Biology subjects

Han, J.

Publications and source records attributed to Han, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

MTB-KB: A Curated Knowledgebase of Mycobacterium tuberculosis Related Studies

Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), has regained its position as the worlds leading killer among infectious diseases. Despite extensive research progress across epidemiology, diagnosis, drug development, treatment regimens, vaccines, drug resistance, virulence factors, and immune mechanisms, MTB-related knowledge remains fragmented across thousands of publications, limiting its effective use. To address this gap, we present MTB-KB, a literature-curated knowledgebase that systematically integrates high-impact findings from eight major sections of TB research. The current release contains 75,170 associations from 1,246 publications, covering 18,439 entities standardized using authoritative databases and WHO-endorsed classifications. A central feature is the interactive knowledge graph, which links cross-section associations to reveal and infer MTB-host interactions, treatment strategies, and vaccine development opportunities. MTB-KB also provides a user-friendly interface with browsing, advanced search, and statistical visualization. Overall, by consolidating dispersed MTB knowledge into a structured and accessible platform, MTB-KB provides a valuable resource for researchers, clinicians, and policymakers, supporting both basic and clinical TB research, enabling evidence-based TB prevention, diagnosis, and treatment, and contributing to global elimination efforts. MTB-KB is accessible at https://ngdc.cncb.ac.cn/mtbkb/.

bioinformatics↗

bioRxiv2026

Precision DNA Impurity Reduction Approaches for Ultra-Pure rAAV Manufacturing

Recombinant adeno-associated virus (rAAV) vectors are a leading platform for gene delivery in basic and clinical research, yet large-scale manufacturing remains constrained by residual nucleic-acid impurities that compromise safety. In this study, we profiled the DNA species packaged within rAAV capsids and identified plasmid backbone sequences and host cell genomic DNA (hcDNA) as predominant contaminants. To mitigate this critical quality attribute, we implemented upstream strategies designed to fragment or excise backbone DNA, including TelN/TelROL excision, I-SceI meganuclease digestion, CRISPR/Cas9 cleavage, and Cre/LoxP recombination. Quantitatively, TelN/TelROL and I-SceI reduced encapsidated plasmid backbone DNA to approximately 20-30% and 20-40% of baseline levels, respectively, while CRISPR/Cas9 lowered it to about 10-20%. Notably, the Cre/LoxP system eliminated detectable plasmid backbone DNA without compromising vector-genome titers, indicating preserved genomic integrity. Additionlly, supplementating cell culture with a caspase inhibitor significantly reduced hcDNA contamination in rAAV particles to 1-5% of the baseline level. Collectively, these interventions provide practical bioprocess frameworks that markedly enhance rAAV purity via targeted DNA minimization and prevention of hcDNA fragmentation, thereby strengthening the safety profile of rAAV therapeutics in alignment with current Good Manufacturing Practice (cGMP) expectations.

molecular biology↗

bioRxiv2026

Bimodal Coupling Optimization in Biological Rhythms: Balancing Energy Efficiency and Functional Demand

Biological rhythms are governed by intricate interactions among oscillatory subsystems, yet how they balance functional demands and energy efficiency remains unclear. We present a bimodal coupling optimization strategy where physiological systems dynamically alternate between synchronized (energy-saving) and desynchronized (function-priority) coupling modes. By employing the water-filling principle developed in communications engineering, we prove synchronized heart rate(HR)-respiration oscillations maximize energy efficiency (oxygen uptake per cardiac work). Then, system modeling confirms task/stress-induced oxygen demands enhance oxygen uptake at the cost of desynchronization and reduced efficiency. Experiments reveal a 70.36% decrease in HR-respiration synchronization during arithmetic versus relaxation, enabling 4.43% higher oxygen uptake but with 11.38% lower energy efficiency. This bimodal coupling optimization strategy is also evident in pancreatic islets, with their insulin/glucagon oscillator alternating between in-phase (energy-saving) and anti-phase (rapid glucose reduction) coupling. This framework, integrating engineering and life sciences, reveals a universal regulatory principle for biological oscillatory systems.

