The notochord is a defining feature of chordates. It acts as mechanical support and a source of signals to surrounding tissues during development. In mammals, notochord-derived cells persist within intervertebral discs, where they form the nucleus pulposus, the cartilage in between vertebrae units that provides the spine with flexibility. Here, we synthesise developmental knowledge with recent advances in notochord biology and insights from single-cell molecular approaches. We discuss the developmental processes from notochord initiation during gastrulation through to disc formation, highlighting signalling pathways that govern axial mesoderm specification and notochordal lineage commitment. Knowledge gained from in vivo studies has guided the development of pluripotent stem cell-based models in mice and humans, including monolayer and micropatterned systems and 3D organoids. These models recapitulate key developmental aspects of notochord formation and pave the way for disease modelling and regenerative applications. We discuss their relevance to the study of developmental disorders arising from notochord dysfunction and notochordal cell roles in disc homeostasis. Finally, we outline remaining questions and examine how developmental insights and stem cell innovations can advance our understanding of tissue formation, function and homeostasis while fostering the integration of basic mechanistic insights with translational applications.
We propose a set of algorithms to identify 'shelved asset candidates' in drug development-drug candidates for which development was discontinued for reasons other than safety or efficacy. Using a variety of microdata sources and classification algorithms, we identify 5523 drug-development programs that appear to have been deprioritized after entering human clinical trials. While many of these assets were likely discontinued for scientifically valid reasons that may not be fully observable in public data, the analysis suggests that a subset may retain scientific or commercial option value under alternative development strategies. These estimates provide a starting point for building a systematic catalog of discontinued assets and for facilitating collaboration among industry sponsors, nonprofit organizations and new developers interested in repositioning or advancing these compounds.
Many congenital conditions and surgical interventions perturb haemodynamics in the proximal pulmonary arteries during postnatal development, thereby altering gene expression and associated changes in vascular structure and function. Among these, pathological conditions include patent ductus arteriosus, pulmonary atresia and stenosis and hypoxemia-induced pulmonary hypertension while surgical interventions include the placement of a Blalock-Thomas-Taussig shunt and the Glenn and Fontan procedures. Despite the significant morbidity associated with these diverse conditions, little attention has been directed to understanding the natural postnatal development of pulmonary arteries from both biological and mechanical perspectives. Without such information, we cannot truly understand the phenotype of the affected pulmonary artery, which is fundamental to improving diagnosis, treatment and prognosis. In this paper, we present novel data from wild-type mice that document normal postnatal changes in select gene expression, wall composition and biomechanical properties of proximal pulmonary arteries. These findings enabled the establishment of a novel, data-informed computational model of pulmonary artery development capable of simulating outcomes in response to perturbations in pulmonary artery haemodynamics.
C.H. Waddington (1905-1975) was a British biologist and perhaps the major figure in developmental biology between the 1940s and 1960s. He is one of the few pre-molecular-age developmental biologists still widely remembered. This is for his pioneering work on using mutations to probe embryogenesis, for his deep analysis of how gene activity drives developmental change (summarised in his illustration of the epigenetic landscape), for his exploration of the mechanics of evolutionary change in the developing phenotype and for his terminology, much of which remains in common usage. Waddington died some 50 years ago, and this short article examines some of his key research papers that underpin these achievements and still remain significant. The supplementary material, available online, includes songs composed for Waddington's 50th birthday.
The vertebrate forelimb initiates as a localized swelling in the somatic lateral plate mesoderm (somatic LPM) in response to TBX5-dependent transcription. The molecular pathways driving limb morphogenesis have been extensively studied but the steps directly preceding limb bud formation remain poorly characterized. To address this, we defined the temporal onset of forelimb initiation in mouse embryos using sequencing based high-throughput approaches (RNA-seq, scRNA-seq, ChIP-seq, and Ribo-ITP) benchmarked to known features in forelimb development, identifying four distinct stages. Using scRNA-seq at the onset of forelimb-specific transcription, we determined the transcriptional profile of the somatic LPM and identified signature genes that distinguish the nascent forelimb from other cell types. This group includes multiple genes involved in neural projection as well as cell adhesion. Interestingly, these genes are highly enriched for TBX5 binding sites, suggesting they are candidate early transcriptional targets of TBX5. As TBX5 is essential for forelimb outgrowth, the identification of these genes suggests new mechanistic models for TBX5-driven limb initiation.
