bioinformatic, molecular, and functional studies to define their regulatory mechanisms. Clinical relevance was evaluated in human arteries. RESULTSHFD selectively increased endothelial SET7 expression in WT mouse aortas. Despite comparable metabolic abnormalities, Setd7EC-KO mice were protected from HFD- induced endothelial dysfunction, oxidative stress, and inflammation. In HAECs, high glucose emerged as the strongest inducer of SET7 expression, promoting pro-inflammatory and pro- oxidant gene expression, monocyte adhesion, and ROS generation. These effects were reproduced by overexpression of catalytically active SET7 and reversed by its inhibition or silencing. Proteomic and ChIP analyses revealed that SET7-dependent H3K4me1 activates transcription of spliceosome components, linking aberrant mRNA splicing to endothelial inflammation and oxidative stress. Moreover, Kme1-proteomics identified endothelial nitric oxide synthase (eNOS) as a direct SET7 substrate. Bioinformatic analyses and mutagenesis experiments demonstrated that SET7-mediated mono-methylation of eNOS at K494 disrupts calmodulin (CaM) binding and impairs NO synthesis. These molecular signatures were also observed in internal mammary arteries from patients with vascular disease and hyperglycemia. CONCLUSIONSSET7 drives endothelial dysfunction through a dual mechanism: 1) H3K4me1-dependent activation of splicing machinery triggering inflammation and oxidative stress, and 2) eNOS mono-methylation at K494 reducing NO bioavailability. Targeting SET7 may therefore represent a promising avenue to safeguard endothelial homeostasis in cardiometabolic disease. GRAPHIC ABSTRACTA graphic abstract is available for this article.

molecular biology↗

bioRxiv2026

FAM136A is an essential chaperone for mitochondrial membrane protein biogenesis

The metabolic and signaling function of mitochondria rely on a network of chaperones within the inner membrane space (IMS) that regulate the biogenesis of nascent mitochondrial proteins. Using a genome wide CRISPRi screen we found that in human cells FAM136A is required for biogenesis of all three voltage-dependent anion channel (VDAC) paralogs, an abundant and essential family of {beta}-barrel metabolite transporters in the outer mitochondrial membrane (OM). FAM136A is a ubiquitously expressed essential gene, that is conserved in metazoa and plants. Using a combination of experiments in human cells and in vitro reconstitution, we determined that FAM136A associates with unfolded VDACs in the IMS; solubilizes nascent VDAC through a direct interaction; and facilitates insertion of VDAC into the OM. FAM136A also binds and chaperones a subset of -helical subunits of the electron transport chain. We therefore conclude that FAM136A is an IMS-resident chaperone, necessary and sufficient to maintain nascent membrane proteins in a folding-competent state to mediate their integration into the bilayer.

molecular biology↗

bioRxiv2026

A curated human lactylome and protein language model framework enable accurate prediction and reveal local determinants of lysine lactylation

Lysine lactylation is a dynamic post-translational modification that can alter protein function and has been implicated in diverse physiological and pathological processes. Accurate identification of lactylation sites is therefore important for defining its regulatory landscape and for generating testable hypotheses about lactylation-associated mechanisms. Here, we introduce CLEAR-Lactyl and AttentionKla. CLEAR-Lactyl is a curated benchmark dataset of human lysine lactylation comprising 16,604 positive sites. AttentionKla is a deep learning framework trained on CLEAR-Lactyl that employs a pre-trained protein language model fine-tuned with LoRA; it significantly outperforms existing tools, and the factors contributing to its performance gain have been dissected through comprehensive ablation studies. Its utility in predicting novel lactylation sites and in sequence-directed modulation of lactylation levels has been experimentally validated in cellular assays. Together, CLEAR-Lactyl and AttentionKla provide a powerful platform for lysine lactylation research and offer an extensible framework for the precise modulation of other post-translational modifications.