systems biology↗

bioRxiv2026

Effects of lumbar disc injury and nociception on trunk motor control during rat locomotion

Intervertebral disc (IVD) injury is a major cause of low-back pain and can lead to structural deficits and mechanical instability. When the IVD is compromised, neuromuscular compensation by paraspinal muscles, such as the multifidus (MF) and longissimus (ML), is critical for maintaining spine stability. However, it is unknown how IVD injury and its interaction with nociception affect neuromuscular control. This study assessed the effects of IVD injury and additional muscle-derived nociception on trunk motor control during locomotion in a rat model. IVD injury was induced via needle puncture at L4/L5. One week later, hypertonic saline was injected into the lumbar MF to induce nociception. Trunk and pelvic kinematics, bilateral EMG activity of MF and ML were recorded during treadmill locomotion at baseline, one week after IVD injury, and immediately following hypertonic saline injection. Trunk and pelvic kinematics and bilateral muscle activation patterns remained largely consistent across conditions. No significant changes were found in stride duration, pelvic, lumbar and spine angle changes, variability, or movement asymmetry. MF activation was bilaterally synchronized, whereas ML showed left-right alternating activation patterns. Following IVD injury, right MF mean activation and EMG variability increased significantly compared to baseline. When muscle-derived nociception was added in the unstable spine (IVD injury) condition, left MF minimum amplitude was significantly reduced, and instability-related increases in right MF mean activation and variability were attenuated, but not fully reversed. These findings suggest that IVD injury, alone or in combination with muscle-derived nociception, elicits localized neuromuscular adaptations without disrupting the global locomotor patterns.

neuroscience↗

bioRxiv2026

Mechanical and morphological effects of intervertebral disc injury: a systematic review of in vivo animal studies

Intervertebral disc degeneration (IVDD) compromises disc structures and mechanics, yet systematic evaluations of the mechanical responses and their relationship to morphological changes in preclinical models remain limited. This systematic review and meta-analysis synthesized mechanical and morphological alterations following experimental disc injury in in vivo animal models. Searches of MEDLINE, EMBASE and Web of Science databases were conducted in accordance with PRISMA guidelines. Study quality and risk of bias were assessed using modified CAMARADES and SYRCLE tools. Twenty-eight studies were included. Pooled analyses showed significant reductions in stiffness, Youngs modulus, and disc height, and significant increases in range of motion and degeneration grade, indicating both mechanical and structural deterioration. Youngs modulus appeared to be the most sensitive marker of functional degeneration. By contrast, creep and other viscoelastic responses showed non-significant changes. High heterogeneity was evident across studies, reflecting variability in injury models, species, timepoints, and testing methods. Evidence of publication bias was detected in several domains, and moderate methodological quality was noted with overall insufficient blinding and lack of sample size calculations. In vivo animal models of IVDD demonstrate robust and consistent mechanical and morphological degeneration after injury. Youngs modulus is a sensitive mechanical indicator, supporting its use in future preclinical research. Standardization of outcome definitions, methodology, and reporting is essential to improve comparability and enhance translation of preclinical findings to clinical research.

bioengineering↗

bioRxiv2026

Pirfenidone improves adipose dysfunction and obesity-driven steatohepatitis via mTORC1 signaling