Chii Jou (Joe) Chan is a Principal Investigator at the Mechanobiology Institute, National University of Singapore. Joe's group focuses on understanding the mechanobiological principles underlying oocyte maturation, follicle growth and collective dynamics during ovarian development and ageing, using ex vivo models and biophysical approaches. We spoke to Joe over Teams to learn more about his transition to becoming a group leader, his multidisciplinary interests spanning the physical sciences, psychology, spirituality and science communications, and his dedication to mentoring early-career researchers.
Microglia, the resident immune cells in the brain, play essential roles in synaptic pruning, neurodevelopment, and the pathogenesis of neuropsychiatric disorders. Since neuronal cells and microglia arise from different embryonic lineages, brain organoids differentiated from human induced pluripotent stem cells (iPSCs) do not typically contain microglial cells, limiting their utility in interrogating neuroimmune interactions in neurodevelopmental and in disease. Reliable methods to generate brain organoids with integrated microglial cells can model important in vivo cellular interactions in an in vitro system. We developed a method to generate microglia-containing cerebral organoids (MG-COs) from human iPSCs using concurrent induction of neuronal and microglial lineages by leveraging the respective patterning molecules for those two lineages during the early stages of embryoid body formation. The resulting MG-COs were characterized with systematic morphological and transcriptomic analyses at specific stages of the differentiation process to confirm lineage-specific differentiation. The transcriptome profiles of MG-COs were compared to cerebral organoids (COs) differentiated without microglial cells to delineate gene expression differences that arise in the setting of concurrent microglia differentiation during development and growth of the organoids. Neuronal network activity in the MG-COs and COs was assessed using microelectrode array (MEA) experiments. MG-COs generated with the protocol resulted in organoids that had a robust population of stable microglial cells integrated in the organoids, as evidenced by the presence of canonical microglial markers alongside neuronal and glial markers in the MG-COs. Transcriptomic profiling of MG-COs identified the presence of immune- and synapse-related genes, including those involved in microglial activation, synaptic plasticity, and neurotransmission in the MG-COs, underscoring the potential of MG-COs as a platform for modeling neuroimmune during neurodevelopment. MG-COs showed a robust response to the inflammatory cytokine IL-17a, which is known to activate microglia. MG-COs demonstrated significantly enhanced neuronal activity earlier in development, when compared to COs, with increased spontaneous firing activity and synchronized bursting in the MG-COs. We developed a robust protocol for generating MG-COs from human iPSCs through concurrent induction of microglial and neuronal cells during embryoid body formation, enabling the growth of cerebral organoids with integrated microglial cells. MG-COs generated using the protocol give rise to three-dimensional structures comprising neuronal, glial, and microglial cells, as evidenced by immunocytochemistry and gene expression. MG-COs exhibited similar composition of neuronal and glial cells, when compared to COs, except for the absence of microglial cells in COs, and the MG-COs showed robust response to inflammatory cytokines. This model provides a physiologically relevant platform for dissecting mechanisms mediating neuroimmune interactions in neurodevelopmental and in disease contexts.
暂无摘要（点击查看详情）
Response evaluation in pleural mesothelioma is challenging because its crescent growth pattern is poorly captured by diameter-based criteria. We aimed to develop and validate artificial intelligence (AI)-assisted volumetric response criteria (ARTIMES) based on automated tumour segmentation and biologically derived thresholds. In this retrospective, multicentre study, we included 10 926 CT scans from 2080 patients from 14 cohorts. A subset totalling 1176 CT scans from routine care (Netherlands Cancer Institute-Antoni van Leeuwenhoek Hospital) and trial cohorts (INITIATE, NivoMes, PEMMELA, LUME-MESO, NVALT19, and MiST1 trials) was annotated by 12 radiologists and 1 pulmonologist, supplemented by 100 negative CT scans, to train a deep-learning segmentation model. Internal testing included 98 CT scans from independent international hospitals in LUME-MESO. External testing included data from the MEDUSA cohort (101 CT scans with radiologist-corrected segmentations) and two fully independent manual segmentation datasets from SAKK17/18 (22 CT scans) and the University of Chicago (15 CT scans). AI segmentations were evaluated through dice similarity coefficient (DSC) and normalised surface distance (NSD) at 3 mm. Progressive disease thresholds were derived using data from patients with multiple CT scans before first-line therapy or receiving only supportive care after first-line treatment (611 CT scans), and partial response thresholds from inter-reader variability (derived from 451 CT scans). ARTIMES was validated using data from eight clinical trials (4674 CT scans; 943 patients) and compared with modified Response Evaluation Criteria in Solid Tumors (mRECIST) using time-varying Cox proportional hazards models and trial-level surrogate endpoint analysis against overall survival using R2 and surrogate threshold effect. DSC was 94-95% in internal testing and 