Biology subjects

Lu, A.

Publications and source records attributed to Lu, A..

At least 19 recordsLinked to original sources

bioRxiv2026

NanoPro - a Framework for Probiotically-Guided Nanovector Therapy

The 'antigen problem', i.e. the disconnect between the broad spectrum of therapeutic modes enabled by the range of viral and synthetic nanoparticles for which workable receptor-targeting architectures exist and the relative dearth of addressable target receptors on most tumors, is a long-standing challenge in targeted tumor nanotherapy. Here we provide in vitro-proof-of-principle for NanoPro, a platform for guiding nanoscale therapeutics to otherwise antigenically indistinct tumors via probiotically-released tumor cell-binding tags, ProTags. These consist of an orthogonal antigen (GFP or ALFA) fused to the heparin-binding domain of placenta growth factor-2 and serve as attachment receptors for ProTag-targeted nanovectors. ProTag release from Escherichia coli Nissle 1917 was facilitated by deletion of the membrane-tethering lpp gene, which increased ProTag supernatant concentrations 16.5-fold compared to the parental strain without impacting viability. HBD-dependent decoration with ProTag in bacterial supernatant followed by treatment with receptor-targeted aGFP- or aALFA-lentiviral vectors resulted in majority transduction of MC-38 and MDA-MB-468 tumor cell lines with antigen specificities of 96.5% and 98.5%, respectively, depending on the choice of nanobody. This ProTag-mediated interaction was notably robust, with selective transduction still observed at 625-fold supernatant dilution, warranting further exploration of the utility of the NanoPro system for tumor-restricted delivery of nanotherapeutics.

synthetic biology↗

bioRxiv2026

Camus: a video-based framework for continuous behavioral monitoring in the mouse home-cage

Home-cage activity is a window into the spontaneous behavioral repertoire of mice. These behaviors are organized across the circadian cycle, and disruptions in their duration, frequency, or organization may provide sensitive measures of neurological or psychiatric dysfunction. While continuous monitoring can help track the dynamics of spontaneous behavior, video recording in conventional laboratory cages is limited by compact cage geometry, opaque cage tops, and obstructed views of animals, food, and water. We therefore developed Camus, a Camera for home-cage recordings of Mus musculus mice. Camus integrates off-the-shelf USB cameras with infrared illumination and custom 3D-printed components for access to food and water without obstructed views. The modular design pairs continuous video acquisition with a manually validated computer-vision model to quantify locomotion, feeding, drinking, and nesting-related behavior across multiday recordings. A single desktop computer can record as many as 20 cages in parallel at an incremental cost of approximately $250 per cage, recording more than 99% of expected frames at 640x360-pixel resolution and 30 frames per second. Camus captured circadian structure in locomotion, feeding, and drinking. Camus also captured nest-building and sex-specific differences in nest dynamics. Using Camus with transgenic 5xFAD mice overexpressing amyloid revealed selective, age-progressive deficits in nesting behavior. Camus provides a scalable, open-source platform that combines accessible hardware, automated video monitoring, and machine-learning based analysis for continuous and potentially longitudinal behavioral phenotyping.

animal behavior and cognition↗

bioRxiv2026

Shifts in the Maternal Gut Microbiome Across Pregnancy are Associated with Energetic Status in Phayre's Leaf Monkeys

During pregnancy, mothers experience physiological changes that support fetal development, including shifts in energy utilization and increasing insulin resistance during late gestation. While these changes benefit the fetus, they can also impose energetic costs that affect the mother's physical condition and metabolic phenotype. Previous studies suggest that the gut microbiome, a key regulator of female metabolism and energy harvest, may play a critical role in mediating these physiological challenges. In this study, metagenomic sequencing of the gut microbiome of 120 samples revealed dramatic shifts in gut bacterial composition and function associated with pregnancy and lactation in 14 wild Phayre's leaf monkeys, Trachypithecus phayrei crepusculus, from two groups at the Phu Khieo Wildlife Sanctuary, Thailand. Alpha diversity, beta diversity, and taxonomic composition all differed between cycling and the 3rd trimester. Furthermore, bacterial dissimilarity between these states was negatively correlated with postpartum physical condition; that is, mothers whose gut microbiota remained more stable during pregnancy recovered sooner after giving birth. Functional profiling revealed a depletion of pathways involved in purine salvage and glutamate degradation during the 3rd trimester. Overall, our study demonstrates that the gut microbiome undergoes substantial changes during pregnancy, and the stability of these microbial communities predicts postpartum maternal health and potentially influence lifetime reproductive output.