Obesity-driven metabolic dysfunction-associated steatotic liver disease (MASLD) and metabolic dysfunction-associated steatohepatitis (MASH) are shaped by depot-specific adipose tissue dysfunction, including maladaptive expansion and visceral adipose tissue (VAT) fibrosis. Pirfenidone, an anti-fibrotic agent, improves experimental liver disease. However, its actions on adipose depots and adipose-liver crosstalk remain unclear. Here, we identify pirfenidone as a modulator of mechanistic target of rapamycin complex 1 (mTORC1)-dependent adipose tissue remodeling with divergent outputs in subcutaneous and visceral fat. In diet-induced obese MASH mice, pirfenidone decreased subcutaneous adipose tissue (SAT), inhibiting mTORC1-driven lipogenesis and enhancing oxidative lipid metabolism. Pirfenidone attenuated VAT fibrosis by suppressing an mTORC1-mothers against decapentaplegic homolog 3 (SMAD3)-yes-associated protein (YAP) axis and extracellular matrix gene programs. Pirfenidone also lowered hepatic triglycerides, improved steatosis and fibrosis, reduced hepatic mTORC1 activity. Conditioned medium from fibrotic adipocytes induced lipogenic, inflammatory, and pro-fibrotic programs in AML12, which effects that were blunted by pirfenidone. These data reveal adipose tissue-centered actions of pirfenidone that link mTORC1 remodeling to improved obesity-associated liver disease.

molecular biology↗

bioRxiv2026

A foundation AI model enhances electron microscopy image analysis

Electron microscopy (EM) and advanced volume EM have extensive applications in deciphering cellular ultrastructures for life sciences. However, quality issues of EM images significantly impede the precise analysis and discovery of nanoscale biological structures. Here, we present an unsupervised Foundation Model for Five Tasks (DF5T) model for image enhancement through denoising, deblurring, super-resolution, two-dimensional (2D) inpainting, and three-dimensional (3D) isotropic restoration. DF5T was trained on an extensive dataset of multi-source membrane-bound organelle EM images, consisting of a total of over 2.25 million images. On unseen data, DF5T outperformed the existing state-of-the-art models in all five tasks. Furthermore, DF5T substantially compensates for missing three-dimensional structural information and reveals significant ultrastructural alterations in organelle geometry following chemical treatment. We demonstrate that DF5T significantly enhances electron microscopy images quality by improving the accuracy of downstream organelle segmentation and 3D structural restoration, thereby contributing to future advances in biological research.

cell biology↗

bioRxiv2026

Non-canonical signaling mechanisms of short-chain fatty acid receptors in glucagon-like peptide-1 (GLP-1) releasing enteroendocrine cells

ObjectivesFree fatty acid receptors 2 and 3 (FFA2 and FFA3) are activated by nutrient-derived metabolites such as short-chain fatty acids (SCFAs) and ketone bodies, produced by the gut microbiota and host, respectively. This study aimed to investigate the intracellular signaling pathways recruited in glucagon-like peptide-1 (GLP-1) releasing enteroendocrine cells following activation of FFA2 and FFA3 to resolve the impact of nutrient status on enteroendocrine cell function. MethodsExperiments were performed using primary mouse colonic cultures and the mouse enteroendocrine cell line, GLUTag cells. Expression analysis by bulk RNA sequencing was used to determine expression of FFA2 and FFA3 in GLP-1 releasing cells. Measurement of GLP-1 secretion by sandwich ELISA was used to assess enteroendocrine cell function. Live-cell measurements of intracellular calcium and cAMP levels were performed to assess canonical second messenger signaling pathways. ResultsA SCFA mixture stimulated GLP-1 secretion from both primary mouse colonic cultures and GLUTag cells. In GLUTag cells, the FFA2 ligand 4-CMTB inhibited GLP-1 release independent of Gaq- and Gai-signaling as neither YM-254890 (Gaq inhibitor) nor pertussis toxin (Gai- uncoupler) altered its effect. However, 4-CMTB did elevate cAMP levels, suggesting an indirect mechanism for the increase in cAMP production. Stimulation of FFA2 with the Gai-biased ligand AZ1729 or the ketone body acetoacetate inhibited GLP-1 release and cAMP accumulation. AZ1729 was insensitive to pertussis toxin and OZITX, supporting atypical FFA2 signaling. Stimulation of FFA3 with AR420626 or the ketone body {beta}-hydroxybutyrate increased GLP-1 secretion from GLUTag cells, an effect that was not mediated by cAMP production. AR420626, but not {beta}-hydroxybutyrate increased intracellular calcium levels. ConclusionsOverall, activation of FFA2 inhibited secretory function in GLP-1-releasing enteroendocrine cells, whereas activation of FFA3 stimulated GLP-1 secretion via distinct intracellular signaling mechanisms. O_FIG O_LINKSMALLFIG WIDTH=184 HEIGHT=200 SRC="FIGDIR/small/708924v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@175dbaforg.highwire.dtl.DTLVardef@a9cc3eorg.highwire.dtl.DTLVardef@1a026e5org.highwire.dtl.DTLVardef@15997af_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG HighlightsO_LIExposure to physiological levels of SCFAs stimulates GLP-1 secretion from colonic EECs C_LIO_LIFFA2 and FFA3 regulate GLP-1 release via non-canonical signaling pathways C_LIO_LIKetone bodies activate SCFA receptors to differentially modulate GLP-1 levels C_LIO_LILigand bias enables nutrient-dependent tuning of EEC gut hormone secretion C_LI

