Biology subjects

Newton, M. D.

Publications and source records attributed to Newton, M. D..

13 recordsLinked to original sources

bioRxiv2026

PIEZO1 mediates mechanosensing and myofibroblastic activation of synovial fibroblasts in post-traumatic osteoarthritis

Fibrosis and inflammation of the synovium are common pathological features of joint diseases. In osteoarthritis (OA), extensive evidence supports that synovial pathology drives symptoms and disease progression, yet the mechanisms underpinning pathological synovial remodeling, including fibrosis, remain unclear. Here, we identify the mechanosensitive ion channel PIEZO1 as a critical regulator of myofibroblast-like activation of synovial fibroblasts (SFs) in post-traumatic osteoarthritis (PTOA). Using multi-omic assessments in human and murine synovium, a murine model of joint injury, histopathology, and functional in vitro phenotyping, we demonstrate that joint injury triggers expansion of myofibroblast-like SFs concurrent with fibrotic remodeling and mechanical stiffening of the synovium. Myofibroblastic commitment of synovial progenitors was associated with activation of the YAP1 regulon, and PIEZO1 agonism drove nuclear accumulation of YAP1 in SFs. PIEZO1 was enriched in synovia of injured joints, and in cultured SFs pharmacologic PIEZO1 activation promoted SMA enrichment and increased matrix contraction, which were both ablated by YAP1 inhibition. PIEZO1 silencing abrogated TGF-{beta}-induced contractility and markedly altered the transcriptomic response to mechanical loading in vitro, including ECM production and neuroinflammatory programs. In vivo, acute intra-articular pharmacologic PIEZO1 activation induced a pro-fibrotic, pro-inflammatory, and anti-adipogenic transcriptomic program in synovium. Collectively, these findings establish PIEZO1 as a key mediator of the pathogenic activation of SFs and identify aberrant mechanosensing as a mechanism underlying synovial fibrosis in PTOA.

cell biology↗

bioRxiv2026

TRF2 mediates force-resistant bridging of distal telomeric DNA repeats

Shelterin binds telomeres, regulates telomere length, and protects chromosome ends from mis-repair, which is essential for genome stability. Telomere end-protection uniquely depends on the TRF2 subunit, which assembles telomeric DNA into a protective T-loop structure in vivo, yet the biochemical mechanism underlying this process remains unresolved. Using single-molecule optical tweezers and atomic force microscopy, we show that the human shelterin complex tethers distal telomeric DNA repeats, looping the intervening DNA. These bridges withstand tens of piconewtons of applied load, rupture at a force that scales with telomeric repeat number and re-form on relaxation. Structure-function analysis demonstrates that this force-resistant tethering is TRF2-dependent under our conditions and depends on multiple interfaces, with the TRFH domain making a major but non-exclusive contribution: introducing the TRF2 TRFH domain into TRF1 is sufficient to confer tethering, whereas its deletion from TRF2 reduces but does not abolish activity. We propose telomeric dsDNA tethering by TRF2 as a candidate first step in T-loop formation, preceding invasion of the telomeric 3' ssDNA overhang.

biophysics↗

bioRxiv2026

Conserved Fibroblast Subsets Drive Shared Fibrotic Mechanisms in Osteoarthritis Synovium and Systemic Sclerosis Skin

Osteoarthritis (OA) and systemic sclerosis (SSc) are diseases with distinct etiologies but similar disease phenotypes, most prominently fibrosis, a process governed by the pathological activation of fibroblasts. Mechanisms underpinning fibrosis in these diseases are widely studied, though have yet to be directly compared. We employed single-cell RNA-seq and high-resolution spatial transcriptomics to describe the functional plasticity and the range of fibroblast activation states in both diseases. We identified disease-enriched fibroblast subsets conserved in both diseases, including fibrogenic myofibroblast-like cells, chemokine- and cytokine-expressing inflammatory fibroblasts, and lining-like fibroblasts. These subsets exhibited convergent fibrotic programs also observed in idiopathic pulmonary fibrosis, as well as overlapping osteochondral transcriptional programs. Xenium 5K spatial transcriptomics revealed that conserved, disease-associated fibroblasts reside in highly similar anatomic niches in OA synovium and SSc skin. These consisted of a fibrotic ECM-rich niche harboring myofibroblast-like cells and an inflammatory niche containing inflammatory fibroblasts adjacent to infiltrating immune cells. Disease-associated transcriptional remodeling converged on shared functional pathways and common putative upstream molecular regulators. These findings identify conserved cellular states, spatial niches, and regulatory programs across OA and SSc, suggesting that fibrotic disease is underpinned by shared pathogenic stromal states and candidate targets for therapeutic strategies are applicable across both diseases.

