Modulation of miRNA expression in glomerular cells is associated with renal disease. Here, we investigated the role of miR-93-5p in mitigating glomerular damage in Alport syndrome and whether the disease-modifying activity of extracellular vesicles from human amniotic fluid stem cells (hAFSC-EVs) is mediated by their miR-93-5p cargo. We identified downregulation of miR-93-5p specifically in glomerular endothelial cells in Alport syndrome along disease progression. Silencing of miR-93-5p in hAFSC-EVs changed the transcriptomic and proteomic profile, regulating EV disease-modifying activity. Compared with naive hAFSC-EVs, silenced hAFSC-EVs did not rescue glomerular endothelial function in vitro and did not restore kidney function in vivo. We established that hAFSC-EVs regulate VEGFR1 and VEGFR2 signaling by miR-93-5p cargo transfer, highlighting that miR-93-5p can restore glomerular endothelial cell biology. Spatial transcriptomics analysis of hAFSC-EV-injected kidneys showed that these EVs can reverse pathways altered during disease progression by stimulating proregenerative processes, specifically in the glomerulus, by regulating miR-93-5p targets. Alteration of glomerular endothelial cell transcriptomics and miR-93-5p targets was also confirmed in biopsies of patients with Alport syndrome using spatial molecular imaging. We demonstrated the critical role of miR-93-5p in glomerular endothelial cells and the capability of hAFSC-EVs to regulate miR-93-5p and its targets in Alport syndrome.

Limb-girdle muscular dystrophy R2 (LGMD R2) is an autosomal recessive disorder caused by dysferlin deficiency, leading to progressive muscle weakness and wasting. The lack of reliable clinical biomarkers has limited disease monitoring and therapeutic evaluation. Here, we identified Disabled-2 (DAB2) as a molecular and clinical indicator of disease state in LGMD R2. Transcriptomic profiling revealed a significant upregulation of DAB2 in induced pluripotent stem cell-derived (iPSC-derived) myotubes from patients, a finding validated in muscle biopsies from 14 dysferlin-deficient individuals and in dysferlin-deficient Bla/J mice, where DAB2 levels increased with disease progression. Importantly, AAV-mediated expression of full-length dysferlin restored DAB2 levels, supporting its value as a dynamic readout of disease activity for both disease monitoring and therapeutic response. Given the established role of DAB2 in clathrin-mediated endocytosis, particularly in LDL receptor internalization and cholesterol homeostasis, and the pathological lipid accumulation reported in LGMD R2, we investigated its contribution to lipid dysregulation. High DAB2 expression paralleled lipid deposition in patient muscles, iPSC-derived myotubes, and mouse tissue, whereas siRNA-mediated DAB2 knockdown reduced lipid accumulation in LGMD R2 myotubes. Collectively, these findings suggest that DAB2 functions as a mechanistic link between dysferlin deficiency, altered lipid handling, and disease severity, and they highlight its potential as a prognostic marker and therapeutic response measure for LGMD R2.

Common variable immunodeficiency (CVID) is the most prevalent symptomatic primary antibody deficiency. For unclear reasons, inflammatory complications, like gastrointestinal (GI) disease, occur in ~50% of CVID cases, worsening morbidity and mortality. NFKB1 variants are among the most frequent genetic variants in CVID. While effect of NFKB1 variants is not well understood, we previously found frameshift heterozygous NFKB1 variants to increase cytokines, monocytes, and inflammatory complications in CVID. In this report, we used induced pluripotent stem cell-derived (iPSC-derived) monocytes (iMONOs) with CRISPR/Cas9-mediated gene editing to study a heterozygous NFKB1 frameshift found in a patient with CVID with severe GI disease. The heterozygous NFKB1 variant similarly reduced NFKB1 protein in CVID patient- and healthy donor-derived iMONOs, but elevated LPS-induced IL-1β release and expression of inflammatory genes, including IL1B, IL6, TNF, and neutrophil chemoattractants, only in CVID patient iMONOs. CVID patient iMONOs also had elevations of IL-12, CCL4, and CCL12 unaffected by presence or absence of the NFKB1 variant. TNF antagonism improved the patient's GI disease, diminishing neutrophilic gastritis, circulating neutrophils, and the neutrophil chemoattractant CXCL1 in the blood. While the biology remains complex, our approach found heterozygous NFKB1 variant-induced inflammatory changes intensified in CVID iMONOs, corresponding with clinical response to TNF antagonism.