zoology↗

bioRxiv2026

Social and reproductive benefits of group fission in wild geladas

Living in large, crowded groups can result in fitness costs due to increased competition and conflict. When dispersing from large groups isn't possible, fissioning into two or more smaller 'daughter' groups may provide an important mechanism for mitigating these costs. Here, we leveraged 15 years of behavioral and demographic data to identify both (i) the social factors that predict group membership decisions and (ii) the adaptive consequences of group fission in the gelada (Theropithecus gelada), a grass-eating primate in which the risk of male infanticide -- the largest fitness cost to females -- is highest in larger groups. After fissioning, females tended to join the same daughter groups as their close kin, closely ranked females, and other strong grooming partners, both female and male. However, females did not join the likely fathers of their dependent infants, even though doing so is expected to prevent infanticide. Group fissions were not preceded by increases in female-female aggression or salient changes in activity budgets but were preceded by increases in infant mortality. In particular, infanticide was elevated prior to fission and plummeted after groups split. Taken together, these data illustrate how animals navigate competing social priorities and highlight the role of fission in ameliorating the costs of group-living.

animal behavior and cognition↗

bioRxiv2026

Transplanted hearts assimilate the recipient's biological age

Background. Despite the growing demand for transplantation, a shortage of donor organs persists, limiting access to this lifesaving procedure. To meet the increasing demand, organs are frequently transplanted across an age discrepancy between donor and recipients. Methods. We delineated biological age dynamics in heterochronic heart transplants performed in both mice and patients. We carried out multiomic profiling and applied advanced biomarkers of aging to understand the interactions between the transplanted organ and the host. Results. We show that the biological age of experimental heart transplants rapidly assimilates the age of recipients. Interestingly, this effect was limited to the grafted tissue without reciprocal effects on systemic biological age of the recipient. These effects were confirmed at the level of DNA methylation and gene expression. Extending our findings clinically using both omics and functional analyses, we show that the biological age of heterochronically transplanted hearts is strongly associated with the age of the recipient, rather than the donor, confirming the clinical relevance of our experimental findings. Conclusions. These data identify the systemic environment as a driving force on tissue biological age. The rejuvenation of older organs in young recipients suggests novel approaches to organ allocation that may expand the pool of transplantable organs.

systems biology↗

bioRxiv2026

Myeloid IRF5 is required for TLR7-driven inflammatory hemophagocyte differentiation and Macrophage Activation Syndrome

In TLR7-driven macrophage activation syndrome (MAS), inflammatory hemophagocytes (iHPCs) differentiate from Ly6CHI monocytes, phagocytose red blood cells and promote disease, including anemia and thrombocytopenia. We demonstrate here that IRF5 is required for iHPC differentiation and MAS in TLR7-overexpressing (TLR7.1) mice. Both constitutive and myeloid-specific Irf5 deletion reduced iHPCs and improved anemia, thrombocytopenia and survival. Furthermore, therapeutic inhibition of IRF5 ameliorated MAS features and reduced splenic and circulating iHPCs. While cell-intrinsic IRF5 expression was required for iHPC differentiation, it was not required for TLR7.1 Ly6CHI monocyte differentiation and monocyte transcriptional programs. We further show that the transcriptome and chromatin landscape changed dramatically as iHPCs differentiated from TLR7.1 Ly6CHI monocytes. Many transcriptional programs gained in iHPCs were enriched in genes associated with IRF5-binding accessible chromatin regions, including those associated with NF-kB signaling, cytokine and chemokine production, and complement activation. Our data suggest that IRF5 collaborates with other transcription factor families, including NF-kB, ETS and AP1 members, to regulate iHPC gene programs. Together, our findings demonstrate that expression of IRF5 in myeloid cells is critical for MAS, for iHPC differentiation, and acts broadly across iHPC-specific gene programs in TLR7-driven inflammation.