cell biology↗

bioRxiv2026

Thrombospondin-2 deficiency primes the synovial joint for aberrant tissue remodeling and injury response

ObjectiveThis study investigates joint injury-induced angiogenesis and the effects of genetic deficiency of thrombospondin-2 (TSP2), an anti-angiogenic factor, in joint homeostasis and post-traumatic osteoarthritis (PTOA). MethodWe utilized a murine non-invasive anterior cruciate ligament rupture (ACLR) model of PTOA and mined published synovial transcriptomics datasets to investigate injury-induced synovial angiogenesis. Spatial transcriptomics and flow cytometry of TSP2-GFP reporter mice were used to assess injury-induced thrombospondin-2 and its cellular origins in synovium. Global TSP2 knockout mice (TSP2-KO) were used to assess the effect of TSP2 deficiency on early and late stages of PTOA development via molecular imaging of inflammation and angiogenesis, histopathology, micro-computed tomography, Raman spectroscopy, and synovium bulk RNA-sequencing. ResultsIntra-articular angiogenesis peaked at 7d post-ACLR and declined but remained elevated above baseline at 28d post-ACLR. We identified synovial crosstalk between endothelial cells and sublining fibroblasts as a key driver of angiogenesis and source of thrombospondin-2 signaling, with TSP2 primarily upregulated in sublining fibroblasts. TSP2-KO mice exhibited increased peri-articular inflammation at 7d post-ACLR and inferior bone quality. Histopathology revealed greater PTOA severity but paradoxically lower synovitis in TSP2-KOs. Additionally, aberrant structural remodeling of the entire knee joint was observed in uninjured and ACLR TSP2-KO limbs. The uninjured TSP2-KO synovial transcriptome demonstrated elevated immune, fibrotic, and angiogenic activation; however, TSP2-KO and WT synovial transcriptomes partially converged upon injury. ConclusionTSP2 is essential for joint homeostasis and trauma response. Global TSP2 deficiency causes premature OA and worsened PTOA, suggesting that therapeutic targeting with TSP2 mimetic could be used to prevent OA.

physiology↗

bioRxiv2026

Wnt/β-catenin signaling regulates fibrotic atrophy of intra-articular adipose tissue in post-traumatic osteoarthritis

Synovial joints like the knee are home to adipose tissue depots whose anatomy and functions are closely intertwined with that of other intra-articular soft tissues such as synovium, underscoring the growing understanding that joints are multi-tissue organs. Traumatic joint injury and the onset of osteoarthritis (OA) dramatically remodel the intra-articular adipose niche, marked by infiltration of fibrotic tissue postulated to underpin OA-associated joint stiffness and pain, yet we know very little about the disease-associated dynamics of joint adipose remodeling nor the mechanisms driving these phenomena. Here, we employed 2D histomorphometry and spatial transcriptomics, alongside 3D osmium tetroxide-enhanced micro-computed tomography to comprehensively define the spatiotemporal, structural, and transcriptional rewiring of joint adipose tissue in a non-invasive mouse model of post-traumatic osteoarthritis (PTOA). These revealed marked loss of intra-articular adiposity accompanied by expansion of fibroblast-rich, collagen-dense tissue with pro-fibrotic hallmarks and Wnt/{beta}-catenin-enriched gene programs. Joint adipose exhibited a distinct transcriptional signature compared to subcutaneous white adipose tissue, pointing to unique, depot-specific functions. Stromal cells isolated from PTOA joints had heightened baseline expression of fibrotic and Wnt pathway genes and exhibited impaired de novo adipogenesis, in contrast to cells derived from healthy joints. In accordance with the destabilized biomechanics of PTOA joints, in vitro modeling demonstrated that prolonged, injurious loading and perturbed Wnt/{beta}-catenin signaling were convergent anti-adipogenic cues that suppressed lipid droplet formation and adipogenic gene induction, while promoting markers of fibrosis in joint-derived stromal cells. Complementary gain-of-function studies using ex vivo joint adipose explants and in vivo joint injections demonstrated that chronic Wnt/{beta}-catenin activation, as seen in OA joints, is sufficient to diminish the intra-articular adipogenic program and shift adipose to a more fibrotic phenotype, independent of joint injury. Collectively, these findings establish a multi-modal framework for quantifying joint adipose atrophy and implicate aberrant Wnt/{beta}-catenin signaling and pathological mechanical loading as key factors impairing de novo adipogenesis and driving fibrotic remodeling of intra-articular adipose tissue in PTOA.