Pancreatic ductal adenocarcinoma (PDAC) is among the most lethal malignancies, characterized by aggressive biology, a dense fibrotic and immunosuppressive microenvironment, and profound resistance to standard therapies. Smart polymeric nanoparticles (SPNs), engineered to sense and respond to biological cues, present a transformative approach to overcome these barriers. This review highlights recent advances in SPNs tailored for PDAC, including systems designed to actively target tumor cells, cancer-associated fibroblasts (CAFs), and cancer stem cells (CSCs), thereby enhancing selective drug delivery and efficacy. SPNs also remodel the desmoplastic stroma or deliver matrix-modulating agents to improve tumor penetration. Furthermore, stimuli-responsive SPNs exploit the unique tumor microenvironment (TME) of PDAC, leveraging pH, hypoxia, or enzymatic triggers to achieve controlled, localized drug release. Beyond these strategies, SPNs have been developed to reprogram tumor immunity, modulate metabolic pathways, and enable precision gene therapy or combination treatments. Incorporating chronotherapy principles, future SPNs are capable of synchronizing drug release with circadian rhythms to maximize therapeutic windows while minimizing toxicity. Emerging concepts, such as integrating biosensors for real-time endogenous signal detection or applying AI-driven design to optimize SPN properties, underscore the future potential of these systems. Together, these multifaceted strategies position SPNs as a powerful platform to tackle the formidable challenges of PDAC and advance toward personalized cancer care.

Intracranial germ cell tumors (iGCTs) are categorized into germinomas (GEs) and non-germinomatous germ cell tumors (NGGCTs), which show divergent clinical outcomes with GEs having a significantly more favorable prognosis. This prognostic disparity suggests distinct biological characteristics, yet the association between tumor stemness and the host immune microenvironment, particularly in pre-treatment peripheral blood, remains poorly understood. Therefore, this study integrated multi-omics data, immune cell enrichment scores, and peripheral blood analyses to elucidate the relationship between cancer stemness indices and immune cells, especially neutrophils; and to evaluate its prognosis and treatment strategy in iGCTs.

The periodontium hosts diverse populations of mesenchymal stem and progenitor cells that are essential for maintaining homeostasis and driving regeneration. These include cells derived from the periodontal ligament, gingiva, and apical papilla. In health and disease, the fate and function of these stem cell populations are shaped by their microenvironment, particularly by inflammatory signals and their resolution. Chronic inflammation, such as that observed in periodontitis, disrupts the regenerative capabilities, impairing stem cell function and biasing differentiation pathways. Inflammation resolution is an active, instructive process that can restore stem cell plasticity and re-establish regenerative potential. Specialized pro-resolving lipid mediators and immune-regulatory cell types play a central role in this reprogramming. We explore how inflammation and its resolution actively shape the behavior of multiple stem cell compartments in the periodontium, highlight the emerging role of spatially organized immunoregulation, and discuss how these insights may be leveraged to develop regenerative therapies for oral and mucosal tissues. We focused on how inflammatory and resolution signals modulate osteogenic programs in periodontal MSCs and contrast these responses with those in bone marrow-derived MSCs, highlighting source-dependent differences in inflammatory susceptibility and regenerative potential.

The impaired healing of diabetic wounds is closely associated with a persistent inflammatory response, wherein macrophages, as crucial immune effector cells in the local wound microenvironment, play a vital role in maintaining inflammatory equilibrium. Increasing evidence indicates that lactate, a product of glycolysis, is now recognized as a novel regulator of macrophage function by influencing gene transcription through protein lactylation on histone and non-histone substrates. This review seeks to outline the impact of chronic inflammation on macrophage phenotype (metabolism and polarization) and to clarify how subsequent protein lactylation alters macrophage biology, thereby impacting the progression of chronic inflammatory conditions such as diabetic wounds. These findings collectively provide new insights into the pathogenesis of impaired diabetic wound healing and underscore the potential of targeting protein lactylation as a therapeutic approach against chronic inflammation.