immunology↗

bioRxiv2026

Behavioral and Functional Profiling of Acomys cahirinus Fibroblasts Reveals Enhanced Matrix Remodeling Capacity

The African spiny mouse (Acomys cahirinus) exhibits a unique capacity among mammals for scarless tissue regeneration, making it a compelling model for investigating the cellular mechanisms underlying regenerative healing. To determine how cellular heterogeneity and specific phenotypes influence fibroblast behavior, we established an immortalized Acomys fibroblast line along with a CRISPR/Cas9-mediated Col3A1 knockout variant and a DNA damage-induced senescent population. Compared with Mus musculus, NIH 3T3 fibroblasts, Acomys cells displayed distinct morphology, similar migration speeds, reduced directional persistence, and greater biophysical heterogeneity. While previous studies have linked regenerative wound healing to the elevated expression of collagen type III (Col3A1), CRISPR-mediated knockout of Col3A1 in Acomys fibroblasts yielded comparable biophysical profiles to wild-type cells in 2D culture. To examine additional contributors to the enhanced wound-like matrix environment, we established a senescence model in which Acomys fibroblasts exhibited elevated resistance to DNA-damaging agents, complete loss of proliferation, and altered single-cell morphology. In 3D collagen gel contraction assays, Col3A1 knockout attenuated matrix remodeling capacity, whereas the introduction of a small fraction of senescent cells enhanced gel contraction and remodeling dynamics, suggesting that senescent fibroblasts can modulate collective matrix behaviors. Together, these findings demonstrate that both Col3A1 expression and senescence-associated cell states contribute to fibroblast-driven matrix remodeling, highlighting Acomys fibroblasts as a valuable model for investigating how cellular heterogeneity and senescence-associated cell phenotypes could influence regenerative wound healing.

bioengineering↗

bioRxiv2026

Structural Connectivity Between the Zinc Linchpin Motif, the cluster, and the active site orchestrates DNA repair in MUTYH

The DNA glycosylase MUTYH protects genomic integrity by excising adenine mispaired with 8-oxoguanine (OG), which initiates base excision repair (BER). The [4Fe-4S] cluster DNA binding domain and Zn linchpin motif of MUTYH are hotspots for inherited cancer associated variants (CAVs) highlighting their critical functions in DNA repair. Here, we present three full-length human MUTYH crystal structures bound to DNA across three catalytic states, representing early and late transition states and product complexes. These structures reveal a previously unrecognized interplay between the Zn site and the Fe-S cluster mediated by His85 and a conserved Arg247/Arg307 bridge spanning [~]15 [A]. Disruption of this network impairs metal loading, reduces the active enzyme fraction, weakens lesion DNA binding, and diminishes OG:A repair in cells. Moreover, the Zn site adopts distinct coordination modes across the reaction coordinate, with a water molecule replacing a cysteine ligand in transition state analog complexes and cysteine coordination restored in a product-mimicked state. Functional analyses show that this ligand switching is dispensable for core glycosylase chemistry in vitro but disproportionately affects repair in cells, suggesting an additional role of the Zn linchpin in cellular OG:A repair beyond intrinsic glycosylase activity, likely involving interactions with BER partners. Together, these findings illustrate how the Zn linchpin enhances Fe-S cluster domain DNA substrate engagement to enable effective DNA repair and provides a rationale for how these functions are compromised by MUTYH CAVs.

biochemistry↗

bioRxiv2026

Type I Interferon-Driven Monocyte Dysregulation and MAS-associated CD8+ T cells During Macrophage Activation Syndrome