cell biology↗

bioRxiv2026

Z-RNA-ZBP1 axis drives Tau-mediated neurodegeneration

Although the causes of Tau aggregates vary, once Tau aggregates are formed, their neurotoxicity significantly contributes to neuronal death and cognitive decline in tauopathies, with Alzheimers disease (AD) being the most well-known example. Despite its central pathogenic role, however, effective therapeutic strategies targeting neurotoxicity of Tau remain poor. Here we demonstrate the pathogenic role of neuronal cell death in Tau-related neurodegeneration. Tau-expressing neurons undergo cell death through Z-DNA-binding protein 1 (ZBP1) activation triggered by endogenous Z-RNAs. These Z-RNAs are derived from reactivated transposable elements (TEs) that are typically silenced within heterochromatin. Tau aggregates show a strong affinity for H3K9me3-modified chromatin, effectively sequestering these epigenetic marks from Heterochromatin Protein 1 (HP1), thereby disrupting the condensation of constitutive heterochromatin. Clinically, an inverse correlation between ZBP1 expression levels in excitatory neurons and cognitive performance in AD patients was observed. Importantly, Zbp1 haploinsufficiency significantly ameliorated cognitive deficits in aged Tau-transgenic mice (24-month-old), highlighting the therapeutic potential of ZBP1 inhibition to strive against neurodegeneration in tauopathies.

neuroscience↗

bioRxiv2026

Programmable RNA detection generates DNA barcodes for multiplexed phage-host interaction screening

Here, we introduce Detectrons, modular biosensors that couples programmable toehold switches with retron-mediated reverse transcription to transduce RNA inputs into unique DNA barcodes. The ability to convert dynamic RNA signals into durable DNA records within living cells unlocks powerful new modes of transcript-based sensing with applications including viral infection detection. Through the construction of a synthetic toehold-retron library and application of machine learning, we uncovered key design principles that improve signal strength and specificity. We applied Detectrons to the multiplexed live-cell detection of specific phage infections, enabling transcript-triggered barcode synthesis and quantitative host susceptibility profiling in pooled bacterial populations. Detectrons are the first RNA-to-DNA transduction system, directly linking transient RNA detection to stable, sequence-encoded DNA outputs. This platform provides a scalable and generalizable strategy for phage screening and for recording transcriptional events in complex bacterial communities.

synthetic biology↗

bioRxiv2026

The genomic basis of heat stress adaptation in indigenous Ethiopian cattle from arid and hot-humid climates

