Search Results (63)

Tooth agenesis is a common developmental anomaly of the human dentition, ranging from hypodontia to oligodontia, yet its marked phenotypic variability remains insufficiently explained. This review synthesizes developmental and molecular evidence on epithelial–mesenchymal interactions during early odontogenesis and proposes a signaling-threshold framework for human tooth agenesis. We focus on the coordinated roles of Wnt/β-catenin, bone morphogenetic protein (BMP), fibroblast growth factor (FGF), and Sonic hedgehog (SHH) pathways and on recurrent disease-associated genes, including MSX1, PAX9, WNT10A, and AXIN2, as quantitative modulators of pathway activity rather than binary determinants of tooth identity. Within this framework, successful tooth initiation may depend on whether integrated signaling output exceeds a field-specific activation threshold within spatially graded developmental regions of the dental arch. Differences in signaling amplitude, duration, and transcriptional responsiveness may therefore account for distal tooth susceptibility, variable penetrance, arch asymmetry, and the broad clinical spectrum from mild hypodontia to severe oligodontia. By integrating molecular genetics with developmental field theory, this model provides a testable systems-level explanation for selective tooth absence and highlights priority directions for future functional and genotype–phenotype studies. Full article

Tooth development or odontogenesis is a complex morphogenetic process that requires tightly regulated interactions between the oral epithelium and mesenchyme of neural crest origin. In this narrative review, we compile existing knowledge regarding gene regulatory networks and epigenetic factors throughout tooth development from initiation to eruption. Signaling between the epithelium and mesenchyme is mediated by four conserved pathways—Wnt/β-catenin, bone morphogenetic protein (BMP), fibroblast growth factor (FGF), and Sonic hedgehog (Shh)—which operate iteratively and interact through extensive crosstalk at each developmental stage. Transcription factors, such as PAX9, MSX1, PITX2, and LEF1, interpret these signals to control cell fate decisions and differentiation. Epigenetic modifications, including DNA methylation, histone modifications, and microRNA-mediated regulation, provide additional layers of control that fine-tune gene expression programs. Unlike existing reviews that address these regulatory mechanisms separately, here we integrate signaling pathways, transcription factor networks, epigenetic regulation, human genetic disorders, dental stem cell biology, and recent single-cell transcriptomic insights into a unified framework. We discuss opportunities to apply developmental biology knowledge towards regenerative dentistry goals, including iPSC-derived dental models and spatially resolved multi-omics approaches, while acknowledging the considerable gap between preclinical findings and clinical applications. Full article

The LAP2–emerin–MAN1-domain (LEM-D) proteins constitute a family of inner nuclear membrane proteins that play essential roles in the spatial regulation of intranuclear signaling. Defined by the conserved LEM domain, these proteins interact with chromatin, nuclear lamins, and barrier-to-autointegration factor (BAF), thereby linking nuclear architecture to signal-dependent transcriptional control. This review summarizes current knowledge on the structural features and molecular functions of representative LEM-D proteins, including LAP2, emerin, and MAN1, with a particular focus on their emerging roles as regulators of intranuclear signaling pathways. We discuss how these proteins modulate the activity of transcription factors involved in Hedgehog, Wnt/β-catenin, STAT3, Notch, and transforming growth factor-β (TGF-β) signaling by temporally retaining them at the inner nuclear membrane and controlling their access to chromatin. Furthermore, this review highlights the physiological and pathological relevance of LEM-D-mediated signaling regulation, especially in the context of muscle development, regeneration, and nuclear envelope-associated diseases such as muscular dystrophies. By integrating structural, signaling, and disease-related perspectives, this review proposes a conceptual framework in which LEM-D proteins function as critical intranuclear signaling hubs. Understanding these mechanisms provides new insights into nuclear signal transduction and suggests potential therapeutic targets for diseases associated with nuclear envelope dysfunction. Full article