Macrophage activation syndrome (MAS) is driven by a hyperinflammatory response characterized by aberrant activation of lymphocytes and phagocytes. While monocytes and macrophages are thought to be important in MAS pathogenesis, their role remains poorly understood. We used bulk and single-cell RNA sequencing (RNA-Seq) on sorted monocytes from children with MAS and healthy controls to identify transcriptional changes during MAS. We defined a MAS signature in classical monocytes that correlated with ferritin and was elevated in monocytes from systemic lupus erythematosus and COVID-19 patients. We also identified a subset of classical monocytes with high levels of interferon-stimulated genes (ISGs) that expanded during MAS. Surprisingly, the transcriptional signature of these cells was driven by type I IFNs, rather than IFN{gamma}. Consistent with this finding, we detected increased levels of circulating IFN{beta} during MAS, suggesting that IFN{beta} plays an unrecognized role in driving MAS monocyte responses. We also identified a MAS-associated CD8+ T cell population with a distinctive transcriptional signature. We used cell-cell communication algorithms to predict increased immunoregulatory interactions between monocytes and T cells during MAS. Together, these results provide new evidence for a role for type I IFN during MAS and identify a unique CD8+ T cell population that may contribute to MAS pathophysiology.

immunology↗

bioRxiv2025

Maternal glucocorticoids and behavior shape offspring developmental trade-offs in wild baboons

Mammalian mothers provide behavioral and physiological signals that offspring use to calibrate development in relation to maternal resources and environmental cues. Infants respond selectively as they prioritize certain developmental systems over others, creating developmental tradeoffs between competing biological systems. Here, we investigate the influence of maternal capital ("investment capacity") on the growth and development of their infants in wild olive baboons (Papio anubis) from Laikipia, Kenya. We posit that maternal capital is influenced by a mothers own early life experiences (e.g., drought, maternal loss) and her current life experiences (e.g., dominance rank, food availability), and is signaled to offspring via maternal effort (i.e., nursing and carrying time) and glucocorticoids. We used behavioral data on 40 infants (43% female) in the first year of life to quantify maternal effort, infant play, and infant independence (i.e., frequency of infant departures from mother). We matched these behavioral data with maternal fecal glucocorticoid measures from lactating mothers, and infant growth measures assessed via photogrammetry. Signals of low maternal capital predicted lower rates of infant play, less behavioral independence, and slower growth. There was a negative relationship between the rate of social contact play and growth rate, indicating a developmental tradeoff. Males were more sensitive than females to some of the maternal signals measured in our study. These results add to a growing body of evidence demonstrating that maternal behavioral and physiological signals shape infant development.

animal behavior and cognition↗

bioRxiv2025

De novo design of phospho-tyrosine peptide binders

Phosphorylation on tyrosine is a key step in many signaling pathways. Despite recent progress in de novo design of protein binders, there are no current methods for designing binders that recognize phosphorylated proteins and peptides; this is a challenging problem as phosphate groups are highly charged, and phosphorylation often occurs within unstructured regions. Here we introduce RoseTTAFold Diffusion 2 for Molecular Interfaces (RFD2-MI), a deep generative framework for the design of binders for protein, ligand, and covalently modified protein targets. We demonstrate the power and versatility of this method by designing binders for four critical phosphotyrosine sites on three clinically relevant targets: Cluster of Differentiation 3 (CD3{varepsilon}), Epidermal Growth Factor Receptor (EGFR), Insulin Receptor (INSR) and Signal Transducer and Activator of Transcription 5 (STAT5). Experimental characterization shows that the designs bind their phosphotyrosine containing targets with affinities comparable to native binding sites and have negligible binding to non-phosphorylated targets or phosphopeptides with different sequences. X-ray crystal structures of generated binders to CD3{varepsilon} and EGFR are very close to the design models, demonstrating the accuracy of the design approach. A designed binder to an EGFR intracellular region phosphorylated upon EGF activation co-localizes with the receptor following EGF stimulation in single-particle tracking (SPT) experiments, demonstrating pY specific recognition in living cells. RFD2-MI provides a generalizable all-atom diffusion framework for probing and modulating phosphorylation-dependent signaling, and more generally, for developing research tools and targeted therapeutics against post-translationally modified proteins.

