The Japanese medaka, Oryzias latipes, has become an important vertebrate model organism for addressing research questions across a broad range of disciplines, including developmental and evolutionary biology, stem cells, gene-environment interactions, behavioral neuroscience, disease modeling, and drug discovery. The medaka community took advantage of the successful completion of the ERC Synergy Grant project IndiGene to gather once again in the beautiful Heidelberg (July 22-25, 2025). Building on the opportunities created by the IndiGene project, which leverages the medaka inbreed panel Medaka Inbred Kiyosu-Karlsruhe as a unique resource for dissecting complex phenotype-genotype relationships, the meeting offered an outstanding update on emerging concepts, technologies, and community resources. By summarizing the content of each session, this report provides an overview of a vibrant and highly productive event that highlights the continued growth and vitality of medaka research.
Facial morphogenesis relies on the coordinated regulation of cellular behaviors that sculpt the face from simple facial prominences to the fully confluent lip and nose. Disruptions to migration of cranial neural crest cells and/or the directed growth of the prominences will lead to abnormalities such as orofacial clefts. Here we review what is known about the roles of the actin cytoskeleton and its key regulators, the small RHO GTPases, during neural crest cell migration and facial development. Although small RHO GTPase signaling has been studied in the context of cancer and vascular pathologies, their role in facial development has received limited attention. In this review, we review the experimental data that connects changes in the function of small Rho GTPases to cytoskeletal dynamics and ultimately to facial morphogenesis. We also highlight human craniofacial disorders resulting from germline or somatic variants of small Rho GTPase pathway genes as well as associations between variants in GTPase-activating proteins (GAPs) and guanidine nucleotide exchange factors (GEFs) and the complex trait, non-syndromic cleft lip with or without cleft palate. The review points to a model where the gain or loss of RHO GTPase pathway components could be centrally involved in many craniofacial disorders and that the Rho GTPases are major regulators of homeostasis during normal development.
BACKGROUND:Endocytosis constitutes a fundamental cellular process governing development through coordinated regulation of plasma membrane remodeling and ciliogenesis, processes essential for cell shape changes and tissue development. Although Twist1 null embryos display complete cranial neural tube (NT) closure defects and conditional knockout in neuroectoderm disrupts cranial neural crest cell fate determination and delamination, the function of TWIST1 in NT morphogenesis remains unknown. We investigated the basis underlying neuroectodermal morphological abnormalities in TWIST1 mutant embryos, specifically the formation of ectopic lateral bending points and cellular disorganization, by examining Twist1's role in cilia formation, adherens junction integrity, and endocytic vesicle dynamics. RESULTS:Immunofluorescence analysis revealed that cytosolic TWIST1 colocalizes with β-catenin and endocytic regulators LRP2 and RAB11B along the apical surface of cranial neuroectoderm. Twist1 knockout resulted in reduced ciliary length and number. Quantitative polymerase chain reaction (PCR) and Western blot analyses demonstrated upregulation of RAB11B and β-catenin at mRNA and protein levels in Twist1 mutants. This molecular dysregulation coincided with increased accumulation of apical endocytic vesicles and altered expression profiles of endocytic component genes, ultimately modifying the apical neuroectodermal cell-cell junctions. CONCLUSION:Our findings establish TWIST1 as a crucial factor for neuroectodermal morphology, demonstrating its importance in ciliogenesis, endocytic vesicle dynamics, and cell-cell integrity.
BACKGROUND:Many maternal mRNAs in Drosophila primordial germ cells (PGCs) are degraded in concert with the synthesis of new transcripts from the zygotic genome during gastrulation and germ band elongation (3-5 h after egg laying [AEL]). However, few studies have focused on maternal mRNA destabilization in PGCs at the blastoderm stage that is prior to zygotic genome activation (ZGA). Thus, the stability of maternal mRNAs at this stage and regulation of their degradation remain poorly understood. To address this gap, we examined the role of Nanos, an RNA-binding protein known to promote mRNA degradation, in blastoderm-stage PGCs. RESULTS:By combining flow cytometry and RNA-sequencing (RNA-seq) analysis of PGCs, we identified the transcripts of 898 genes that were increased in nanos- PGCs. Among them, 298 genes encode maternal transcripts that were downregulated by Nanos in PGCs. CONCLUSIONS:Our results show that Nanos downregulates maternal mRNA expression in PGCs before ZGA in Drosophila. As Nanos in C. elegans PGCs has also been reported to promote maternal-to-zygotic transition (MZT) via maternal mRNA downregulation during a transcriptionally silent state, our findings highlight the importance of investigating the function of Nanos for understanding the MZT in PGCs across various animal species.
