Biology subjects

Thomopoulos, S.

Publications and source records attributed to Thomopoulos, S..

13 recordsLinked to original sources

bioRxiv2026

The Regional Vulnerability Index (RVI) as a Neuroimaging-Based Biomarker for Autism: Associations with Likelihood, Cognition, and Longitudinal Social Outcomes

Autism spectrum disorder (ASD) is a complex neurodevelopmental condition with symptoms spanning cognitive, social and behavioral domains and leading to lifelong challenges. Autism is heritable but specific genetic and environmental factors that shape its early neurodevelopmental trajectory remain unknown. Despite the clinical variability, neuroimaging findings from Enhancing Neuro Imaging Genetics through Meta Analysis (ENIGMA)-ASD consortium identified stable and replicable patterns of cortical and subcortical differences that were consistent with those reported by an independent consortium, the Cognitive Genetics Collaborative Research Organization (COCORO) in Japan. Here we developed and evaluated a regional vulnerability index (RVI), a similarity metric that quantifies how closely a persons brain resembles the specific pattern of an individual with autism. RVI-ASD is based on combining the regional effect sizes for regional brain measurements published by the ENIGMA-ASD group with microstructural white matter integrity differences reported by COCORO. RVI-ASD showed significantly higher effect size for case-control differences relative to any individual brain measure (d=0.30 vs. d=0.01-0.21) in individuals with autism, particularly in the adolescent-to-adult sample (N=2,577; Mean age = 16.1; SD=5.0). We next calculated RVI-ASD in the baseline and follow-up (ages 10 and 12) data from normally developing participants of the ABCD study (N=4,201). We tested the longitudinal stability, heritability, genotype-by-age interaction and sensitivity of RVI-ASD to known factors and cognitive measurements. RVI-ASD were stable on the 2-year follow up (ICC=0.76-0.92); showed significant heritability (h{superscript 2}=0.55-0.83, p<10-16) but was not affected by gene-by-age interaction. RVI-ASD showed significant positive correlation with paternal age, while correlation with maternal age was non-significant. Baseline and follow-up RVI-ASD were negatively correlated with cognitive measures including total, fluid and crystallized intelligence (r=-0.09 to -0.11, p<10-6). RVI-ASD scores tracked with core autism phenotypes including poor eye contact and rigid routines (p < .01). In a sub-sample of children with symptoms of autism (N=20), we found that earlier age of symptom onset was strongly correlated with higher White Matter RVI (r = -0.61), linking early behavioral emergence to the neuroanatomical signature. Longitudinal changes in subcortical RVI-ASD are significantly correlated with change in social functioning. The RVI-ASD is a neuroimaging-based biomarker linked to stable and reproducible brain patterns in autism. RVI-ASD allows researchers to study associations with factors associated with the likelihood for autism and cognition across large and inclusive non-clinical samples, thus moving beyond simple case-control models to understand the biological pathways of autism.

neuroscience↗

bioRxiv2026

SPECTRA: Spatial Inference for Tractometry Toward Precision Mapping of White Matter Microstructure

Diffusion MRI tractometry characterizes white matter microstructure along fiber bundles, but standard along-tract profiling collapses measurements across the bundle cross-section, obscuring radial heterogeneity and producing spatially inconsistent units of inference. We present SPECTRA (Spatial Inference for Tractometry), a framework designed to address these limitations through a unified design of parameterization and statistical inference. First, we propose a 2D bundle parameterization that extends along-tract profiling to include a radial dimension defined on the atlas bundle. Second, we develop a two-stage hierarchical false discovery rate (hFDR) procedure for multi-bundle inference, which aggregates evidence at a coarser spatial scale before proceeding to finer-grained inference, with spatial scales derived from a Matern kernel. Across extensive simulation conditions, we found that hFDR improves statistical power and reduces the sample size required to detect effects compared to global FDR correction, while maintaining appropriate error control. We further characterized how sensitivity-specificity tradeoffs depend on sample size, the magnitude, spatial extent, and configurations of effects, thereby providing practical guidance for tractometry study design. In an empirical analysis of mild cognitive impairment and dementia in more than 4,000 subjects across 63 bundles, SPECTRA revealed spatially localized patterns that were absent in 1D profiles. Together, these results demonstrate that spatially resolved parameterization and adaptive error control jointly enable precise mapping of white matter microstructure in large-scale tractometry studies. SPECTRA is openly available as a Python package.

neuroscience↗

bioRxiv2025

Tendon fibroblast inflammatory responses depend on NF-κβ and JAK/STAT signaling and alter mechanotransduction pathways