bioinformatics↗

bioRxiv2026

Evolutionary Origins and Synthetic Reconstruction of Gingerols

How new enzymatic activities become integrated with existing metabolic networks to generate lineage-restricted plant chemistry remains a central question in metabolic evolution, exemplified by gingerol biosynthesis in Zingiberaceae, whose complete enzymatic basis has remained elusive. Here, we resolve this problem by elucidating the evolutionary origins and the full biosynthetic pathway of gingerol through single-cell transcriptomics, functional screening, structural biology, comparative genomics and pathway reconstruction. A coordinated metabolic program operates in ginger oil cells, thereby guiding the identification of diketide-CoA synthases, gingerol synthases (GS) and gingerol reductases that together constitute the complete pathway. GS remodels the conserved type III polyketide synthase scaffold to organize a fatty acyl-CoA and a phenylpropanoid-derived intermediate for gingerol formation. Furthermore, GS arose through duplication and limited active-site remodeling of a curcumin synthase-like enzyme, accompanied by coordinated recruitment of precursor-supply and reduction pathways. Translating these principles into yeast achieves the first de novo microbial production of 6-gingerol from glucose at 12.4 mg/L. These findings reveal the evolutionary logic by which plants recruit and coordinate novel enzymatic activities to establish lineage-restricted metabolic program, providing a framework for understanding and engineering specialized metabolism across the plant kingdom.

synthetic biology↗

bioRxiv2026

Medulloblastoma Forms Symbiotic Metabolic Partnerships with Macrophages to Establish Leptomeningeal Metastases

Leptomeningeal metastases are the primary source of morbidity and mortality for pediatric medulloblastoma patients. Due to limited surgical sampling of metastases in patients, little is understood of the mechanisms of metastasis. Here, we identify biologically distinct quiescent small metastases (designated as micrometastases) and mitotically active larger metastases (macrometastases). Macrometastases are more metabolically active than micrometastases and contain higher levels of lipids, particularly cholesterol. Macrometastases secrete CXCL12, which attracts lipid-laden macrophages into the tumor. Lipid-laden macrophages upregulate the cholesterol transporter ABCG1, promoting the efflux of free cholesterol, which is then taken up by tumor cells via the HDL receptor SCARB1. CXCL12-driven macrophage recruitment and exogenous cholesterol are sufficient and necessary to drive progression of medulloblastoma leptomeningeal metastases in vivo. High fat diets drive metastatic progression in vivo. Dietary or pharmacological interventions targeting the CXCL12-SCARB1-cholesterol axis represent therapeutic strategies to either prevent or treat medulloblastoma leptomeningeal metastases.

cancer biology↗

bioRxiv2026

An integrated single-cell atlas of human lung across the lifespan

The healthy adult lung is largely quiescent but can respond to injury and replace damaged or lost cells. However, the identities and origins of regenerative cell states remain poorly understood. Here we present the Human Developmental Lung Cell Atlas (HDLCA), a curated single-cell reference atlas of the respiratory system across the lifespan, integrating 253 datasets from 225 studies, and comprising over 18 million cells from 3,198 samples and 2,460 individuals across 34 anatomical locations in both health and disease. The HDLCA defines 142 consensus lung cell types, including 13 rare and 8 previously undescribed ones. Notably, we identify a rare intermediate alveolar epithelial progenitor (Int AP) population in normal lungs, with transcriptional signatures shared by alveolar type 2 (AT2) and alveolar type 1 (AT1) cells. Trajectory inference indicates that Int AP cells arise from both AT2 and SCGB1A1+ secretory cells and give rise to AT1 cells, with Hippo-YAP/TAZ signalling governing lineage specification. Int AP cells are associated with genetic susceptibility to idiopathic pulmonary fibrosis and chronic obstructive pulmonary disease, and their dysfunction may contribute to abnormal alveolar repair and regenerative failure in both diseases. The HDLCA provides a unified atlas-level reference for mapping respiratory cellular diversity, uncovering reparative cell dynamics and informing regenerative and cell-based therapeutic strategies.

bioinformatics↗

bioRxiv2026

Compact red-shifted near-infrared fluorescent proteins enable deep-tissue SWIR imaging with in vivo optical clearing.

Compact fluorescent proteins (FPs) with red-shifted emission are needed for deep-tissue short-wavelength infrared (SWIR) imaging. We engineered a GAF domain from the JSC1 cyanobacteriochrome of thermophilic Leptolyngbya sp. into three monomeric, biliverdin-binding FPs of 19.1 kDa: miRFP729nano, miRFP732nano and miRFP735nano, with excitation/emission maxima of 714/729, 716/732 and 719/735 nm, respectively. Their off-peak fluorescence beyond 1,000 nm was several-fold higher than that of miRFP718nano previously used for SWIR imaging. miRFP732nano functioned as a fusion tag, a component of target-stabilized nanobodies, and a reporter of NF-{kappa}B and AP-1 transcriptional activities. It enabled single-laser, dual-color three-photon imaging with EGFP to depths of [~]950 m in cortex and [~]300 m in spinal cord. In mice, miRFP732nano supported SWIR imaging of skeletal muscle, inflammatory signaling and intracellular targets. Combining SWIR detection with biocompatible 4-aminoantipyrine-based in vivo tissue clearing enhanced signal and image sharpness. These red-shifted NIR FPs expand the genetically encoded toolkit for deep-tissue imaging.

bioengineering↗

bioRxiv2026

The diversity of disease-associated natural human antibody specificities declines dramatically in Alzheimers disease.