African zebu cattle (Bos indicus) exhibit remarkable adaptation to extreme thermal conditions, yet the genomic bases of this resilience are not fully elucidated. Ethiopia provides a unique natural setting where closely related zebu populations have divergently adapted to hot-arid (DHETZ) and hot-humid (HHETZ) climates. In this study, we performed whole-genome sequencing of 46 Ethiopian zebu cattle from five populations and compared them with Asian zebu, Sudanese zebu, African taurine, and European taurine breeds. By integrating genome-wide SNP analysis, population genetic structure assessment, and multiple selection scans (iHS, Hp, XP-EHH, and XP-CLR), we identified distinct and shared selection signatures between DHETZ and HHETZ cattle. Ethiopian zebu closely clustered with Sudanese zebu but showed clear divergence from Asian zebu and taurine breeds. Although DHETZ and HHETZ cattle exhibited minimal genetic differentiation, reflecting their shared ancestry, each group displayed unique selection signals. DHETZ cattle showed strong selection in genes involved in oxidative stress regulation, protein folding, mitochondrial function, and vascular remodeling (e.g., SESN2, DNAJC8, GRPEL2, ABLIM3, and AFAP1L1). In contrast, HHETZ cattle displayed signatures in genes associated with immune responses, energy metabolism, and angiogenesis inhibition (e.g., MYD88, PRKACA, PRKACB, and WIF1). Several genes, including VEGFC, TNIP3, and DMXL2, were under selection in both groups, suggesting conserved mechanisms of thermotolerance and reproductive adaptation. These findings reveal a dual pattern of genomic adaptation: while core heat-response pathways are shared, population-specific signatures reflect distinct metabolic and vascular strategies for coping with arid versus humid heat stress. This study provides novel insights into the genomic architecture of environmental adaptation in tropical cattle and offers valuable markers for breeding climate-resilient livestock.

genomics↗

bioRxiv2026

Accurate somatic variant detection from formalin fixed, paraffin embedded tissue (FFPE) derived WES and WGS by DeepOmicsFFPE-PLUS, a sequence context-based transformer

Formalin-fixed paraffin-embedded (FFPE) tissues represent a vast archival resource for genomic studies, yet their utility remains constrained by fixation-induced DNA damage and subsequent sequencing artifacts. To comprehensively characterize and address this challenge, we analyzed matched FFPE and fresh-frozen tumor samples from two institutions, spanning different storage durations, DNA qualities, sequencing platforms (WES and WGS), exome capture kits, and somatic variant callers. We found that FFPE-induced artifacts exhibit strong batch- and age-specific patterns, with a predominance of C:G>T:A substitutions, which particularly complicate the accurate identification of low allele frequency true variants. Enzymatic repair methods partially alleviated these artifacts but remained insufficient. To overcome these limitations, we developed DeepOmicsFFPE-PLUS(https://github.com/Theragen-Bio/DeepOmicsFFPE-PLUS), an advanced AI-based tool to accurately distinguish true somatic variants from FFPE-specific artifacts. DeepOmicsFFPE-PLUS demonstrated consistently superior performance across diverse conditions, achieving high sensitivity and specificity--even for low-frequency variants--outperforming existing tools. Application of our model to WGS data further enabled recovery of biologically relevant mutational signatures, including restoration of microsatellite instability (MSI)-associated signatures initially obscured by FFPE artifacts. Our findings underscore the necessity of artifact-aware variant calling in FFPE genomics and establish DeepOmicsFFPE-PLUS as a robust tool for artifact removal, enabling high-fidelity downstream analyses and personalized therapeutic target discovery.

cancer biology↗

bioRxiv2026

Novel repressors of cambium activity in Arabidopsis

Wood is the greatest reservoir of terrestrial biomass and an essential carbon sink. Formed of xylem, it is derived from the cambium, a meristematic zone within plant stems from which phloem also forms. In Arabidopsis, cell division within the cambium is promoted by three major factors: auxin, cytokinin, and the TDIF-PXY ligand-receptor pair. Meristems and other stem cell populations are typically regulated by a balance between cell division-promoting factors and those that repress cell division to control meristem size, however few factors with cambium-repressing activity are known. Here we combined transcriptomics and transcriptional network analysis, which led to identification of related homeodomain zinc-finger transcription factors, ATHB23, ATHB30, and ATHB34, that repress cambium activity. These factors inhibit cambium activity by directly binding of promoters from a subset of auxin, cytokinin and TDIF-PXY transcriptional target genes, resulting in attenuation of their transcription. Our findings thus reveal a new mechanism underpinning balanced cambium activity.