bioengineering↗

bioRxiv2025

Peptide-based ligand antagonists block a Vibrio cholerae adhesin

Vibrio cholerae, the causative agent of cholera, uses surface proteins such as the repeats-in-toxin (RTX) adhesin FrhA to colonize hosts and initiate infection. Blocking bacterial adhesion represents a promising therapeutic strategy to treat infections without promoting drug resistance. FrhA contains a peptide-binding domain (PBD) that is key for hemagglutination, human epithelial cell binding, and V. cholerae biofilm formation. Previous studies identified a lead pentapeptide ligand with the sequence Ala-Gly-Tyr-Thr-Asp (AGYTD) that blocks V. cholerae colonization of the mouse small intestine at high micromolar concentrations. A structure-guided approach has now identified a minimal D-amino acid-containing tripeptide motif with higher affinity for the FrhA-PBD and predicted metabolic stability. Our results contribute to the development of anti-adhesion strategies to combat infections.

microbiology↗

bioRxiv2025

Development of LYTACs via incorporating a nucleolin-targeting and lysosome-directed aptamer

Lysosomal targeting chimeras (LYTACs) represent an emerging class of bifunctional molecules that bridge extracellular target proteins with intrinsic lysosome-targeting receptors (LTRs) on the cell surface, facilitating endocytic internalization and subsequent lysosomal degradation of the targets. However, the therapeutic potential of LYTACs has been limited by the scarcity of suitable intrinsic LTRs. We previously identified an aptamer, SAPT8, that selectively targets nucleolin, a shuttling protein overexpressed on the surface of pathogenic FLSs in rheumatoid arthritis (RA), and induced its lysosomal degradation. In this study, we repurposed SAPT8 as a tumor-targeting and lysosome-directed ligand, leveraging the elevated expression of NCL on tumor cell surfaces. By conjugating SAPT8 with either the c-Met-binding aptamer SL1 or the small molecule inhibitor Tepotinib, we engineered novel LYTACs that demonstrated potent tumor-targeting capability and induced concurrent degradation of both c-Met and NCL, leading to significant antitumor effects. Furthermore, fusion of SAPT8 with VEGFR-2-targeting aptamer Apt02 generated LYTACs that simultaneously degraded VEGFR-2 and NCL, effectively suppressing RA-FLS activity. These results establish SAPT8 as a versatile platform for developing next-generation LYTACs, overcoming current limitations in extracellular protein degradation by circumventing dependence on endogenous LTRs. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=69 SRC="FIGDIR/small/672993v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@975b74org.highwire.dtl.DTLVardef@f55565org.highwire.dtl.DTLVardef@b9639corg.highwire.dtl.DTLVardef@13aaba7_HPS_FORMAT_FIGEXP M_FIG C_FIG

pathology↗

bioRxiv2025

Human progenitor T-cell differentiation regulated by the mechanical resistance of thymus-mimetic extracellular matrices

Therapeutic T-cell engineering ex vivo from human hematopoietic stem cells (HSCs) focuses on recapitulating notch1-signaling and 4{beta}1-integrin-mediated adhesion within the thymic niche with supportive stromal cell feeder-layers or surface-immobilized recombinant protein-based engineered thymic niches (ETNs). The relevant Notch1-DLL-4 and 4{beta}1-integrin-VCAM-1 interactions are known to respond to mechanical forces that regulate their bond dissociation behaviors and downstream signal transduction, yet manipulating the mechanosensitive features of these key receptor-ligand interactions in thymopoiesis has been largely ignored in current ETN designs. Here, we demonstrate that human T-cell development from cord blood-derived CD34+ HSCs is regulated via molecular cooperativity in notch1 and integrin-mediated mechanotransduction. Mechanically confining interpenetrating network (IPN) hydrogel-based 3D cell culture comprised of collagen type I and alginate polysaccharides functionalized with DLL-4 and VCAM-1 is used as a model viscoelastic 3D ETN to manipulate human progenitor (pro)T-cell differentiation. This ETN enables orthogonal control of the mechanical and biomolecular features of the thymic niche, including thymopoietic ligand density, modulus, and viscoelastic properties (e.g., stress relaxation kinetics). We identify that soft, viscous matrices that enhance activation of the notch1-pathway, and subsequently notch1 intracellular domain (NICD) nuclear import sustain the T-cell development gene regulatory network during proT-cell differentiation. Conversely, stiff, elastic matrices inhibit HSC commitment to the T-lineage, and rather promotes Myeloid-cell differentiation. Our observations indicate mechanical reciprocity in signaling pathways indispensable to thymopoiesis, and highlights extracellular matrix mechanics as a variable in controlling hematopoietic stem cell fate decisions.