Alzheimers disease (AD) is the leading cause of dementia and administration of monoclonal antibodies against A{beta} amyloid are associated with disease modifying effects leading to FDA approval for some antibodies. Naturally-occurring human antibodies (NAbs) are believed to be the front line of defense against a variety of diseases, so we investigated the specificity of NAbs in AD and cognitively normal (NC) individuals using epitomic profiling (EP). We found that the diversity of antibody-specific peptide epitope segments (ES) declines dramatically (26-fold) in the AD compared to NC populations. Many of these differentially expressed ES (DEES) map to amyloid sequences that accumulate in AD, such as A{beta}, tau, -synuclein, TDP43 and TMEM106b. NAbs that target amino terminal A{beta} epitopes are elevated in AD (residues 1-6 and 18-21) and NAbs that target different A{beta} epitopes are elevated in NC (residues 5-10 and 35-41). DEES that map to 2N4R tau are highly cross correlated in the population implying that that the antibodies may be polyspecific or that a set of antibodies are coordinately regulated. We used weighted gene correlation network analysis (WGCNA) to identify co-expressed DEES and UMAP to embed DEES in both AD and NC populations that bind to the same antibody or co-expressed set of antibodies. An average of approximately 25 DEES cluster in each WGCNA group. A major WGCNA cluster associated with AD contains 3 groups of overlapping DEES that assemble into longer linear epitopes. One of these 3 groups contain sequences that map to the amino terminus of A{beta}. DEES elevated in AD may be useful blood biomarkers for AD. The DEES clusters elevated in NC may be associated with protection against misfolded protein amyloid seeding and propagation and maintaining the resilience of neuronal populations.

neuroscience↗

bioRxiv2026

Proprotein convertase activity regulates cumulus-oocyte-complex matrix integrity and cumulus cell migration during ovulation via a GDF9-dependent mechanism

Cumulus cells have well-established roles early in ovulation but the key molecules that drive their behavior in later stages, leading to follicle rupture, remain underexplored. Here, we observed that inhibition of proprotein convertases (PCSKs) via a pan-inhibitor (PCI) impaired follicular rupture and disrupted the cumulus matrix integrity within intact follicles. Reduced cumulus cell adherence to the cumulus-oocyte-complex (COC) matrix was also observed in isolated COCs and notably occurred late during the maturation window without affecting oocyte maturation. Visualization of PCSK transcript and protein expression, as well as selective inhibition of specific PCSKs, determined that the observed phenotype in COCs is likely attributed to PCSK5A inhibition. We conducted bulk RNA-sequencing and proteomics of PCI-treated COCs which revealed that PCSK inhibition caused dysregulation of extracellular matrix organization, cell migration/adhesion, and TGF-{beta} signaling pathways. Subsequent validation showed that this inhibition translated to disrupted matrix organization and altered migratory and adhesive behaviors in cumulus cells. The TGF-{beta} ligand GDF9 has a predicted PCSK cleavage site, and supplementation with GDF9 rescued matrix integrity suggesting its role as a downstream substrate of PCSKs to regulate matrix organization. Altogether, this study identified PCSK5A and GDF9 as key regulators of COC matrix integrity and cumulus cell migration during late ovulation. These findings highlight novel factors required for follicle rupture which can be leveraged for the development of fertility therapeutics and contraceptives.

cell biology↗

bioRxiv2026

Evaluation of gaseous ozone technology for decontaminating porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV) from non-porous surface in truck cabins