plant biology↗

bioRxiv2026

Machine Learning Identifies Distinct Treg-Mediated Remodeling in HFpEF Hearts Treated with Neonatal Mesenchymal Stem Cells and Their Secretome

BackgroundHeart failure with preserved ejection fraction (HFpEF) remains a major therapeutic challenge due to its complex pathophysiology and pronounced heterogeneity. Regenerative approaches using neonatal mesenchymal stromal cells (nMSCs) and their secretome (SEC) have shown promise in other heart failure contexts. ObjectivesHowever, the effect of these therapies in HFpEF, and the underlying molecular mechanisms and causal pathways remain poorly understood. MethodsHFpEF was established in two distinct murine models, followed by treatment with either nMSCs or SEC. Functional and histological endpoints were assessed. We developed a novel machine learning framework, VIPcell, which integrates data augmentation, Partial Least Squares (PLS) regression, and causal structure inference to identify genes causally linked to cardiac function using single-nucleus RNA sequencing (snRNA-seq) data. VIPcell was applied to heart tissues from treated HFpEF animals to uncover key regulators of cardiac remodeling. ResultsBoth nMSC and SEC therapies significantly improved diastolic function in two independent rodent HFpEF models. These improvements were associated with reduced inflammation, attenuated myocardial fibrosis, and improved exercise capacity. Intercellular communication analysis revealed widespread, system-level signaling in nMSC-treated hearts, compared to more localized endothelial-cardiomyocyte crosstalk in SEC-treated hearts. Causal inference via VIPcell suggested overlapping upstream regulators in both treatment groups, particularly genes involved in regulatory T cell (Treg) biology and immunomodulatory signaling pathways, including FOXO signaling, NLRP3 inflammasome inhibition, and Tie2 activation. In vivo validation confirmed selective expansion of Tregs following nMSC and SEC therapy. In vitro, nMSCs induced significantly greater Treg expansion compared to multiple adult stem cell types. Critically, chemical depletion of Tregs abrogated the therapeutic effects of both treatments, establishing Tregs as central mediators of diastolic function recovery in the HFpEF preclinical model. ConclusionsnMSC and SEC therapies improve diastolic function in HFpEF through distinct remodeling mechanisms converging on Treg-mediated immune modulation. VIPcell supported identification of causal regulators, highlighting Treg-related signaling as a key driver of myocardial recovery in HFpEF. These findings offer mechanistic insight into cellular therapies for HFpEF and support the development of targeted, Treg-focused interventions.

physiology↗

bioRxiv2026

DISCO-LAMP: A Novel discontinuous LAMP assay for isothermal antigen detection

Proximity ligation assay (PLA), in which the ligation of two DNA probes is greatly accelerated by the associating target molecules, has emerged as a highly sensitive technique for protein detection. The detection of the ligated DNA typically relies on PCR, which requires temperature cycling. In this study, we report on a novel discontinuous (DISCO)-LAMP assay that enables the wash-free detection of PLA products via loop-mediated isothermal amplification (LAMP). Due to the exponential amplification nature of LAMP, a careful balance between efficient amplification of the ligated full-length DNA and minimal background amplification from the individual constituent probes is essential but often challenging to achieve. After extensive template/primer design and assay optimization, DISCO-LAMP assay achieved a detection limit of 1 fM for the ligated DNA probe while maintaining undetectable background amplification at 1 nM of each individual probe. DISCO-LAMP detected Shiga toxin 2 (Stx2) with a limit of detection (LoD) of 100 fM when functionalized with Stx2-binders, as well as both Wuhan-1 and Omicron spike protein when functionalized with DS16, a newly engineered DARPin targeting a conserved epitope on the SARS-CoV-2 Spike protein. We believe DISCO-LAMP represents a versatile and efficient LAMP-based PLA technology that is readily adaptable for sensing diverse targets.