cell biology↗

bioRxiv2025

Spatial transcriptomic profiling of decalcified murine musculoskeletal samples via Xenium Prime 5K

Successful generation of high-quality spatial transcriptomics data from murine musculoskeletal tissues has been impeded by the challenge of preserving RNA integrity through the harsh tissue processing steps required for histological sectioning. In particular, the need to thoroughly fix and decalcify mineralized tissues has proven problematic. We detail a comprehensive sample processing pipeline for three common murine musculoskeletal tissue samples, enabling high-quality transcript detection via imaging-based spatial transcriptomics using the Xenium Prime 5K platform from 10x Genomics. Our protocol outlines methodological details for transcardiac perfusion, fixation, decalcification, paraffin processing, and a sample co-embedding strategy facilitating anatomically consistent and simultaneous sectioning of multiple samples onto the spatial transcriptomics slide. Rigorous quality control demonstrates high-quality tissue-specific outcomes across intact knee joints, tibiae, and lumbar spines from adult mice. Our pipeline enabled 70-91% high-quality transcripts across synovium, meniscus, patellar tendon, articular cartilage, subchondral bone, cortical bone, bone marrow, muscle, fracture callus, and dorsal root ganglion tissues. The average number of detected transcripts varied markedly between tissue types - soft tissues such as synovium, patellar tendon, muscle, bone marrow, and callus exhibited ~200 - 400 transcript per cell; mineralized tissues such as subchondral bone, meniscus, and cortical bone exhibited ~ 13 - 150 transcripts per cell; highly active neuronal tissues such as dorsal root ganglion neurons yielded 750 - 1100 transcripts per cell. Canonical cell markers within each tissue confirmed successful identification and representation of key cell types. Through rigorous sample quality assessment at multiple stages of processing, this protocol yields high-quality RNA transcript detection while preserving critical anatomical context and will serve as a valuable tool enabling spatial transcriptomic profiling of intact musculoskeletal tissue samples. Lay summarySpatial transcriptomics is a powerful scientific tool that characterizes genetic coding material ("transcripts") of specific cell types in their native anatomical context. However, successfully applying this tool to musculoskeletal tissues has been challenging because preserving transcript integrity in these tissues requires additional care. The authors of this publication developed a specialized method for preparing tissue samples from mice that works with the spatial transcriptomics platform, 10x Genomics Xenium Prime 5K. This protocol improves sample quality while preserving high-quality genetic information in various mouse musculoskeletal tissues, making it easier to explore their functions. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=168 SRC="FIGDIR/small/693132v1_ufig1.gif" ALT="Figure 1"> View larger version (87K): org.highwire.dtl.DTLVardef@4c4389org.highwire.dtl.DTLVardef@e607bcorg.highwire.dtl.DTLVardef@5f957org.highwire.dtl.DTLVardef@34ce27_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

bioRxiv2025

Binding Kinetics Oppositely Regulates type II Topoisomerase Relaxation and Decatenation Activities

Type II Topoisomerases (topo II) are critical to simplify genome topology during transcription and replication. They identify topological problems and resolve them by passing a double-stranded DNA segment through a transient break in another segment. The precise mechanisms underpinning topo IIs ability to maintain a topologically simple genome are not fully understood. Here, we investigate how binding kinetics affects the resolution of two distinct forms of topological entanglement: decatenation and torsional relaxation. First, by single-molecule measurements, we quantify how monovalent cation concentration affects the dissociation rate of topo II from DNA. Second, we discover that increasing dissociation rates accelerate decatenation while slowing down relaxation catalytic activities. Finally, by using molecular dynamics simulations, we uncover that this opposite behaviour is due to a trade-off between search of target through facilitated diffusion and processivity of the enzyme in catenated versus super-coiled DNA. Thus, our findings reveal that a modulation of topo II binding kinetics can oppositely regulate its topological simplification activity, and in turn can have a significant impact in vivo.

biophysics↗

bioRxiv2025

NERVE GROWTH FACTOR IS SUFFICIENT TO CAUSE MULTIPLE OSTEOARTHRITIS-RELEVANT PATHOLOGICAL FEATURES IN NAIVE MURINE KNEE JOINTS