Porcine reproductive and respiratory syndrome virus (PRRSV) and porcine epidemic diarrhea virus (PEDV), both economically detrimental to the swine industry, can be spread through contaminated truck cabins, posing significant transport biosecurity risks. This study evaluated the effectiveness of gaseous ozone technology in decontaminating PRRSV and PEDV on non-porous surfaces in truck cabins. An incomplete factorial study comprising 26 treatment groups, including controls, and ozone treatments at three capacities (30, 38, and 68 g/h) was conducted over varied exposure times (0.5, 1, or 2 hours) in a climate-controlled truck cabin, where PRRSV or PEDV contaminated rubber coupons were subjected to treatments under continuous environmental monitoring, followed by virus elution and titration in cell cultures. Statistical analyses included regression models and ANOVA with Tukey's comparisons, standard deviations for ozone machines, and Pearson correlations between ozone concentration and environmental factors. Ozone treatments showed variable results with less than two-log viral titer reduction. Ozone concentrations varied across identical setups (SD: 4.75 ppm for 30 g/h, 5.43 ppm for 38 g/h machines) during the first 30 minutes, while across the entire study period, ozone concentration showed weak negative correlation with virus titer (p > 0.05), moderate positive correlation with temperature (r = 0.5, p < 0.0001), and moderate negative correlation with humidity (r = -0.56, p < 0.0001). In conclusion, ozone treatments showed inconsistent and limited effectiveness in PRRSV and PEDV decontamination, influenced by temperature and humidity under the tested conditions.

microbiology↗

bioRxiv2026

Noncanonical Circular RNAs and Potential Functions

Circular RNAs (circRNAs) are ubiquitous in eukaryotes; dysregulated circRNA expression is linked to diseases, including lung cancer. In contrast to canonical circRNAs arising from exon-intron boundaries, noncanonical circRNAs originating within exonic, intronic, and intergenic regions have typically been dismissed as transcriptional noise or technical artifacts. To explore circRNA diversity and appreciate their functions, we developed an algorithm to identify both canonical and noncanonical circRNAs without relying on genome annotation, enabling the identification of circRNAs of all types and in newly sequenced or poorly annotated species. Results from lung cancer cells revealed that noncanonical circRNAs constituted over two-thirds of the circRNA population and were expressed more abundantly than canonical circRNAs, and genes with fewer and shorter exons were hotspots for noncanonical circRNA and circRNA isoform production. Further analyses showed that many noncanonical circRNAs were indeed endogenous circRNAs transcribed within cells rather than experimental artifacts, were potentially translated into proteins or peptides, and were conserved across species. Moreover, we validated 65 noncanonical circRNAs in NCI-H23 cells using multiple bioassays and demonstrated that both exonic and intergenic noncanonical circRNAs influenced cell viability. CircRNA profiles in tumor and tumor-adjacent tissues of lung cancer patients revealed tissue-specific expression and differentially expressed canonical and noncanonical circRNAs from cognate genes involved in cancer-related pathways, indicating their potential clinical relevance. This study confirmed the authenticity of noncanonical circRNAs and provided the first experimental evidence that noncanonical circRNAs influence cancer cell phenotypes. These findings broaden our understanding of circRNA biology, highlighting their widespread genomic distribution, diverse functions, and potential clinical relevance.

molecular biology↗

bioRxiv2026

Diagnostic Performance of Fluorescence-Based Rapid On-Site Specimen Evaluation for Helicobacter pylori Antimicrobial Susceptibility Testing Before and After Algorithm Optimization: A Two-Round Comparative Study