Tendon pathologies, including both chronic injuries and acute tendon tears, are some of the most common musculoskeletal injuries. Recent studies have suggested the importance of inflammation in the healing process in both acute and chronic tendon injury. However, there remain gaps in knowledge that hinder progress in the development of therapeutics to improve healing. A more complete characterization of the inflammatory response in tendon is needed, by defining the relative roles of different molecular pathways, and determining how these pathways interact with tendon mechanobiology. To investigate these questions, an in vitro model was developed, wherein the complexity of the in vivo healing environment was simulated by applying M1 macrophage conditioned media (M1-CM) to tendon fibroblasts (TFs). Characterization of the M1-CM and its effect on TFs revealed a robust inflammatory response, including upregulation of over 500 genes and increased secretion of several cytokines in TFs. The NF-{kappa}{beta} and JAK/STAT signaling pathways were necessary for the response to M1-CM, and each pathway was responsible for different downstream responses to inflammation in TFs. When considering the role of mechanical loading in tendon responses to inflammation, it was found that TF responses to loading were altered by the presence of an inflammatory stimulus. Analysis of the genes that responded differently to loading with inflammation present suggested changes in pathways involving extracellular matrix organization and G protein signaling. Mathematical modeling based upon these results revealed time-dependent suppression of mechanosensitivity, suggesting that therapeutic timing of inflammatory or anti-inflammatory interventions could restore or attenuate mechanical responsiveness to modulate rehabilitation outcomes. Results reveal that inflammation disrupts mechanosensitivity in tendon healing, and suggest potential pathways for therapeutic intervention.

cell biology↗

bioRxiv2025

Musculoskeletal architecture of the shoulder: A comparative anatomy study in bats and mice informing human rotator cuff function

Overhead motion in humans often leads to shoulder injuries, a consequence of the evolutionary trade-off in glenohumeral joint anatomy that balances stability with mobility. Bats consistently engage in overhead motion during flight, subjecting their shoulders to substantial loading throughout their relatively long lifespan. Remarkably, despite the demands placed on a bats shoulder, instability and rotator cuff tears, which could be fatal to bats in short order, are not observed in nature. We were thus inspired to study functional adaptations in the shoulders of bats that enable this overhead motion. Comparative anatomical studies of the shoulders of bats and mice, similarly-sized quadrupeds, were performed and interpreted using a mathematical model. Scapular anatomy indicated a more prominent role for the infraspinatus muscle in the bat compared to the mouse. Measurements of bat and mice shoulders revealed that the bat glenoid had a larger curvature and arc length than that of mice, providing a larger articulating surface area with and deeper enclosing surface of the humeral head. Modeling results predicted that the bat shoulder is stable over a dramatically larger range of angles compared to the mouse shoulder. These results suggested that adaptations to constraints imposed by the bony anatomy and rotator cuff tendons of the shoulder may contribute to the ability of bats to sustain overhead motion in a high stress, repeated loading environment without injury. Results suggest that bats have evolved unique adaptations in their glenohumeral bony anatomy that reduce stress on the supraspinatus, enhance joint stability, and optimize strength across a broad range of motion.

physiology↗

bioRxiv2025

Image-Based Meta- and Mega-Analysis (IBMMA): A Unified Framework for Large-Scale, Multi-Site, Neuroimaging Data Analysis

The increasing scale and complexity of neuroimaging datasets aggregated from multiple study sites present substantial analytic challenges, as existing statistical analysis tools struggle to handle missing voxel-data, suffer from limited computational speed and inefficient memory allocation, and are restricted in the types of statistical designs they are able to model. We introduce Image-Based Meta- & Mega-Analysis (IBMMA), a novel software package implemented in R and Python that provides a unified framework for analyzing diverse neuroimaging features, efficiently handles large-scale datasets through parallel processing, offers flexible statistical modeling options, and properly manages missing voxel-data commonly encountered in multi-site studies. IBMMA produced stronger effect sizes and revealed findings in brain regions that traditional software overlooked due to missing voxel-data resulting in gaps in brain coverage. IBMMA has the potential to accelerate discoveries in neuroscience and enhance the clinical utility of neuroimaging findings.

neuroscience↗

bioRxiv2023

The subacromial bursa is a key regulator of the rotator cuff and a new therapeutic target for improving repair