Extracellular vesicles (EVs) are lipid-enveloped nanovesicles rich in microRNAs, proteins and lipids, that serve as potent mediators of intercellular communication. While EVs have demonstrated pro-regenerative potential in 2D and preclinical models, their impact on skin regeneration and aging processes in 3D reconstructed skin models has remained less explored. In this study, EVs from adipose-derived stem cells and umbilical cord-derived mesenchymal stem cells (UC-MSCs) were evaluated using both 2D primary skin cells and 3D full-thickness reconstructed skin models. EVs stimulated fibroblast and keratinocyte proliferation, increased epidermal thickness, and enhanced the presence of collagen IV in the dermal-epidermal junction (DEJ) and fibrillin 1 in the extracellular matrix. Bulk transcriptomic analysis of the 3D reconstructed skin revealed gene expression profiles impacted by the addition of EVs. Additionally, miRNA-seq and proteomics of extracellular vesicle contents revealed miRNAs and proteins that may be drivers of the biological activities observed in 3D models, suggesting EVs activate processes associated with skin regeneration. This holistic approach demonstrated that EVs previously linked to pro-regenerative behaviors also modulate biomarkers associated with cutaneous aging in full-thickness 3D reconstructed models. This work not only provides mechanistic insights but also paves the way for the development of next-generation regenerative skincare active ingredients.

Successful induction of gonadal somatic cell-like cells (GSCLCs) from mouse embryonic stem cells (mES) is important for studying ovarian somatic cell differentiation, development and their function for oocyte genesis and maturation. This study demonstrates the successful differentiation of GSCLCs from mES in vitro by utilizing novel green-synthesized Fe3O4 nanoparticles (G-Fe3O4-NP).

Atrial fibrillation (AF) is the most common cardiac arrhythmia, linked to greater risk of heart failure, stroke and death. Inflammation has been connected to AF emergence, however mechanisms of inflammation-caused AF remain thus far elusive, leading to a lack of mechanism-based treatments. An isogenic, 3D tissue model containing hiPSC-derived atrial-like cardiomyocytes (aCM), cardiac fibroblasts (cfb), and cardiac macrophages was engineered using custom injection-molded pillar devices. Electrophysiological changes were examined via sharp electrode recordings, calcium imaging, and multi-electrode assays. Gene function was interrogated using siRNA knock-down, lentiviral overexpression, and pharmacological modulation. In silico tissue and whole-heart models validated findings under simulated stress and heterogeneous conditions. Activation of M1 macrophages led to a 50% reduction in contraction amplitude, action potential spike amplitude (aCM+cfb+M1: 61.3 mV ±13.9 vs control: 71.6 mV ±14.5, p < 0.01) and increased beat irregularity (M1: 150.7% ± 388.9 vs control, p < 0.001). Calcium transient amplitude was reduced (12.3 a.u. ± 14.7, p < 0.05) and upstroke velocity slowed. SCN5A knock-down reduced contraction amplitude (-51.9% ± 37.2, p < 0.01) without inducing arrhythmias, whereas combined GJA5 and ATP1A1 knock-down induced significant irregularity (403% ± 371.3, p < 0.001), increased conduction heterogeneity (+18%), and reduced velocity (-52.4%). In silico modeling confirmed that paired 50% downregulation of sodium-potassium pump and tissue conductivity induced AF under tachycardia even without ectopic activity. This work reveals a novel, inflammation-driven mechanism for AF initiation. Combined downregulation of GJA5 (connexin 40) and ATP1A1 (NaK ATPase) disrupted intercellular connectivity and ion flux, establishing a substrate for arrhythmogenesis. These results were robust across in vitro, genetic/pharmacological, and in silico models, defining new avenues for translational intervention.

The meniscus, a critical fibrocartilaginous structure in the knee joint that cushions load and stabilizes movement, suffers from poor self-healing potential following tears. This impaired repair not only fails to restore joint function but often progresses to osteoarthritis, posing significant clinical challenges. Regrettably, current therapeutic approaches, such as surgical suturing or partial resection, have limited efficacy in achieving functional regeneration of the meniscus. To address these bottlenecks, we developed a multifunctional composite hydrogel system integrating methacrylated silk fibroin (SilMA), cerium dioxide (CeO2) nanozymes and tetrahedral framework nucleic acid (tFNA)-miRNA-455. The SilMA hydrogel, leveraging photocrosslinking technology for on-demand solidification, offers injectability (enabling minimally invasive delivery), strong tissue adhesion and robust mechanical support-effectively bridging meniscal tear gaps and creating a scaffold for cell infiltration. Embedded CeO2 nanozymes act as potent reactive oxygen species (ROS) scavengers and nanozyme-mediated ROS clearance mitigates inflammation and fosters a regeneration-conducive microenvironment. Moreover, tFNAs serve as a biocompatible, stable delivery vector for miRNA-455, protecting the nucleic acid from degradation and ensuring its efficient cellular uptake. This targeted delivery drives chondrogenic differentiation of synovial mesenchymal stem cells (SMSCs), directly promoting fibrocartilage formation. This synergistic strategy unites structural reinforcement, immunomodulation and stem cell regulation, overcoming conventional carrier limitations (cytotoxicity and poor stability) and demonstrating significant potential for meniscal repair. Ultimately, it offers a promising solution for cartilage regeneration and meniscus function restoration, with broad implications for clinical translation.