ObjectiveThis study was designed to evaluate the diagnostic performance of fluorescence-based rapid on-site specimen evaluation (F-ROSE) for antimicrobial susceptibility testing of Helicobacter pylori (H. pylori) and to compare test performance before and after iterative optimization of fluorescence image acquisition and of the artificial intelligence (AI) recognition algorithm, using two consecutive rounds of paired testing, so as to provide trial data supporting clinical implementation of rapid susceptibility testing. MethodsForty patients with a urea breath test (UBT) or rapid urease test (RUT) positive for H. pylori within the preceding 2 weeks, together with strongly positive endoscopic findings, were prospectively enrolled. In order of enrollment they were allocated to two rounds in which F-ROSE was compared with culture-based susceptibility testing. Twenty patients were tested in round 1 on an automated fluorescence immunoassay scanner running the original algorithm; a further 20 were tested in round 2 with the optimized algorithm. With in vitro culture and E-test as the reference standard, sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV) and accuracy of F-ROSE were calculated for each round for amoxicillin, levofloxacin hydrochloride and clarithromycin, and agreement between methods was assessed with Cohens kappa. Receiver operating characteristic (ROC) analysis was used to identify the optimal cutoff of the fluorescence residual rate (FRR) and to determine how far threshold adjustment improved performance. ResultsCulture succeeded in 15 patients in round 1 and in 14 patients in round 2, leaving 29 evaluable samples. Overall diagnostic performance after algorithm optimization was clearly better than before. Pooled across the three antibiotics, sensitivity was 92.9%, specificity 71.0% and accuracy 77.8% before optimization; after optimization sensitivity rose to 100.0%, specificity increased slightly to 74.2% and accuracy to 81.0%. NPV reached 100.0% for all three agents after optimization, and no resistant isolate was missed. The gain was largest for clarithromycin, for which sensitivity rose from 85.7% to 100.0%, accuracy from 66.7% to 78.6% and kappa from 0.348 to 0.571, indicating a clear improvement in agreement between the two methods. ROC analysis showed that drug-specific optimal cutoffs derived from the Youden index improved specificity appreciably compared with the uniform 50% FRR threshold currently applied, the gain being most evident for levofloxacin hydrochloride. ConclusionsWith sharper fluorescence images and an improved AI recognition algorithm, F-ROSE performs better in H. pylori susceptibility testing, and the reduction in missed resistant strains is particularly noteworthy; the assay is therefore a plausible option for rapid susceptibility screening in clinical practice. Multicenter studies with larger samples are still required to confirm the stability of the technique.

microbiology↗

bioRxiv2026

Mechanisms regulating combination effect of antibody-drug conjugates and cancer immunotherapy

Antibody-drug conjugates (ADCs) have emerged as a transformative class of cancer therapeutics with important challenges still to be addressed. Combination of ADC with immunotherapy is a promising strategy but mechanisms and effective application remain to be determined. We evaluated ADC combinations with T cell engagers (TCEs) and checkpoint inhibitors (CPI). ADC-TCE combinations produced robust antitumor activity independent of antigen and payload and persisted despite ADC-related T cell loss. Efficacy was dominated by a direct effect of ADC on tumor cells. ADCs induced autophagy that upregulated TNF receptors (TNFRs) and mannose-6-phosphate receptors (M6PR). When ADCs were combined with TCEs TNF released by T cells was primarily responsible for potent antitumor effect of combination. In contrast, M6PR was dispensable for ADC-TCE activity but critical for combinations with CPI expanded antigen-specific T cells via enhanced granzyme B uptake. These data reveal a unifying, target- and payload-agnostic mechanism enabling rational ADC-immunotherapy combinations. SignificanceThis is first evidence that ADC-induced tumor cell autophagy via up-regulation of TNFR and M6PR could be responsible for potent antitumor effect of combination of ADC with TCE. TCEs exploit a TNF-TNFR axis, whereas antigen-specific T cells leverage granzyme B-M6PR uptake. This mechanistic framework explains broad ADC-TCE synergy and guides rational selection of ADC-immunotherapy combinations beyond checkpoint blockade.

immunology↗

bioRxiv2026

Ribonucleotide Reductase Inhibition Overcomes FLT3 Inhibitor Resistance in Acute Myeloid Leukemia

Internal tandem duplication mutations in FLT3 (FLT3ITD) occur in approximately 30% of patients with acute myeloid leukemia (AML) and are among the most common genetic alterations in this disease. FLT3ITD is a major driver of AML and is associated with poor clinical outcomes. Although FLT3 inhibitors (FLT3is) have significantly improved outcomes for patients with FLT3ITD+ AML, acquired resistance remains a major barrier to durable clinical benefit. Reactivation of RAS/MAPK signaling, often driven by activating NRAS mutations, is a major mechanism of FLT3i resistance in AML; however, effective strategies to overcome this resistance remain lacking. Here, we identify ribonucleotide reductase (RNR) as a critical therapeutic vulnerability in NRAS-driven FLT3i-resistant FLT3ITD+ AML. Activation of RAS signaling through SPRY3 loss or oncogenic NRAS mutations confers robust resistance to FLT3is, whereas pharmacologic inhibition of RNR with multiple inhibitors, as well as siRNA-mediated RNR suppression, reverses FLT3i resistance and restores FLT3i sensitivity across multiple FLT3ITD+ AML models in vitro. In vivo, clofarabine, an FDA-approved RNR inhibitor (RNRi), significantly overcomes NRAS mutation-driven FLT3i resistance. In combination with FLT3 inhibition, clofarabine markedly suppresses the progression of FLT3i-resistant AML and significantly prolongs survival in cell line-derived xenograft (CDX) models. Importantly, the therapeutic efficacy of the gilteritinib/clofarabine combination was independently validated in two genetically distinct patient-derived xenograft (PDX) models harboring different NRAS mutations, demonstrating robust reduction of leukemia burden and confirming the generalizability of RNR inhibition in primary FLT3i-resistant AML. Together, these findings identify a previously unrecognized therapeutic vulnerability in FLT3i-resistant FLT3mut+ AML and establish RNR inhibition as an effective strategy to overcome FLT3i resistance, providing a strong rationale for the clinical evaluation of RNRis in combination with FLT3is in patients with resistant AML. SignificanceAlthough FLT3 inhibitors (FLT3i) are an important therapeutic advance in FLT3ITD+ AML, resistance commonly develops. We identified ribonucleotide reductase (RNR) as a new key vulnerability in NRAS-driven FLT3i-resistant AML and demonstrated that multiple RNRis, including the FDA-approved agent clofarabine, restore FLT3i sensitivity and enhance antileukemic activity, supporting a clinically actionable combination strategy.

