In preprints: re-examining the role of oxygen in mammalian embryogenesis

Developmental biology has traditionally focused on embryo-intrinsic mechanisms, from gene regulatory networks to coordinated cell behaviours. By comparison, the contribution of environmental factors to embryogenesis has received less attention. This emphasis partly reflects the classical model organisms of the field, many of which are oviparous and develop within relatively self-contained environments. In contrast, viviparous species, particularly placental mammals, embryos of which develop entirely within maternal tissues, are exposed to dynamic physiological conditions throughout gestation. How mammalian embryos adapt to these environmental constraints, and whether such conditions actively shape developmental programmes, remains incompletely understood.One physiological variable that changes drastically during mammalian gestation is oxygen levels. Early mouse and human embryos develop in relatively hypoxic environments due to limited maternal blood supply before placental circulation. Oxygen levels increase only after the establishment of effective maternal–foetal exchange (Dunwoodie, 2009). Early hypoxia has therefore often been viewed as a constraint that embryos must tolerate. However, accumulating evidence challenges this view. Firstly, genetic depletion of Hif1a, a central regulator of cellular hypoxia responses, disrupts multiple tissues during early organogenesis (Iyer et al., 1998). Secondly, elevating oxygen levels before placentation can result in developmental abnormalities, including neural tube defects (Morriss and New, 1979; Sakai et al., 2023). Furthermore, recent work further indicates that hypoxia can regulate lineage specification and developmental timing in a tissue-specific manner during early gestation (Zhu et al., 2024 preprint). Together, these findings suggest that oxygen availability may function not merely as a permissive condition, but as an active developmental regulator.Three recent preprints extend this emerging perspective by examining three distinct developmental contexts: trophoblast maturation (Lattner et al., 2025 preprint), somitogenesis (Anderson et al., 2025 preprint) and postnatal tendon–enthesis development (Steltzer et al., 2025 preprint). Although each study addresses a different stage and tissue, all converge in dissecting the contribution of HIF1A-dependent and HIF1A-independent mechanisms. They together provide additional evidence that oxygen signalling is integrated into developmental programmes.Trophoblast lineages develop within a physiologically low-oxygen environment in early mammalian gestation. Consistently, HIF1A is robustly expressed in trophoblast populations, including cytotrophoblasts (CTBs), extravillous trophoblasts (EVTs) and syncytiotrophoblasts (SCTs), and genetic perturbation of HIF1A in mouse models disrupts placental development. However, whether hypoxia promotes or impairs trophoblast maturation has remained controversial.Using a human trophoblast organoid system capable of differentiating into multiple trophoblast lineages, Lattner et al. (2025, preprint) systematically dissected the contributions of oxygen and HIF1A activity in trophoblast maturation. Their data indicate that low oxygen conditions consistently impair aspects of trophoblast maturation. Intriguingly, HIF1A signalling is still active even under high oxygen, suggesting that HIF1A functions are not strictly coupled to hypoxia. To further explore this point, the authors generated and examined Hif1a knockout organoids and found overlapping and distinct roles of hypoxia and HIF1A in regulating trophoblast development. For example, CTB expansion appears to be promoted by hypoxia independently of HIF1A, whereas HIF1A alone contributes to EVT morphogenesis.These findings highlight a layered regulatory logic in which hypoxia and HIF1A signalling can converge or diverge during trophoblast development.The bilateral somites are derived from presomitic mesoderm (PSM), which is generated in an oscillatory manner from the posterior trunk. During early organogenesis, the PSM displays elevated Hif1a expression and increased glycolytic activity, potentially induced by Hif1a. Previous work suggests that glycolytic flux regulates the pace of somitogenesis, and that hypoxia promotes the expression of PSM specifiers (Zhu et al., 2024 preprint). However, a comprehensive assessment of the roles of Hif1a and hypoxia in the somitogenesis process has been lacking. Anderson et al. (2025, preprint) addressed this question by generating conditional Hif1a knockout mouse lines in progenitor tissues giving rise to somites, including mesoderm and PSM.They found that depletion of Hif1a at the stage of mesoderm specification results in malformed vertebrae, with disrupted anterior–posterior polarity, left–right asymmetry and supernumerary thoracic vertebrae. In contrast, depletion