BACKGROUNDNerve growth factor (NGF), a key mediator of pain and inflammation, is increased in joints with osteoarthritis (OA). Neutralizing NGF with monoclonal antibodies has shown analgesic effects in painful knee OA, but clinical development was stopped due to side effects in the joints. Knowledge about the biological effects of long-term exposure of joint tissues to NGF is limited. Therefore, we aimed to explore the effects of repeated intra-articular (IA) injections of NGF into the knee joints of healthy mice on pain and sensitization, as well as joint innervation and structure. METHODSWe conducted five experiments in male C57BL/6 mice. In Experiment 1, NGF (50ng or 500ng) or vehicle was injected IA into the knee of naive wildtype (WT) mice, twice a week for 4 weeks. We assessed knee swelling, knee hyperalgesia and histopathology. In Experiment 2, mice were injected with 500ng NGF or vehicle, twice a week for 4 weeks and microCT of the knee was performed. In Experiment 3, NaV1.8-tdTomato reporter mice were injected with 500ng NGF or vehicle, twice a week for 4 weeks, and joint innervation was assessed. In Experiment 4, WT mice received 500ng NGF or vehicle twice a week for 4 weeks and were used for single cell RNA sequencing (scRNAseq) of the synovium. In Experiment 5, L3-L5 DRGs of mice that received 3 IA injections of 500ng NGF or vehicle twice a week were used for bulk RNA sequencing. RESULTSRepeated bi-weekly IA injections of NGF caused knee hyperalgesia in naive mice. NGF caused dose-dependent knee swelling, synovial pathology, increased bone mineral density and trabecular bone thickness in the medial subchondral bone, growth of pre-osteophytes in the medial compartment, but no cartilage degeneration. NGF injection caused sprouting of NaV1.8+ neurons in the medial but not the lateral synovium. ScRNAseq of the synovium revealed upregulated genes related to neuronal sprouting, synovial fibrosis and ossification, confirming histopathological findings. Bulk RNA seq of DRG showed upregulated pathways related to axonal growth. CONCLUSIONSIn healthy mouse knees, NGF induced mechanical sensitization, synovitis, neoinnervation in the medial synovium, subchondral bone changes and pre-osteophyte growth in the medial compartment, thus capturing many pathological changes observed in OA, except cartilage damage.

neuroscience↗

bioRxiv2025

CXCL16 mediates nociception and inflammation in murine post-traumatic osteoarthritis

This study investigates the role of the chemokine CXCL16 and its receptor, CXCR6, in post-traumatic osteoarthritis (PTOA) and joint nociception, highlighting the potential of targeting the CXCL16-CXCR6 axis for therapeutically managing joint inflammation and pain. Following joint injury in mice, the CXCL16-CXCR6 signaling axis is activated in synovium, driven by synovial fibroblasts and macrophages. Human OA synovium also exhibited increased CXCL16 and CXCR6 gene expression. CXCL16 stimulated a pro-inflammatory response in fibroblasts and macrophages, contrasting with an anti-inflammatory response observed in mesenchymal progenitor cells. In mice, repeated intra-articular CXCL16 injections induced histological synovitis and sex-dependent activation of inflammatory and fibrotic transcriptional programs in synovium. Repeated CXCL16 joint injections also induced knee hyperalgesia, which was mitigated by co-administration of the CXCR6 antagonist, ML339. A single intra-articular injection of CXCL16 induced acute knee hyperalgesia as early as 30 minutes post-injection, which was completely abrogated by ML339 co-treatment, suggesting direct CXCL16 binding to nociceptor-expressed CXCR6. In a murine PTOA model, systemic CXCR6 antagonism with ML339 alleviated knee hyperalgesia and altered circulating immune cell profiles. Direct stimulation of mouse dorsal root ganglion-derived nociceptive neurons with CXCL16 induced rapid calcium signaling, which was abolished by co-treatment with ML339. These findings establish CXCL16 as a regulator of joint inflammation and identifies the CXCL16-CXCR6 binding mechanism as key in mediating pain-related behaviors and nociceptor activation, offering a therapeutic target for PTOA-related inflammation and pain management. One Sentence SummaryCXCL16 regulates synovial inflammation and mediates joint nociception via CXCR6, highlighting its potential as a therapeutic target for post-traumatic osteoarthritis.

physiology↗

bioRxiv2025

A standardized, open-source, portable model for noninvasive joint injury in mice

Preclinical models of osteoarthritis (OA) are crucial for the study of disease mechanisms and for the development of critically-needed disease-modifying therapeutics. While surgical OA models, such as the destabilization of the medial meniscus (DMM), have been the gold standard in the field for decades, noninvasive joint loading-based models have increased in popularity and utility. To facilitate standardization of the noninvasive anterior cruciate ligament rupture (ACLR) model in mice, we present the Mobile Joint-Injury Operator (MoJO) - an open-source protocol with accompanying fixtures and data, designed for a low-cost, commercially-available, portable uniaxial testing system with a small footprint. We provide 3d-printable fixture designs and a rapid, highly-repeatable ACLR-mediated joint injury protocol that results in the expected post-traumatic osteoarthritis phenotype in male and female C56Bl/6 mice. We then describe the expected mechanical data from the injury procedure and offer various troubleshooting strategies. Finally, we summarize the resultant PTOA phenotype by knee hyperalgesia testing, {micro}CT imaging, flow cytometry, and histological assessment. Increased standardization of this model is a critical aspect of the overall refinement of animal models of OA.