Bone defects represent a significant clinical challenge, frequently resulting in nonunion and impaired function. Although autologous bone grafts are considered the gold standard owing to their excellent biocompatibility, their application is constrained by limited donor availability, thereby driving the need for alternative biomaterials. In this study, we report the synthesis of copper-aluminum layered double hydroxide (CuAl-LDH) nanosheets as a bioactive platform for bone regeneration. The nanosheets were systematically characterized using transmission electron microscopy, energy-dispersive spectroscopy and dynamic light scattering, confirming uniform morphology, precise elemental composition and colloidal stability. To enable localized therapeutic delivery, CuAl-LDH nanosheets were incorporated into gelatin methacryloyl (GelMA) hydrogels to form a nanocomposite hydrogel (Gel-CAL). Mechanical testing demonstrated that tuning the CuAl-LDH concentration (0.01-0.1 wt%) significantly enhanced the compressive modulus of the hydrogel, while rheological analysis revealed rapid light-induced gelation kinetics, making it suitable for minimally invasive, in situ implantation. The nanocomposite exhibited sustained release of Cu2+ ions over 40 days and displayed strong antibacterial activity against Escherichia coli. In vitro studies using rat bone marrow mesenchymal stem cells showed that Gel-CAL effectively reduced intracellular reactive oxygen species levels and upregulated key osteogenic markers, including alkaline phosphatase. In a rat subchondral bone defect model, micro-computed tomography and histological analyses at 5 weeks post-implantation revealed that Gel-CAL induced a significantly higher new bone volume fraction compared to GelMA alone. These results demonstrate that CuAl-LDH nanosheets serve as a multifunctional biomaterial that integrates mechanical reinforcement, antibacterial properties and osteogenic stimulation, offering a promising strategy for bone regeneration.

Two-dimensional (2D) electronic materials are emerging candidates for flexible neural interfaces, yet their biocompatibility remains unclear because most studies use exfoliated flakes or suspensions. Here, we report a systematic in vitro comparison of large-area, electronics-grade, chemical-vapor-deposited graphene, MoS2, PtSe2, and PtTe2, together with flaky MoS2 and thin-film metals, as substrates for mouse neural stem cells. All large-area 2D materials support neural stem cell viability and show live-dead and metabolic readouts comparable to laminin-coated glass. Each material also supports robust neuronal differentiation, with extensive βIII-tubulin expression. Flaky MoS2 uniquely promotes strong neuronal maturation, yielding substantially higher fractions of NeuN-positive neurons, whereas PtSe2 biases differentiation toward glial lineages, including oligodendrocyte- and astrocyte-like cells. These findings establish large-area 2D materials as biocompatible, tunable platforms for neural interfacing and highlight material format as a key design variable for future bioelectronic devices.

Acute myeloid leukemia (AML) is characterized by high relapse and mortality rates. Our previous investigation identified enoyl-CoA hydratase domain-containing protein 3 (ECHDC3) as being of prognostic significance in AML; however, the underlying pathways remain elusive. The intricate crosstalk among genetic abnormalities, metabolic pathways, and protein dysfunctions underpins the complexity contributing to its poor prognosis.

To develop an immunodeficient retinal degenerate (RD) rat model with fluorescent label for studying retinal degeneration and transplant-host connectivity.

remains challenging. To test the hypothesis that SVs from people with congenital heart disease (CHD) disrupt developmental chromatin interactions, we developed CardioAkita, a machine-learning model that predicts how variants alter 3D chromatin structure. Analyzing previously genotyped de novo SVs (dnSVs), we observed a positive association between CHD severity and CardioAkita scores across dozens of families. From whole-genome sequencing of three individuals with CHD we predicted disruptive dnSVs. Induced pluripotent stem cells engineered to harbor these variants confirmed CardioAkita's predictions of 3D chromatin changes, and further revealed aberrant expression of local genes including cardiac developmental genes, suggesting that chromatin reorganization plays a significant mechanistic role in the genetic etiology of CHD. Our findings highlight the potential for models of 3D chromatin organization to predict the pathogenicity and underlying mechanisms of SVs in human disease.