bioengineering↗

bioRxiv2026

Exploring Multi-Scale Local and Global Features in Whole Slide Images Using State Space Models

Whole slide image (WSI) classification is crucial in computational pathology, yet the gigapixel scale of WSIs makes it challenging to extract discriminative and compact WSI-level features for disease diagnosis. In this paper, we propose MambaWSI, a novel method that leverages the state space model (SSM) for WSI classification by exploring multi-scale local and global features. Unlike existing approaches that sequentially traverse WSI tiles and rely on vanilla SSMs for long-range dependency modeling, we exploit a traversal strategy in a higher-dimensional discrete space that preserves spatial proximity, enabling a first-local-then-global feature extraction process. Furthermore, to align with the clinical workflow of pathologists when examining WSIs at multiple scales, we propose a two-stage hierarchical fusion strategy: inter-scale feature alignment and aggregation, followed by attention-based fusion across magnifications, integrating complementary information from multiple magnifications. Experiments on two datasets demonstrate that MambaWSI outperforms state-of-the-art methods in classification performance.1

pathology↗

bioRxiv2026

PCRD-seq: Proximity Crosslinking-induced RNA Depletion for Low-Input Subcellular Transcriptome Profiling

Chromatin-associated RNAs play critical roles in regulating chromatin organization and transcription, underscoring the importance of their study. Proximity labeling has emerged as a promising and versatile technique for profiling chromatin-associated RNAs with high spatiotemporal resolution. While being a powerful technique, traditional proximity labeling methods depend on complex, high-input enrichment protocols, which significantly limit their wide practical application. Here, we developed a straightforward, enrichment-free chromatin-associated RNA profiling strategy: Proximity Crosslinking-induced RNA Depletion sequencing (PCRD-seq). This approach leverages the proximity crosslinking between chromatin and its surrounding RNAs induced by singlet oxygen generated by HoeDBF, a photosensitizer targeting chromatin region. The proximity crosslinking hinders the release of chromatin-associated RNAs during routine TRIzol extraction, consequently leading to a specific depletion of these RNAs. This method was successfully applied to investigate the role of U1 snRNA in RNA chromatin retention and the differences in chromatin-associated transcriptomes between two ovarian cancer cell lines with opposite metastatic capability. Moreover, our PCRD-seq exhibits potential in profiling nuclear lamina-associated RNAs, which paves the way for its application to profile RNAs associated with other chromatin subdomains. The minimal cell input and simple workflow endow PCRD-seq as a transformative tool for wide applications.

cell biology↗

bioRxiv2026

Mitochondrial Double-Stranded RNA Triggers Ferroptosis via PKR-ISR Signaling in Renal Ischemia-Reperfusion Injury

Renal ischemia-reperfusion (IR) injury remains a leading cause of acute kidney injury, although the precise molecular pathways responsible for tissue injury are not fully understood. In this study, we demonstrate that IR initiates ferroptosis through activation of the PKR-dependent integrated stress response (ISR), which is driven by the accumulation of mitochondrial double-stranded RNA (dsRNA). Our mechanistic investigations reveal that IR perturbs mitochondrial homeostasis, leading to the accumulation of mitochondrial dsRNA and its subsequent release into the cytosol, thereby activating the dsRNA-dependent kinase PKR. Activation of PKR results in eIF2 phosphorylation and maladaptive ISR signaling, which facilitates ferroptosis and impairs renal function. Notably, genetic ablation of PKR or pharmacological intervention to inhibit ISR significantly reduced ferroptosis and preserved renal function. Collectively, these results identify the mitochondrial dsRNA-PKR-ISR axis as a critical mediator of ferroptotic renal injury and highlight its potential as a therapeutic target in ischemic acute kidney injury.

cell biology↗