bioengineering↗

bioRxiv2025

Disparate social structures are underpinned by distinct social rules across a primate radiation

Over six decades of research on wild baboons and their close relatives (collectively, the African papionins) have uncovered substantial variation in their behavior and social systems. While most papionins form discrete social groups (single-level societies), a few others form small social units that are nested within larger supergroups (multi-level societies). These two systems are generally thought to be qualitatively distinct, but data from wild populations increasingly suggest that there may be areas of overlap. To quantify this potential gradient in social structure, a more systematic, comparative analysis is needed. Here, we constructed a database of behavioral and demographic records spanning 135 group-years, 28 social groups, 13 long-term field studies, and 11 species to quantify variation in grooming network structure, and identify the individual and dyadic properties (e.g., kinship and social status effects) that underlie this variation. Consistent with accumulating observations in the field, the single-level species could be divided into two categories: cohesive and cliquish. Cohesive single-level networks were dense, kin-biased, and moderately rank-structured, while cliquish single-level networks were more differentiated, slightly more kin-biased, and strongly rank-structured. As expected, multi-level networks were very modular and shaped by females ties to specific dominant males but varied in their kin biases. Taken together, these data suggest that (i) kin and rank biases are widespread but vary in their strength; (ii) male-centered subgroups are exclusive to multi-level systems; and (iii) increases in network modularity can emerge in response to heightened nepotism and male-centered clustering. SIGNIFICANCE STATEMENTWhat forces explain variation in primate societies? While kinship and dominance shape the social lives of many of our close relatives, it is unclear how their effects differ across species. Using a new database comprising decades of field research, we found that baboons and their close relatives fell into three general patterns: one in which groups were cohesive, kin-biased, and moderately rank-biased, another in which groups were more cliquish and nepotistic, and a third in which groups were divided into clusters centered on dominant males. Distinct primate societies may thus reflect differences in the strength of females nepotistic biases and the degree of males social influence.

animal behavior and cognition↗

bioRxiv2025

Targeting nucleolin facilitates the development of blood-tumor barrier-penetrating and glioblastoma-specific PROTACs

Targeted therapy for glioblastoma (GBM) is challenged by the blood-tumor barrier (BTB). Extracellular vesicles (EVs) from GBM cells play a role in transforming BBB into BTB, although the mechanisms are not fully understood. This study identifies nucleolin (NCL), a nucleomembrane shuttling protein, as being transferred from GBM cells to the surface of brain capillary endothelial cells, facilitating BTB formation. The aptamer AS1411, which targets NCL, is shown to cross the BTB via receptor-mediated transcytosis (RMT) and selectively recognize GBM cells in an NCL-dependent manner. Beyond its targeting capabilities, AS1411 has been repurposed to recruit the E3 ligase MDM2 in PROTACs, leveraging the intracellular interaction of NCL with MDM2. Utilizing AS1411s multifunctionality in BTB penetration, GBM cell targeting, and MDM2 recruitment, we conjugated AS1411 to VEGFR2 or EGFR ligands to create PROTAC degraders. These constructs induce NCL- and MDM2-dependent ubiquitination and degradation of VEGFR2 or EGFR, demonstrating significant anti-GBM efficacy both in vitro and in vivo, with no toxicity to normal cells. Overall, NCL from GBM-derived EVs emerges as a crucial mediator of BTB formation and serves as a receptor for AS1411-mediated RMT, paving the way for developing PROTACs that effectively traverse BTB and target GBM. GRAPHICAL ABSTRACTS O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=139 SRC="FIGDIR/small/666084v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@79778org.highwire.dtl.DTLVardef@6984d8org.highwire.dtl.DTLVardef@1909eddorg.highwire.dtl.DTLVardef@1adf342_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Arabidopsis REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA Polymerase IV transcription complexes.