The mechanism(s) driving selective expansion of mutant hematopoietic stem and progenitor cells (HSPC) in clonal hematopoiesis (CH) are incompletely understood. Here, we address the role of metabolism in selection for HSPC with loss of function mutations in TET2 . Loss of Tet2 in murine HSPC triggers overexpression of glycolysis and oxidative phosphorylation genes and increased oxidative metabolism via an enlarged mitochondrial network. However, Tet2 -deficient HSPC maintain a normal redox state. Strikingly, compound loss of the rate-limiting pentose phosphate pathway (PPP) enzyme glucose-6-phosphate dehydrogenase (G6PD) triggers increased reactive oxygen species and impairs the fitness of Tet2 -deficient HSPC. We find that aberrant oxidative metabolism is also a feature of HSPC in human CH and clonal cytopenia of unknown significance (CCUS). Overall, our data point to aberrant metabolism as a critical and conserved driver of selection in TET2 -deficient CH and identify the PPP as a crucial compensatory pathway needed to maintain their selective advantage.

Maintenance of the gas exchange surface throughout life and regeneration of the lung after injury requires tight regulation of epithelial cell fate and function. Alveolar epithelial type 2 (AT2) cells serve as the progenitors of the distal epithelium, differentiating into alveolar epithelial type 1 (AT1) cells or proliferating to maintain the quorum of AT2 cells. Here we describe the role of the chromatin regulator polycomb repressive complex 2 (PRC2) in the maintenance of AT2 cell fate in the adult alveolus. Cross-species single-cell transcriptomic analyses identified PRC2 activation in proliferative AT2 populations. PRC2 loss of function in human iPSC-derived AT2 (iAT2) cells and primary murine AT2 cells in vitro resulted in loss of AT2 cell state and emergence of programs reminiscent of alveolar-basal intermediate (ABI) cell states, while overexpression of the PRC2 enzymatic component EZH2 in human iAT2 cells augmented the AT2 cell program. Genetic loss of PRC2 function in the AT2 lineage in adult mice in vivo led to emphysematous remodeling of the lung and induced a time-dependent series of transitions of AT2 cells through an alveolar-basal intermediate (ABI) state into Krt5+ basal-like cells. Comparison of murine ABI cells to human disease-associated ABI cells demonstrates de-repression of canonical PRC2 targets during transition to ABI and basal-like states in human fibrosis, implicating PRC2 is a conserved regulator of AT2 cell fate. Together, these findings define PRC2 complex function during AT2 cell self-renewal as a critical guardrail for maintaining epithelial cell fate in the adult lung.

The rapid convergence of advanced microscopy and deep learning is transforming cell biology by enabling imaging systems in which optical encoding and computational inference are jointly optimized for volumetric information capture and interpretation. However, broadly accessible three-dimensional imaging at high spatiotemporal resolution remains constrained by volumetric reconstruction throughput, susceptibility to artifacts, and the burden of collecting modality-matched training data. Here, we introduce PAVR, a physics-aware light-field imaging platform that integrates single-shot volumetric acquisition with fast, end-to-end volumetric reconstruction. PAVR is trained entirely using in silico system responses, avoiding reliance on external high-resolution ground-truth modalities and enabling sample-independent reconstruction across diverse biological contexts. Using fixed and live mammalian cells, we demonstrate multicolor volumetric imaging of subcellular organelles, three-dimensional tracking of autofluorescent particles, and high-speed visualization of organelle remodeling and interactions. We further extend PAVR to quantify coupled morphological and functional dynamics in beating human induced pluripotent stem cell-derived cardiomyocytes under pharmacological perturbation. Together, PAVR establishes a scalable hardware-software platform for high-throughput volumetric imaging and quantitative analysis of dynamic cellular systems in both basic and translational settings.

A preeminent goal of virology is to discover cellular genes that mediate virus entry. Genome-wide loss-of-function screens can illuminate single genes necessary for virus entry, but are stymied by genetic redundancy. Here we report a genome-wide CRISPR activation screening strategy to discover single genes that are sufficient for viral entry into normally-uninfectable cells. Sequential rounds of viral infection vastly enhanced screening sensitivity. This sequential screening strategy was generalizable to two unrelated viruses-Ebola and rabies viruses-and could broadly accelerate the discovery of viral entry factors.