BACKGROUND:The brown anole is a model species of the genus Anolis, a squamate (encompassing lizards and snakes) group widely studied in evolutionary, behavioral, and developmental biology. Full genome annotation, the establishment of gene editing techniques, and comprehensive description of reproductive tract morphology and embryogenesis in this species have laid the foundation for functional studies. However, analysis of brown anole oogenesis is still required and vital to optimize genome modification, mutant line establishment, and analyses of the evolution of reproductive developmental mechanisms. RESULTS:Here, we characterize ovary morphology and gametogenesis in the female brown anole, Anolis sagrei, using brightfield imaging, microCT, histology staining, electron microscopy, and confocal imaging. We define 10 stages of oocyte maturation, which commences inside the oogonial nest within the germinal bed and concludes with the mature follicle ready to ovulate based on follicle size, yolk acquisition, and follicular, cellular, and basement membrane architecture. CONCLUSIONS:We describe the complete oogenesis of the brown anole in 10 stages and report that oogenesis is highly conserved within iguanians, a suborder of lizards. With our staging framework, we lay the foundation for functional studies of oogenesis and optimized gene-editing.
Maternal effects, encompassing both genetic (maternally expressed gene products) and non-genetic (maternal state) influences, are powerful determinants of offspring phenotype, yet their RNA-level mechanisms remain incompletely resolved. In parallel, epitranscriptomics, an emerging field centered on chemical modifications to RNA, has revealed new layers of gene regulation with implications for cell fate, plasticity, and response to environmental cues. In this perspective article, a conceptual link is proposed between maternal effects and epitranscriptomic mechanisms, focusing on how maternal environments may shape offspring phenotypes through RNA modifications. Evidence is examined from diverse systems, including maternal deposition of modified RNAs, environmental modulation of RNA-modifying enzymes, and early developmental windows sensitive to maternal inputs. A clear distinction is drawn between placenta-mediated pathways that reprogram trophoblast/placental epitranscriptomics and direct fetal-tissue routes that act within developing organs. Although causal demonstrations are still emerging, convergent observations indicate that maternal environments can tune the offspring epitranscriptome with lasting phenotypic consequences. To articulate this emerging connection, the concept of “ maternal RNA imprinting ” is proposed, the idea that offspring development is shaped by maternal cues via targeted RNA modifications. This article aims not only to synthesize emerging insights across fields but also to stimulate interdisciplinary discussion and encourage investigation into the unexplored intersections of maternal biology and RNA regulation.
BACKGROUND:EGF-CFC proteins are a bilaterian innovation, but they are best known for their roles in Nodal signaling during gastrulation and left-right patterning in vertebrates. Species with multiple family members show evidence of functional specialization. For example, in mouse, Cripto is required for gastrulation, whereas CFC1 is involved in left-right patterning. However, members of the EGF-CFC family across model organisms exhibit limited sequence conservation beyond the EGF-CFC domain, posing challenges for determining their evolutionary history and functional conservation. RESULTS:In this study, we describe the evolutionary history of the EGF-CFC family of proteins across several branches of deuterostomes, with a particular focus on vertebrates. We trace the EGF-CFC gene family from a single gene in the deuterostome ancestor through its expansion and functional specialization in tetrapods, and subsequent gene loss and translocation in eutherian mammals. Mouse Cripto and CFC1, zebrafish Tdgf1, and each Xenopus EGF-CFC gene (Tdgf1, Tdgf1.2 and Cripto.3) are all descendants of the ancestral deuterostome Tdgf1 gene. CONCLUSIONS:We propose that subsequent to EGF-CFC family expansion in tetrapods, Tdgf1B (Xenopus Tdgf1.2) acquired specialization in the left-right patterning cascade, and then after its translocation in eutherians to a different chromosomal location, CFC1 has maintained that specialization.