cancer biology↗

bioRxiv2026

Reversing aging-like 3D genome disorganization in a Drosophila interphase model

Recent experimental evidence suggests that aging may arise from the progressive deterioration of the epigenetic landscape, while reversing the trend can result in cell and tissue rejuvenation. A mechanistic understanding of how restoration of a key component of this landscape - the 3D structure of the genome - can be accomplished is lacking. Here we investigate lamina-dependent disruption and recovery of the 3D architecture of the Drosophila melanogaster genome at TAD resolution ([~] 100 kb), using a model of the entire nucleus; weakening of chromatin-lamina interactions mimics an aging-associated loss of chromatin organization. We characterize this loss using the Shannon entropy of appropriately normalized Hi-C contact matrices. Our main finding is that lamina-depletion-induced increases in Hi-C map disorder, deterioration of chromosome territories, and cell-to-cell conformational heterogeneity are largely reversible when WT-like LAD-nuclear-envelope interactions are restored. The original and recovered conformational states of chromatin are nearly indistinguishable by bulk Hi-C contact matrix; the corresponding Pearson correlation coefficient is 0.999902. The direct experimentally testable prediction is that restoration of functional LAD-lamina interactions will promote recovery of young/WT-like 3D chromatin architecture after lamina-dependent architectural disruption.

genomics↗

bioRxiv2026

Glomerulus-Targeted Nanotherapy via Collagen IV-α3 Binding Enhances Renal Immunoregulation in Lupus Nephritis

Lupus nephritis requires long-term immunosuppressive therapy, which is often associated with severe systemic side effects. Therefore, new therapeutic strategies that maintain high efficacy while minimizing adverse effects is essential. Although nanomedicine has advanced systemic and kidney-targeted drug delivery, a reliable method for glomerulus-specific delivery is lacking. Collagen IV (Col4)-alpha 3, located in the glomerular basement membrane (GBM) at the blood-tissue interface through fenestrated capillary endothelium, represents an ideal target for glomeruli delivery. Herein, we developed a novel liposomal nanoparticle conjugated with a Col4-alpha 3 binding peptide (Col4-3-NPs) for selective glomerular targeting. Prednisolone-loaded Col4-3-NPs were administered to lupus-prone mice twice weekly for 8 weeks. Kidney injury and function were evaluated biweekly, and renal immune cell populations were analyzed by flow cytometry at study completion. The results show that rhodamine-labeled NPs predominantly accumulate in kidney glomeruli 48 hours after intravenous injection. The Col4-NP system demonstrated stable and prolonged release of the encapsulated drug for over 48 hours. Lupus-prone mice treated with prednisolone-loaded Col4-NPs showed significantly improved renal function and histology, including a 30% increase in glomerular filtration rate (GFR), a 56% reduction in proteinuria, and decreased IgG deposition and fibrosis. Notably, treatment also enhanced renal regulatory T cell (Treg) populations. These findings suggest that glomerulus-targeted Col4-3-NPs hold significant translational promise. This platform may offer an effective, site-specific treatment for lupus nephritis while minimizing systemic side effects and could be adapted for other glomerular diseases requiring targeted therapy.

physiology↗