71-80% with manual segmentations. NSD was 98% and 81-93%, respectively. ARTIMES demonstrated superior patient-level prognostic performance compared with mRECIST (concordance index 0·83 [95% CI 0·79-0·87] vs 0·73 [0·66-0·80]; p=0·023) and detected progression a median of 5 weeks earlier (124 days [95% CI 115-126] vs 162 days [138-167]; p<0·0001). At the trial level, ARTIMES-based progression-free survival showed stronger correlation with overall survival (R2 88% [95% CI 42-100]) than did mRECIST-based progression-free survival (R2 6% [0-97]) and demonstrated a surrogate threshold effect at a progression-free survival hazard ratio of less than 0·82; no threshold was observed for mRECIST. Baseline AI-derived tumour volume independently predicted overall survival and outperformed T stage and WHO performance status. ARTIMES-based progression-free survival improves prognostic stratification and shows better trial-level surrogacy for overall survival compared with mRECIST-based progression-free survival. Pending prospective validation, ARTIMES could potentially facilitate a more reliable response evaluation in pleural mesothelioma. Asbestos-Related Disease Section (SAGA) of the Dutch Society of Pulmonology and Tuberculosis (NVALT), Dutch Cancer Society, and Dutch Ministry of Health, Welfare and Sport.
Motivated by the growing use of unanchored indirect treatment comparisons (ITCs) in the absence of head-to-head trials, this paper evaluates and compares methods for estimating treatment effects across two data sources for continuous and binary outcomes. Within the Neyman-Rubin causal framework, we target the population average treatment effect for the treated, which in our setting quantifies the counterfactual difference between receiving treatment 0 and treatment 1 among individuals in Study 1, the population for which individual patient data (IPD) may not be accessible. We review six existing methods based on propensity score weighting and outcome regression and introduce a novel doubly robust (DR) estimator tailored to settings in which IPD is unavailable for the target population. Through a simulation study and a clinical case study, we demonstrate that doubly robust estimators consistently perform well across a range of practical settings. In particular, we recommend the proposed DR estimator for unavailable IPD settings.
Human body form reveals cumulative effects of ecological and socio-cultural factors. China's provides an exceptional context for investigating these multifactorial influences, not only because of its extensive geographic and cultural diversity, but also because recent decades have been marked by rapid economic development, urbanisation, migration, and the population-level trauma of the Great Famine. Using anthropometric data from > 90,000 adults across 213 geo-referenced groups from mid-late-20th and early-21st centuries, we applied Bayesian hierarchical models to assess the roles of climate, altitude, urban-rural status, linguistic affiliation, and time in shaping stature, body mass, relative sitting height, and body breadth. Substantial secular increases in body size, particularly body mass, were associated with recent economic development and urbanisation. Males and females responded similarly across environmental and temporal gradients, indicating limited sex-based differentiation. Northern groups remained taller and heavier than their southern counterparts. Notably, maximum precipitation, not temperature, emerged as the strongest climatic correlate, likely reflecting indirect effects of subsistence and disease burden. Relative sitting height increased modestly over time, while relative body breadth showed a stable east-west gradient, potentially shaped by population history. Regional exceptions, including highland Tibetan and Sherpa populations and northeastern groups, along with widening divergence among linguistic subgroups, underscore the persistent roles of migration, developmental constraints and potential high-altitude adaptation. These findings show that recent changes in human body form in China cannot be understood as simple outcomes of modernisation alone, but instead reflect layered interactions among ecology, population history, socio-economic transformation, and cohort-specific historical experience.
Collective cell migration is essential for development and tissue homeostasis, yet how integrin-extracellular matrix adhesion coordinates migratory force generation in vivo remains poorly understood. Here, we have used the zebrafish posterior lateral line primordium (pLLP) as a model for epithelial collective cell migration. We show that integrins α3 and α6b are expressed in different, yet overlapping, domains of the pLLP and function redundantly to support migration. The systematic combination of itga6b, itga3b and itga3a mutants disrupts integrin β1 localization, increases protrusive activity and impairs migration, revealing a spatially organized, partially redundant adhesion system. We further identify laminin α5 (Lama5) as a key component of the basement membrane (BM) underlying the migrating pLLP. While loss of Lama5 alone compromises BM integrity and pLLP morphology without impairing migration, simultaneous depletion of lama5 and itga6b leads to severe migration defects, with the formation of invadopodia-like structures and ultimately the stalling of migration. Together, these findings reveal a robust, redundant adhesion machinery that ensures persistent collective migration in vivo, and they establish fundamental principles of integrin-mediated adhesion that are relevant to development and disease.