Colorectal cancer (CRC) ranks among the leading causes of cancer-related morbidity and mortality worldwide. Despite progress in understanding its molecular intricacies, the management of CRC, especially in advanced stages, remains a significant clinical hurdle. This review delves into the evolving landscape of stem cell-based therapeutic strategies in CRC, with a specific focus on the interplay between cancer stem cells (CSCs) and CRC pathogenesis and treatment resistance. Highlighting the pivotal roles of CSCs in tumor initiation, progression, metastasis, and recurrence, the review comprehensively examines their involvement in CRC, ranging from normal colonic tissue to cancer initiation. The potential of stem cells for medicinal purposes in CRC management is explored, encompassing diverse modalities such as transplantation, differentiation therapy, immunotherapy, and gene/cell-based approaches. Challenges and opportunities associated with these strategies are also evaluated, providing insights into their clinical potential and limitations. The review also appraises preclinical investigations contributing to the understanding of CRC and stem cells. Current clinical trials, patient stratification strategies, and regulatory considerations related to stem cell-based therapies in CRC are scrutinized. Furthermore, the review explores emerging trends and future directions, including developments in stem cell technologies and ethical considerations. It highlights the transformative potential of stem cell-based therapeutic strategies in CRC.
BACKGROUND:Histone post-translational modification (PTM) is an important epigenomic regulation content and an essential process regulating gene expression. Histone lysine lactylation is the newly identified histone PTM that utilizes the lactyl moiety for its modification. Although histone lysine lactylation is considered an essential outcome of the Wardburg effects and the interconnection between cellular metabolism and gene regulation, the developmental contexts involving this PTM are largely unknown. In this study, we comprehensively observed histone lysine lactylation during Drosophila oogenesis, one of the developmental contexts in which chromatin regulation plays crucial roles. RESULTS:Our study revealed that lactylation on the specific histone lysine mainly occurs in the oocyte karyosome and condensed meiotic chromosome, suggesting histone lysine lactylation has a vital role in female meiosis. Interestingly, one of the histone lysine lactylations, lactylation of lysine 14 of histone H3, is intensively observed in the meiotic germline in the mouse ovary, suggesting that lactylation has an evolutionarily conserved role. CONCLUSIONS:Our results revealed that histone lysine lactylation is predominantly present in transcriptionally repressive meiotic chromatin, which contradicts the previously reported function of histone lactylation in transcriptional activation. This study, therefore, provides the first fundamental information to understand the role of histone lysine lactylation in the germline and repressive chromatin.
Gfi1 plays an important role in the development of hair cells (HCs), as indicated by its ability to regulate the expression of HC-related genes while the organ of Corti is developing. Given that the HCs and the supporting cells (SCs) are coming from a common stem/progenitor cell pool, it is conceivable to regenerate HCs from SCs that ectopically express Gfi1. The focus of this review was to elucidate the role of Gfi1 in controlling the development of HCs by dissecting the phenotypes of the inner ear in Gfi1-mutated mouse lines. In addition, we reviewed studies of regeneration in the mammalian inner ear, by which we discussed the novel function of Gfi1 as an essential factor in guiding non-HCs toward an HC destiny in coordination with Atoh1 and Pou4f3. Finally, we summarized the known Gfi1-specific Cre/CreER/reporter mouse lines and highlighted the pros and cons of each line, with the aim of providing insights for use in future studies. In summary, a better understanding of Gfi1 and its diverse roles is beneficial for advancing studies of HC regeneration in the inner ear.
BACKGROUND:Previously, we explored the role of Sox9 in the second heart field (SHF) in atrioventricular septation. For that study, we created a SHF-specific Sox9 knockout mouse. In addition to the presence of primary atrial septal defects in half of the offspring, we found that virtually all specimens also developed a ventricular septal defect. Histological analysis suggested that the ventricular septal defects resulted from developmental perturbation of the mesenchymal structures within the outflow tract. In the current study, we investigated the role of Sox9 in the SHF in the development of these tissues. RESULTS:Sox9 is expressed in all mesenchymal cell populations in the developing outflow tract, including a cohort of endocardial-derived cells that originate from the SHF-derived endocardium. SHF-specific deletion of Sox9 inhibits the formation of this cell population and ultimately leads to truncation of the mesenchymal outlet septum. This prevents complete fusion of this outlet septum with the atrioventricular mesenchymal complex, resulting in ventricular septal defects. CONCLUSIONS:In combination with our first paper on the role of Sox9 in atrioventricular septation, data presented in this study demonstrate that Sox9 expression in the SHF is of critical importance for the proper formation of the septal structures in the developing heart.