While the PI3K/Akt/mTOR pathway is a well-established drug target in T-cell acute lymphoblastic leukemia (T-ALL), the contribution of the Hedgehog (Hh) pathway in T-ALL malignancy remains poorly defined. We investigated the effects of pharmacological inhibition of key signaling nodes in these pathways using T-ALL cell lines (Jurkat, Molt-4, DND-41, and ALL-SIL). Cells were treated with the Gli1 inhibitor Gant-61, the Smoothened inhibitors GDC-0449 and Glasdegib, the Akt inhibitor MK-2206, and the mTOR inhibitor RAD001, both alone and in combination. Analyses of cell viability, cell cycle progression, apoptosis, autophagy, protein expression, and in situ intracellular distribution revealed potent cytotoxic activity of Gant-61 and MK-2206, while Smo and mTOR inhibitors showed limited efficacy. Combined Gli1 and Akt inhibition induced synergistic suppression of proliferation, enhanced G0/G1 arrest, increased apoptosis, and promoted autophagy, accompanied by reduced nuclear Gli1 and decreased Akt phosphorylation. These findings demonstrate a functional interaction between Hh/Gli1 and PI3K/Akt pathways in T-ALL and identify Gli1 as a critical, druggable node. Dual targeting of Gli1 and Akt represents a potential therapeutic strategy to overcome resistance and improve treatment outcomes in T-ALL. Full article

Background/Objectives: Non-syndromic tooth agenesis (NSTA) is a congenital condition that causes the absence of one or more teeth without accompanying systemic abnormalities, which significantly affects quality of life. Genetic factors, including mutations in several specific genes, contribute to the pathogenesis of NSTA. This study investigates a novel EVC2 mutation in a patient with NSTA and explores its potential pathogenic mechanism, with the aim of enriching the spectrum of pathogenic genes. Methods: Whole-exome sequencing (WES) was performed on peripheral blood samples from a patient diagnosed with NSTA. Bioinformatics analysis was utilized to identify the mutation and assess its potential impact on protein structure and function. Molecular dynamics simulations were conducted to analyze structural alterations in the EVC2 protein. The binding affinity between EVC2, EVC, and Smoothened (SMO) was to determine the effect of mutation on protein–protein interaction. Protein localization and expression were analyzed using immunofluorescence and Western blotting. Reverse transcription quantitative PCR (RT-qPCR) was employed to evaluate downstream signaling pathway alterations. Results: A novel EVC2 mutation (c.1657_1660delinsA, p.Glu553_leu554delinsMet) was identified in the proband, and the mutation was maternally inherited. Molecular dynamics simulations revealed that the mutation resulted in a decrease in α-helical content and significant conformational changes in the protein structure. This led to reduced binding affinity between EVC2 and its ligands EVC and SMO, destabilizing the structural integrity of the protein complex. Despite these structural changes, EVC2 protein localization and expression were unaffected. Furthermore, a downregulation of GLI1 and SHH expression was observed, indicating impaired Hedgehog (Hh) signaling. The downregulation of the Hh signaling pathway impairs the tooth development process and may lead to the occurrence of tooth agenesis. Conclusions: A novel EVC2 mutation was identified in a patient with NSTA. Based on molecular dynamics simulations, it is hypothesized that this EVC2 variant could contribute to the pathogenesis of NSTA by impairing the EVC2-EVC-SMO complex formation, which may lead to downregulation of downstream GLI1 and SHH. These findings provide new insights into the molecular mechanisms underlying EVC2-mediated NSTA, suggesting that disruption of Hh signaling may represent a critical pathogenic mechanism. Full article