The robust patterning of cell fates during embryonic development requires precise coordination of signalling gradients within defined spatial constraints. Using a geometrically confined in vitro system derived from human embryonic stem cells, we demonstrate that patterning of neuromesodermal progenitors (NMPs) during axial elongation is driven by boundary-dependent mechanisms. Despite extensive work on radial fate patterning in confined 2D systems, the quantitative role of boundary conditions in shaping spatiotemporal dynamics remains unclear. Here, we show that a minimal reaction-diffusion model coupled with a simplified gene regulatory network accurately predicts spatial patterns across diverse geometries. Guided by its predictions, we identify Wnt signalling as a key component of the activator signal. Inhibition of Wnt secretion preserved initiation of patterning but disrupted subsequent morphogenesis, indicating distinct mechanisms govern pattern establishment versus maintenance. Our findings reveal how geometry encodes positional information that directs molecular patterning, providing insight into how spatial constraints and signalling dynamics guide robust tissue self-organisation during development.
The development of complex tissues relies on the precise assignment of cell identity. At the molecular scale, this process depends on the deposition of epigenetic modifications-such as methylation-that are regulated by complex biochemical networks and occur at specific regions on the DNA and chromatin. Here we show that despite the complexity of epigenetic regulation, dynamical scaling and self-similarity of DNA methylation marks emerge in embryonic development. Drawing on single-cell multi-omics experiments, super-resolution microscopy and statistical physics, we demonstrate that these phenomena originate in dynamical feedback between DNA methylation and the formation of nanoscale dynamic chromatin aggregates. These nanoscale processes lead to genome-wide increase in DNA methylation marks following a power law and self-similar correlation functions. Using this framework, we identify methylation patterns that precede gene expression changes in embryonic symmetry breaking. Our work identifies linear sequencing measurements as a laboratory to study mesoscopic biophysical processes in vivo.
Orofacial clefts, including cleft palate (CP), are among the most common types of birth defects. CP results from a failure of palatal shelf fusion during development. Previous human studies have shown that mutations in the RhoA GTPase Activating Protein 29 (ARHGAP29) gene are linked to CP, yet the role and tissue-specific requirements for ARHGAP29 during palatogenesis remain unknown. Here, we use tissue-specific deletion of Arhgap29 in mice to provide the first direct evidence that ARHGAP29 is essential for palatal elevation and fusion. We demonstrate that ectodermal conditional loss of Arhgap29 induces a significant delay in palatogenesis at embryonic (E) day 14.5 and a significant, complete cleft of the secondary palate at E18.5 -which is not observed when Arhgap29 is lost later in development using K14-Cre and K6-Cre. Phenotypic analyses of palatal shelves at E14.5 reveal a disorganized and thicker epithelium. Loss of Arhgap29 increases palatal epithelial cell area and upregulates markers of contractility including alpha-smooth muscle actin and phospho-myosin regulatory light chain implicating cell morphology and contractility as potential drivers of CP.
Artery endothelial cells (ECs) arise through different pathways, including differentiation from mesodermal cells (vasculogenesis) or from already established vein or capillary plexus ECs (angiogenesis), the latter being most common during embryonic development and regeneration. Understanding the vein-to-artery (v2a) transition could improve revascularization therapies, but progress is limited by a lack of human models. Here, we develop a human pluripotent stem cell (hPSC) differentiation protocol that models the v2a EC conversion. Comparing v2a and mesoderm-to-artery (m2a) transcriptomes with publicly available single cell RNA sequencing (scRNA-seq) data from human embryos showed they reflected angiogenesis- and vasculogenesis-derived artery ECs, respectively. This reductionist system revealed that VEGF activation alongside PI3K inhibition was sufficient for vein ECs to acquire arterial identity within 48 hours. We model a critical step in vascular development and define the minimal signals required for artery differentiation from veins, providing a framework to promote this conversion in revascularization or therapeutic contexts.