Rotator cuff injuries result in over 500,000 surgeries performed annually, an alarmingly high number of which fail. These procedures typically involve repair of the injured tendon and removal of the subacromial bursa. However, recent identification of a resident population of mesenchymal stem cells and inflammatory responsiveness of the bursa to tendinopathy indicate an unexplored biological role of the bursa in the context of rotator cuff disease. Therefore, we aimed to understand the clinical relevance of bursa-tendon crosstalk, characterize the biologic role of the bursa within the shoulder, and test the therapeutic potential for targeting the bursa. Proteomic profiling of patient bursa and tendon samples demonstrated that the bursa is activated by tendon injury. Using a rat to model rotator cuff injury and repair, tenotomy-activated bursa protected the intact tendon adjacent to the injured tendon and maintained the morphology of the underlying bone. The bursa also promoted an early inflammatory response in the injured tendon, initiating key players in wound healing. In vivo results were supported by targeted organ culture studies of the bursa. To examine the potential to therapeutically target the bursa, dexamethasone was delivered to the bursa, prompting a shift in cellular signaling towards resolution of inflammation in the healing tendon. In conclusion, contrary to current clinical practice, the bursa should be retained to the greatest extent possible and provides a new therapeutically target for improving tendon healing outcomes. One Sentence SummaryThe subacromial bursa is activated by rotator cuff injury and regulates the paracrine environment of the shoulder to maintain the properties of the underlying tendon and bone.

bioengineering↗

bioRxiv2022

Tenotomy-induced muscle atrophy is sex-specific and independent of NFκB

The nuclear factor-{kappa}B (NF{kappa}B) pathway is a major thoroughfare for skeletal muscle atrophy and is driven by diverse stimuli. Targeted inhibition of NF{kappa}B through its canonical mediator IKK{beta} effectively mitigates loss of muscle mass across many conditions, from denervation to unloading to cancer. In this study, we used gain- and loss-of-function mouse models to examine the role of NF{kappa}B in muscle atrophy following rotator cuff tenotomy - a model of chronic rotator cuff tear. IKK{beta} was knocked down or constitutively activated in muscle-specific inducible transgenic mice to elicit a 2-fold gain or loss of NF{kappa}B signaling. Surprisingly, neither knockdown of IKK{beta} nor overexpression of caIKK{beta} significantly altered the loss of muscle mass following tenotomy. This finding was consistent across measures of architectural adaptation (fiber cross-sectional area, fiber length, fiber number), tissue pathology (fibrosis and fatty infiltration) and intracellular signaling (ubiquitin-proteasome, autophagy). Intriguingly, late-stage tenotomy-induced atrophy was exacerbated in male mice compared to female mice. This sex specificity was driven by ongoing decreases in fiber cross-sectional area, which paralleled the accumulation of large autophagic vesicles in male, but not female muscle. These findings suggest that tenotomy-induced atrophy is not dependent on NF{kappa}B and instead may be regulated by autophagy in a sex-specific manner.

physiology↗

bioRxiv2022

The role of TGFβ signaling in Gli1+ tendon and enthesis cells

The development of musculoskeletal tissues such as tendon, enthesis, and bone relies on proliferation and differentiation of mesenchymal progenitor cells. Gli1+ cells have been described as putative stem cells in several tissues and are presumed to play critical roles in tissue formation and maintenance. For example, the enthesis, a fibrocartilage tissue that connects tendon to bone, is mineralized postnatally by a pool of Gli1+ progenitor cells. These cells are regulated by hedgehog signaling, but it is unclear if TGF{beta} signaling, necessary for tenogenesis, also plays a role in their behavior. To examine the role of TGF{beta} signaling in Gli1+ cell function, the receptor for TGF{beta}, TbR2, was deleted in Gli1-lineage cells in mice at P5. Decreased TGF{beta} signaling in these cells led to defects in enthesis formation by P56, including deficient bone morphometry underlying the enthesis and decreased mechanical properties. In vitro experiments using Gli1+ cells isolated from mouse tail tendons demonstrated that TGF{beta} controls cell proliferation and differentiation through canonical and non-canonical pathways and that TGF{beta} directly controls the tendon transcription factor scleraxis by binding to its distant enhancer. These results have implications in the development of treatments for tendon and enthesis pathologies.

developmental biology↗

bioRxiv2022

A unique mineralizing pool of Gli1+ stem cells builds the tendon enthesis and demonstrates therapeutic potential

The enthesis, a fibrocartilaginous transition between tendon and bone, is necessary for the transfer of force from muscle to bone to produce joint motion. The enthesis is prone to injury due to mechanical demands, and it cannot regenerate. A better understanding of how the enthesis develops will lead to more effective therapies to prevent pathology and promote regeneration. Here, we used single-cell RNA sequencing to define the development transcriptome of the entheses over postnatal stages. Six resident cell types, including enthesis progenitors and mineralizing chondrocytes, were identified along with their transcription factor regulons and temporal regulation. Following our prior discovery of the necessity of Gli1-lineage cells for enthesis development and healing, we then examined their transcriptomes at single cell resolution and demonstrated their clonogenicity and multipotency. Transplantation of these Gli1- lineage cells to enthesis injuries improved healing, demonstrating their therapeutic potential for enthesis regeneration. HighlightsO_LIThe transcriptome and differentiation trajectory of enthesis stem cells during postnatal development are defined at single cell resolution. C_LIO_LITranscription factor regulons drive enthesis stem cell differentiation. C_LIO_LIGli1-lineage enthesis stem cells demonstrate in vivo and in vitro clonogenicity and multipotency. C_LIO_LITransplantation of Gli1-lineage enthesis stem cells to enthesis injuries improves healing. C_LI

developmental biology↗

bioRxiv2021

Neonatal enthesis healing involves non-inflammatory formation of acellular scar through ECM secretion by resident cells