BACKGROUND:Skeletal muscle stem cells (MuSCs) played an important role in maintaining the proper function of muscle tissues. In adults, they normally remained in a quiescent state and activated upon stimulation to undergo self-renewal or myogenic differentiation. This process was complexly regulated by cytokines, and the molecular mechanisms that promoted MuSCs activation remained largely unknown. RESULTS:Here, we analyzed transcriptome data from MuSCs activated by different stimuli using weighted gene co-expression network analysis (WGCNA) and identified the key long non-coding RNA SNHG1 (lncSNHG1), which promotes the transition from the quiescent to the activated state of MuSCs. Overexpression of lncSNHG1 was able to promote the proliferation and differentiation of MuSCs, whereas knockdown resulted in the opposite results. Mechanistically, the disruption of the Wnt/β-catenin pathway blocked the quiescence exit induced by lncSNHG1. CONCLUSIONS:We conclude that lncSNHG1 is a key factor that promotes the transition from the quiescent to the activated state of MuSCs and promotes cell proliferation and differentiation through the Wnt/β-catenin pathway.
In recent years, the importance of placental function for fetal neurodevelopment has become increasingly studied. This field, known as neuroplacentology, has greatly expanded possible etiologies of neurodevelopmental disorders by exploring the influence of placental function on brain development. It is also well-established that brain development is influenced by craniofacial morphogenesis. However, there is less focus on the impact of the placenta on craniofacial development. Recent research suggests the functional influence of placental nutrients and hormones on craniofacial skeletal growth, such as prolactin, growth hormone, insulin-like growth factor 1, vitamin D, sulfate, and calcium, impacting both craniofacial and brain development. Therefore, interactions between the placenta and both fetal neurodevelopment and craniofacial development likely influence the growth and morphology of the head as a whole. This review discusses the role of placental hormone production and nutrient delivery in the development of the fetal head-defined as craniofacial and brain tissue together-expanding on the more established focus on brain development to also include the skull (or cranium) and face.
BACKGROUND:Freshwater salinization is an emerging stressor in amphibian populations, and embryonic stages are most vulnerable. To better understand the variation in embryonic osmoregulation, we challenged embryos of two phylogenetically diverse anuran species, Xenopus laevis and Lithobates (Rana) sylvaticus, along a gradient of non-lethal salinities. We hypothesized embryos at higher salinities will display epidermal plasticity as a coping response and increase energy expenditure related to osmoregulation demands, thereby reducing energy for growth and development. RESULTS:Scanning electron microscopy revealed an extra mucus-secreting cell type and higher ionocyte proportions in the X. laevis epidermis, suggesting more osmoregulatory machinery than L. sylvaticus. Under elevated salinity, X. laevis displayed greater increases in goblet cell proportions, mucus secretion, and reductions in ionocyte apical area compared with L. sylvaticus. Although both species increased oxygen consumption rates and reduced body length with elevated salinity, these effects were proportionally greater in L. sylvaticus at the highest salinity, and only this species slowed developmental rates. CONCLUSION:These findings support the hypothesis that frog embryos respond to salinity by altering the cellular landscape of their epidermis. We show that epidermal cell types, as well as the magnitude of epidermal plasticity and energetic trade-offs in response to salinity, vary among amphibian species.
BACKGROUND:Longitudinal skeletal growth takes place in the cartilaginous growth plates. While growth plates are found at either end of conventional long bones, they occur at a variety of locations in the mammalian skeleton. For example, the metacarpals and metatarsals (MT) in the hands and feet form only a single growth plate at one end, and the pisiform in the wrist is the only carpal bone to contain a growth plate. We take advantage of this natural anatomical variation to test which components of the PTHrP/Ihh feedback loop, a fundamental regulator of chondrocyte differentiation, are specific to growth plate function. RESULTS:Parathyroid hormone-like hormone (Pthlh), the gene that transcribes parathyroid hormone-related peptide (PTHrP), is expressed in the reserve zone of the growth plate-forming end of the MT. At the opposite end, the absence of a PTHrP+ reserve zone results in premature chondrocyte differentiation and Indian hedgehog (Ihh) expression. Pthlh is expressed in the reserve zone of the developing pisiform, confirming the existence of a true growth plate. CONCLUSION:A pool of PTHrP+ reserve zone chondrocytes is a defining characteristic of growth plates, and its patterning may be key to evolved differences in growth plate location in the mammalian skeleton.