physiology↗

bioRxiv2020

Single-molecule analysis reveals cooperative stimulation of Rad51 filament nucleation and growth by mediator proteins

Homologous recombination (HR) is an essential DNA double-strand break (DSBs) repair mechanism frequently inactivated in cancer. During HR, RAD51 forms nucleoprotein filaments on RPA-coated resected DNA and catalyses strand invasion into homologous duplex DNA. How RAD51 displaces RPA and assembles into long HR-proficient filaments remains uncertain. Here, we employ single-molecule imaging to investigate the mechanism of nematode RAD-51 filament growth in the presence of BRC-2 (BRCA2) and RAD-51 paralogs, RFS-1/RIP-1. BRC-2 nucleates RAD-51 on RPA-coated DNA, while RFS-1/RIP-1 acts as a chaperone to promote 3 to 5 filament growth via highly dynamic engagement with 5 filament ends. Inhibiting ATPase or mutation in RFS-1 Walker box leads to RFS-1/RIP-1 retention on RAD-51 filaments and hinders growth. rfs-1 Walker box mutants display sensitivity to DNA damage and accumulate RAD-51 complexes non-functional for HR in vivo. Our work reveals the mechanism of RAD-51 nucleation and filament growth in the presence of recombination mediators.

biophysics↗

bioRxiv2020

Traumatic Joint Injury Induces Acute Catabolic Bone Turnover Concurrent with Articular Cartilage Damage in a Rat Model of Post-Traumatic Osteoarthritis

ObjectiveAssess acute alterations in bone turnover, microstructure, and histomorphometry following noninvasive anterior cruciate ligament rupture (ACLR). MethodsTwelve female Lewis rats were randomized to receive noninvasive ACLR or Sham loading (n=6/group). In vivo CT was performed at 3, 7, 10, and 14 days post-injury to quantify compartment-dependent subchondral (SCB) and epiphyseal trabecular bone remodeling. Near-infrared (NIR) molecular imaging was used to measure in vivo bone anabolism (800 CW BoneTag) and catabolism (Cat K 680 FAST). Metaphyseal bone remodeling and articular cartilage morphology was quantified using ex vivo CT and contrast-enhanced {micro}CT, respectively. Calcein-based dynamic histomorphometry was used to quantify bone formation. OARSI scoring was used to assess joint degeneration, and osteoclast number was quantified on TRAP stained-sections. ResultsACLR induced acute catabolic bone remodeling in subchondral, epiphyseal, and metaphyseal compartments. Thinning of medial femoral condyle (MFC) SCB was observed as early as 7 days post-injury, while lateral femoral condyles (LFC) exhibited SCB gains. Trabecular thinning was observed in MFC epiphyseal bone, with minimal changes to LFC. NIR imaging demonstrated immediate and sustained reduction of bone anabolism ([~]15-20%), and a [~]32% increase in bone catabolism at 14 days, compared to contralateral limbs. These findings were corroborated by reduced bone formation rate and increased osteoclast numbers, observed histologically. ACLR-injured femora had significantly elevated OARSI score, cartilage thickness, and cartilage surface deviation. ConclusionACL rupture induces immediate and sustained reduction of bone anabolism and overactivation of bone catabolism, with mild-to-moderate articular cartilage damage at 14 days post-injury.

physiology↗

bioRxiv2018

Comparative genomics of ten new Caenorhabditis species

The nematode Caenorhabditis elegans has been central to the understanding of metazoan biology. However, C. elegans is but one species among millions and the significance of this important model organism will only be fully revealed if it is placed in a rich evolutionary context. Global sampling efforts have led to the discovery of over 50 putative species from the genus Caenorhabditis, many of which await formal species description. Here, we present species descriptions for ten new Caenorhabditis species. We also present draft genome sequences for nine of these new species, along with a transcriptome assembly for one. We exploit these whole-genome data to reconstruct the Caenorhabditis phylogeny and use this phylogenetic tree to dissect the evolution of morphology in the genus. We show unexpected complexity in the evolutionary history of key developmental pathway genes. The genomic data also permit large scale analysis of gene structure, which we find to be highly variable within the genus. These new species and the associated genomic resources will be essential in our attempts to understand the evolutionary origins of the C. elegans model.

evolutionary biology↗