Wound healing is a well-orchestrated process that typically recruits the immune and vascular systems to restore the structure and function of the injured tissue. Injuries to the enthesis, a hypocellular and avascular tissue, often result in fibrotic scar formation and loss of mechanical properties, thereby severely affecting musculoskeletal function and life quality. This raises questions about the healing capabilities of the enthesis. Here, we established an injury model to the Achilles entheses of neonatal mice to study the possibility that at an early age, the enthesis can heal more effectively. Histology and immunohistochemistry analyses revealed an atypical process that did not involve inflammation or angiogenesis. Instead, neonatal enthesis healing was mediated by secretion of collagen types I and II by resident cells, which formed a permanent hypocellular and avascular scar. Transmission electron microscopy showed that the cellular response to injury, including ER stress, autophagy and cell death, varied between the tendon and cartilage ends of the enthesis. Single-molecule in situ hybridization, immunostaining, and TUNEL assays verified these differences. Finally, gait analysis showed that these processes effectively restored function of the injured leg. Collectively, these findings reveal a novel healing mechanism in neonatal entheses, whereby local ECM secretion by resident cells forms an acellular ECM deposit in the absence of inflammation markers, allowing gait restoration. These insights into the healing mechanism of a complex transitional tissue may lead to new therapeutic strategies for adult enthesis injuries.

molecular biology↗

bioRxiv2021

Effects of tendon viscoelasticity in the distribution of forces over sutures in a model tendon-to-bone repair

Tears to the rotator cuff often require surgical repair. These repairs often culminate in re-tearing when sutures break through the tendon in the weeks following repair. Although numerous studies have been performed to identify suturing strategies that reduce this risk by balancing forces across sutures, none have accounted for how the viscoelastic nature of tendon influences load sharing. With the aim of providing insight into this problem, we studied how tendon viscoelasticity, tendon stiffness, and suture anchor spacing affect this balancing of forces across sutures. Results from a model of a three-row sutured re-attachment demonstrated that optimized distributions of suture stiffnesses and of the spacing of suture anchors can balance the forces across sutures to within a few percent, even when accounting for tendon viscoelasticity. Non-optimized distributions resulted in concentrated force, typically in the outermost sutures. Results underscore the importance of accounting for viscoelastic effects in the design of tendon to bone repairs.

bioengineering↗

bioRxiv2021

Toughening mechanisms for the attachment of architectured materials: The mechanics of the tendon enthesis

Architectured materials offer tailored mechanical properties but are limited in engineering applications due to challenges in maintaining toughness across their attachments. The enthesis connects tendon and bone, two vastly different architectured materials, and exhibits toughness across a wide range of loadings. Understanding the mechanisms by which this is achieved could inform the development of engineered attachments. Integrating experiments, simulations, and novel imaging that enabled simultaneous observation of mineralized and unmineralized tissues, we identified putative mechanisms of enthesis toughening in a mouse model and then manipulated these mechanisms via in vivo control of mineralization and architecture. Imaging uncovered a fibrous architecture within the enthesis that controls trade-offs between strength and toughness. In vivo models of pathology revealed architectural adaptations that optimize these trade-offs through cross-scale mechanisms including nanoscale protein denaturation, milliscale load-sharing, and macroscale energy absorption. Results suggest strategies for optimizing architecture for tough bimaterial attachments in medicine and engineering. TeaserThe architecture of the tendon-to-bone attachment is designed for toughness.

bioengineering↗

bioRxiv2018

Functional grading of pericellular matrix surrounding chondrocytes: potential roles in signaling and fluid transport

The extracellular matrix surrounding chondrocytes within cartilage and fibrocartilage has spatial gradients in mechanical properties. Although the function of these gradients is unknown, the potential exists for cells to tailor their mechanical microenvironment through these gradients. We hypothesized that these gradients enhance fluid transport around the cell during the slow loading cycles that occur over the course of a day, and that this enhancement changes the nature of the mechanical signals received at the surface of the cell. To test this hypothesis, we studied the effect of these gradients on the mechanical environment around a chondrocyte using a closed form, linearized model. Results demonstrated that functional grading of the character observed around chondrocytes in articular cartilage enhances fluid transport, and furthermore inverts compressive radial strains to provide tensile signals at the cell surface. The results point to several potentially important roles for functional grading of the pericellular matrix.

bioengineering↗