BACKGROUND:While heart function is broadly conserved across vertebrates, the cellular phenotype of muscle cells (cardiomyocytes) varies across taxa and throughout ontogeny. Emerging evidence suggests that some attributes may correlate with the capacity for spontaneous cardiomyocyte replacement following injury. For example, among non-regenerating taxa like adult mammals and birds, cardiomyocytes are polyploid, rarely proliferate, and are large in size. In contrast, in regeneration-competent zebrafish and amphibians, cardiomyocytes are diploid, spontaneously proliferate, and are comparatively small. For other species, less is known. RESULTS:Here, we investigate these attributes in the squamate Eublepharis macularius, the leopard gecko. Using the nuclear counterstain DAPI to measure fluorescence intensity as a proxy for DNA content, we found that >90% of adult cardiomyocytes are diploid. Using serial histology and immunostaining for markers of DNA synthesis and mitosis, we determined that adult gecko cardiomyocytes spontaneously proliferate, albeit at significantly lower levels than previously reported in subadults. Furthermore, using wheat germ agglutinin, we found that the cross-sectional area is maintained across ontogeny and that gecko cardiomyocytes are 10× smaller than those of mice. CONCLUSIONS:Taken together, our data show that gecko cardiomyocytes share several key cellular attributes with regeneration-competent species and that postnatal ventricular growth occurs via cardiomyocyte hyperplasia.
Cilia are specialized structures found on a variety of mammalian cells, with variable roles in the transduction of mechanical and biological signals (by primary cilia, PC), as well as in the generation of fluid flow (by motile cilia). Their critical role in the establishment of a left-right axis in early development is well described, as well as in the defense immune function of multiciliated upper airway epithelium. By contrast, detailed analysis of the ciliary status of specific cell types during organogenesis and postnatal development has received less attention. In this study, we investigate the progression of ciliary status within the endothelium and mesenchyme of the lung. Remarkably, we find that pulmonary endothelial cells (ECs) lack PC at all stages of development, except in low numbers in the proximal portions of older pulmonary arteries. Mesenchymal cells, by contrast, widely exhibit PC in early development, and a large subset of PDGFRα+ fibroblasts maintain PC into adulthood. The dynamic and differential ciliation of multiple cellular populations in the developing lung both challenges prior assertions that PC are found on all cells and highlights a need to understand their spatiotemporal functions.
Sonic Hedgehog (SHH) is an evolutionarily conserved signaling pathway essential for embryonic development, tissue homeostasis, and tumorigenesis. Aberrant activation of the SHH pathway induces various types of cancer and different types of immune dysregulation. SHH is an extremely important morphogen during lung development, as it regulates the interaction between epithelial and mesenchymal transitions (EMT) in the airways. Cigarette smoking triggers the EMT and activates the SHH signaling pathway, which leads to lung damage and the development of various lung diseases, such as COPD, a smoker's disease. SHH also directs the gut–lung axis (GLA) formation via epithelial–mesenchymal signaling. The abruption or alteration of GLA formation is also responsible for COPD pathogenesis. In this review, we elucidate an overview of the SHH pathway and its inhibitor HHIP, SHH's prominence during lung development, and the dysregulation of the SHH signaling pathway in COPD pathogenesis and its link with COPD clinical features. We also provide insights into the SHH pathway linked with the nicotine pathway and gut–lung axis and their influence on COPD pathogenesis.
Background: Fibroblast Growth Factor 9 (Fgf9) and its paralog Fgf20 are expressed in the developing stomach. We investigate the role of these growth factors during gastric development, using combinations of null alleles. Results: Analysis of expression databases showed that Fgf9 is expressed in gastric endoderm and surrounding mesoderm such as the mesothelium as early as E8.5, and Fgf20 is expressed in the gastric progenitors of the glandular stomach. To explore whether Fgf9 and Fgf20 are important for gastric development, we examined embryonic stomachs from Fgf9 and Fgf20 null (Fgf9(LacZ/LacZ) and Fgf20(Cre.GFP/Cre.GFP)) mice during development. At E18.5, Fgf9(LacZ/LacZ) stomachs were hypoplastic, lacking the squamous forestomach. No changes to glandular stomach differentiation were observed using representative markers of glandular lineages. Fgf9(LacZ/LacZ )stomachs were smaller during early development (E12.5 and E15.5). RNA-seq analysis of Fgf9(LacZ/LacZ) mice at E15.5 showed that squamous-epithelium-associated transcripts were underrepresented, and glandular epithelial transcripts were overrepresented. Analysis of gastric patterning at E12.5 revealed loss of early squamous progenitors in the epithelium, characterized by loss of SOX2(+); GATA4(-) cells. We further show that loss of Fgf20 does not alone impact gastric development nor modify the Fgf9(LacZ/LacZ )phenotype. Conclusions: Fgf9 drives gastric growth and squamous epithelial identity during gastric development.