The C. elegans germline is one of the foremost models for the study of germ cell biology. We created an integrated ratiometric calcium reporter to assess calcium levels in the C. elegans germ line. The reporter reveals changes in basal cytoplasmic calcium levels during hermaphrodite sexual development. Oogenic cells have elevated calcium levels, while spermatogenic cells have significantly reduced levels of calcium. There are a small number of germ cells in the bend region of mid-to-late L4 hermaphrodite germ lines with elevated calcium levels that are correlated with the spermatogenesis-to-oogenesis transition. We identified GON-2 as a calcium channel that is required for the maintenance of normal calcium levels in the germline. Significantly, basal calcium levels correlate with germ cell proliferation. Starvation and inactivation of pro-proliferation signaling pathways reduce basal calcium levels, while proliferating germline tumor cells have elevated basal calcium levels. Experimentally altering calcium levels leads to a concomitant increase or decrease in the proliferation rate of germ stem cells. These results imply that basal cytoplasmic calcium acts as a rheostat to regulate germ stem cell proliferation.
Distortions in autobiographical memory processing are implicated in the onset and maintenance of multiple mental health problems in adults. While reduced personal memory specificity has been identified as a transdiagnostic risk factor in adolescents, less is known about other domains of memory processing, including biases in the accessibility and affective intensity of negative and positive memories. We administered a novel recall paradigm, the Good Day-Bad Day task (Hitchcock et al., Journal of Experimental Psychology: General, 2019, 149, 198), to assess autobiographical memory fluency for positive and negative events, memory specificity, and the Fading Affect Bias (FAB) - the extent to which the emotional intensity associated with positive memories fades less than for negative memories overtime - in adolescents, aged 16-18, at high (n = 201, Mage = 17.20, SD = 0.60, 84.6% female, 2% other) and low clinical risk (n = 117, Mage = 17.10, SD = 0.60, 77.8% female) of affective disorder. We found that superior recall for positive relative to negative events and a strong FAB were associated with good mental health. Risk of affective disorder was associated with a significant reduction in these positive biases and recall of a higher number of negative memories compared with Low-Risk adolescents. Memory specificity did not differ by risk status. Findings extend research on autobiographical memory processing to two novel domains in adolescence and further elucidate how differences in autobiographical memory recall may underlie mental health, with implications for the development of memory-based interventions.
Craniosynostosis, the premature fusion of calvarial bones, is a common congenital defect often attributed to the loss of fibrous sutures or excessive ossification. Recent studies have reported aberrant cartilage formation near affected sutures, suggesting a previously unrecognized role for cartilage in suture morphogenesis and maintenance. The tectum transversum (TTR), a transient cartilage adjacent to the coronal suture, has been considered absent in humans. By analyzing published human embryonic datasets, we demonstrate that the TTR is in fact a conserved structure in humans. We further investigated the developmental dynamics and function of the TTR in mice. Spatial transcriptomic analyses reveal that the TTR mediates critical tissue-tissue interactions and may serve as a physical and molecular barrier restricting BMP signaling activation within the coronal suture, potentially modulated by the underlying dura mater. These findings identify the TTR as a conserved regulator of coronal suture morphogenesis and provide new mechanistic insight into the etiology of coronal craniosynostosis.
Definitively detecting the presence and location of pain and lameness in a dog can be challenging. Clinical gait analysis can be a useful tool to understand, diagnose, monitor, rehabilitate, and design treatment plans for a variety of musculoskeletal and neurological abnormalities. However its use to detect and distinguish abnormalities can still be limited, particularly in cases of subclinical lameness or multi-limb involvement. This study aimed to develop a proof-of-concept model for machine learning-assisted detection of lameness using temporospatial and kinetic gait parameter measurements. A total of 119 clinically normal dogs and 54 injured dogs were measured using a pressure-sensitive treadmill at the walk, while 98 clinically normal dogs and 31injured dogs were measured at the trot. A classification model was trained on 85% of the data for each gait style using an f1 scoring method and tested with the remaining 15% of the data. The walking classification model successfully identified all clinical lameness cases in the test data, but was not able to detect subclinical lameness cases. The trotting classification model was successful in detecting one of two subclinical lameness cases. Point biserial correlation analysis suggests unique patterns of parameters may enable future models to distinguish lameness locations. These findings support the development and implementation of machine learning methods to detect abnormalities in canine gait, including cases of subclinical lameness, and to assist in determining the location and type of lameness a dog may be experiencing to provide a better understanding of where and how to utilise further diagnostic methods.