of Hif1a within the developing somites themselves produced comparatively milder phenotypes. These findings suggest that hypoxia influences early specification and patterning processes rather than acting within somites per se. The combined defects in patterning and somite number indicate that HIF1A may regulate two distinct processes during somitogenesis: the establishment of anterior–posterior identity and oscillatory segmentation clock dynamics that determine somite number.To investigate the mechanisms underlying anterior–posterior patterning defects, the authors examined earlier progenitor populations and found that Hif1a is required for proper specification of neural–mesoderm progenitors (NMPs), thereby accounting for the observed patterning abnormalities. Analysis of the segmentation clock revealed that specific Notch signals that are associated with the left–right asynchrony and alterations in vertebral number were disrupted following Hif1a depletion.Interestingly, the phenotypes associated with the Hif1a knockout were partially alleviated by hyperoxic treatment. Together with the observation that Hif1a loss induces intracellular hypoxia within PSM tissues, this finding points to the involvement of additional hypoxia-responsive pathways, potentially acting downstream or in parallel to Hif1a, in regulating somite patterning and oscillatory dynamics.Taken together, this study suggests that the hypoxia responsive pathways (both Hif1a-dependent and -independent) are organised as complex network that are embedded in the gene regulatory network regulating developmental processes.The enthesis is a specialised structure at the bone–muscle attachment site that is essential for mobility and tendon function. Unlike bone cells, enthesis cells at postnatal stages are highly proliferative and undergo extensive extracellular matrix (ECM) remodelling. Given the established role of HIF1A in regulating bone morphogenesis and proliferation, Steltzer et al. (2025, preprint) investigated whether HIF1A also functions in enthesis development, a tissue closely related to bone.Interestingly, the authors found that, at postnatal stages, the enthesis exhibits higher levels of hypoxia compared with surrounding tissues, including bone and tendon, and that a hypoxic gradient is present within the tissue. This observation suggests that hypoxia-responsive pathways may be active in supporting enthesis cell function. To test this, the authors conditionally depleted Hif1a in the enthesis and observed abnormal enthesis morphogenesis. These defects were accompanied by detachment of tendon from bone, reduced grip strength, altered calcaneal architecture, impaired force transmission and ectopic mineralisation. Histological and cell proliferation analyses further revealed that these phenotypes were associated with reduced enthesis cell number and disrupted ECM organisation.To better understand how Hif1a regulates cell survival and matrix organisation, the authors used mouse tail tendon fibroblasts as a model system and performed bulk RNA sequencing on wild-type and Hif1a mutant cells cultured under low (1%) or high (20%) oxygen conditions. Loss of Hif1a led to downregulation of ECM-remodelling factors, including regulators of the BMP pathway required for ossification, consistent with their induction under hypoxic conditions. However, in contrast to hypoxia treatment, Hif1a deletion had only modest effects on anaerobic metabolic pathways such as glycolysis, suggesting that metabolic rewiring in tendon fibroblasts may occur largely independently of HIF1A.Overall, these findings support the view that the hypoxic environment uniquely present in the enthesis promotes cell survival, ECM remodelling and glycolytic features through both HIF1A-dependent and HIF1A-independent mechanisms.Together, these studies join forces with previous work to push toward a conceptual shift: oxygen availability is not merely a background condition of mammalian development, but an instructive input. Across embryonic and postnatal contexts, hypoxia and HIF1A signalling influence lineage specification, patterning, morphogenesis and tissue maturation.Importantly, by manipulating oxygen levels and genetic depletion of Hif1a, the three pieces of work together suggest that the relationship between oxygen and HIF1A activity is neither uniform nor linear: HIF1A can act in contexts under high oxygen, and hypoxia can regulate responses that are only partially dependent on HIF1A. Important follow–up questions remain: are hypoxia-responses graded or threshold-based? How is tissue-specific HIF1A activity achieved in the absence of severe hypoxia? And what additional pathways mediate oxygen-dependent developmental processes independently of HIF1A?Overall, investigating the emerging ‘oxygen biology in development’ promises to clarify how environmental variables are incorporated into developmental programmes.