DNA methylation plays crucial roles in gene regulation and transposon silencing. In plants, the maintenance of DNA methylation is controlled by several self-reinforcing loops involving histone methylation and non-coding RNAs. However, how methylation is initially patterned at specific loci is unknown. Here, we describe four Arabidopsis REM transcription factors, VDD, VAL, REM12 and REM13, that recognize specific sequence regions, and together with the protein GENETICS DETERMINES EPIGENETICS1 (GDE1), recruit RNA polymerase IV transcription complexes to generate 24-nucleotide small interfering RNAs (24nt-siRNAs) that guide DNA methylation to specific loci. In the absence of GDE1, Pol IV transcription complexes redistribute to sites bound by a different factor called REM8. These results suggest that REM proteins act as sequence specific DNA binding proteins that pattern siRNAs and methylation at specific sites in the genome, highlighting the role of genetic information in determining epigenetic patterns.

plant biology↗

bioRxiv2025

Biomaterial-based 3D human lung models replicate pathological characteristics of early pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive and incurable lung disease characterized by tissue scarring that disrupts gas exchange. Epithelial cell dysfunction, fibroblast activation, and excessive extracellular matrix deposition drive this pathology that ultimately leads to respiratory failure. Mechanistic studies have shown that repeated injury to alveolar epithelial cells initiates an aberrant wound-healing response in surrounding fibroblasts through secretion of mediators like transforming growth factor-{beta}, yet the precise biological pathways contributing to disease progression are not fully understood. To better study these interactions there is a critical need for lung models that replicate the cellular heterogeneity, geometry, and biomechanics of the distal lung microenvironment. In this study, induced pluripotent stem cell-derived alveolar epithelial type II (iATII) cells and human pulmonary fibroblasts were arranged to replicate human lung micro-architecture and embedded in soft or stiff poly(ethylene glycol) norbornene (PEG-NB) hydrogels that recapitulated the mechanical properties of healthy and fibrotic lung tissue, respectively. The co-cultured cells were then exposed to pro-fibrotic biochemical cues, including inflammatory cytokines and growth factors. iATIIs and fibroblasts exhibited differentiation pathways and gene expression patterns consistent with trends observed during IPF progression in vivo. A design of experiments statistical analysis identified stiff hydrogels combined with pro-fibrotic biochemical cue exposure as the most effective condition for modeling fibrosis in vitro. Finally, treatment with Nintedanib, one of only two Food and Drug Administration (FDA)-approved drugs for IPF, was assessed. Treatment reduced fibroblast activation, as indicated by downregulation of key activation genes, and upregulated several epithelial genes. These findings demonstrate that human 3D co-culture models hold tremendous potential for advancing our understanding of IPF and identifying novel therapeutic targets. Statement of significanceThis study leverages advanced biomaterials and biofabrication techniques to engineer physiologically relevant, patient-specific, and sex-matched models of pulmonary fibrosis, addressing the critical need for pre-clinical therapeutic drug screening platforms. These human 3D lung models successfully replicated key features of fibrotic lung tissue. Tuning microenvironmental stiffness of 3D PEG-NB hydrogels to match fibrotic lung values and exposing human iATII cells and fibroblasts to pro-inflammatory biochemical cues recreated hallmark characteristics of in vivo fibrosis pathogenesis, including epithelial differentiation and loss, as well as fibroblast activation. The utility of these models was further validated by demonstrating responsiveness to Nintedanib, a clinically available treatment for IPF. These findings highlight the transformative potential of well-defined biomaterial-based 3D models for elucidating complex disease mechanisms and accelerating therapeutic drug discovery for chronic pulmonary diseases like idiopathic pulmonary fibrosis. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=176 SRC="FIGDIR/small/637970v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@bd8ed0org.highwire.dtl.DTLVardef@eb3489org.highwire.dtl.DTLVardef@1c64d6aorg.highwire.dtl.DTLVardef@49f60_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