Mealybugs are high-priority quarantine pests in fresh-produce trade due to cryptic habits, broad host ranges, and market-access risks. Phytosanitary irradiation (PI) provides a non-residual, process-controlled option that is increasingly integrated with modified-atmosphere (MA/MAP) logistics. Because molecular oxygen enhances indirect radiation damage (oxygen enhancement ratio, OER), oxygen limitation may modulate PI outcomes in mealybugs. The Jack Beardsley mealybug (Pseudococcus jackbeardsleyi) has an IPPC-adopted PI treatment of 166 Gy (ISPM 28, PT 45). We exposed adult females to 166 Gy under air and 1% O₂ and generated whole-transcriptome profiles across treatments. Differentially expressed genes and co-differentially expressed genes (co-DEGs) were integrated with protein–protein interaction (PPI) and regulatory networks, and ten hubs were validated by reverse transcription quantitative PCR (RT-qPCR). Hypoxia attenuated irradiation-induced transcriptional disruption. Expression programs shifted toward transport, redox buffering, and immune readiness, while morphogen signaling (Wnt, Hedgehog, BMP) was coherently suppressed; hubs including wg, hh, dpp, and ptc showed stronger down-regulation under hypoxia + irradiation than under irradiation alone. Despite these molecular differences, confirmatory bioassays at 166 Gy under both atmospheres (air and 1% O₂) achieved complete control. These results clarify how oxygen limitation modulates PI responses in a quarantine mealybug while confirming the operational efficacy of the prescribed 166 Gy dose. Practically, they support the current international standard and highlight the value of documenting oxygen atmospheres and managing dose margins when PI is applied within MA/MAP supply chains. Full article

To investigate the impacts of dietary Bacillus-based probiotics and yeast-derived prebiotics on the hepatic transcriptome profile, 500 Hisex White laying hens were randomly allotted into five dietary treatments from 37 to 52 weeks of age: control; control + Bacillus subtilis; control + Bacillus subtilis and Bacillus licheniformis; control + Bacillus coagulans; and control + Saccharomyces cerevisiae yeast cell wall. Transcriptome analysis revealed a substantial number of differentially expressed genes exclusively between the control and prebiotic groups, identifying 2221 genes (FDR ≤ 0.05), with 980 genes upregulated (log₂ fold change 0.69 to 24.62) and 1241 downregulated (log₂ fold change −0.74 to −26.46). The top 10 upregulated KEGG pathways included protein export, glycerophospholipid metabolism, tryptophan metabolism, amino acid biosynthesis, alanine, aspartate, and glutamate metabolism, cofactor biosynthesis, propanoate metabolism, ABC transporters, 2-oxocarboxylic acid metabolism, and protein processing within the endoplasmic reticulum. In contrast, the most prominently downregulated pathways encompassed fructose and mannose metabolism, hedgehog signaling, PPAR signaling, Notch signaling, GnRH signaling, cell adhesion molecules, cytokine–cytokine receptor interactions, apelin signaling, glycosaminoglycan degradation, and RIG-I-like receptor signaling. These findings advance understanding of the hepatic transcriptomic response to yeast-derived prebiotics and identify key molecular pathways that could be targeted to enhance metabolic function in laying hens. Full article

Tooth development (odontogenesis) is regulated by interactions between epithelial and mesenchymal tissues through signaling pathways such as Bone Morphogenetic Protein (BMP), Wingless-related integration site (Wnt), Sonic Hedgehog (SHH), and Fibroblast Growth Factor (FGF). Mesenchymal stem cells (MSCs) derived from dental tissues—including dental pulp stem cells (DPSCs), periodontal ligament stem cells (PDLSCs), and dental follicle progenitor cells (DFPCs)—show promise for regenerative dentistry due to their multilineage differentiation potential. Epigenetic regulation, particularly DNA methylation, is hypothesized to underpin their distinct regenerative capacities. This study reanalyzed publicly available DNA methylation data generated with Illumina Infinium HumanMethylation450 BeadChip arrays (450K arrays) from DPSCs, PDLSCs, and DFPCs. High-confidence CpG sites were selected based on detection p-values, probe variance, and genomic annotation. Principal Component Analysis (PCA) and hierarchical clustering identified distinct methylation profiles. Functional enrichment analyses highlighted biological processes and pathways associated with specific methylation clusters. Noncoding RNA analysis was integrated to construct regulatory networks linking DNA methylation patterns with key developmental genes. Distinct epigenetic signatures were identified for DPSCs, PDLSCs, and DFPCs, characterized by differential methylation across specific genomic contexts. Functional enrichment revealed pathways involved in odontogenesis, osteogenesis, and neurodevelopment. Network analysis identified central regulatory nodes—including genes, such as PAX6, FOXC2, NR2F2, SALL1, BMP7, and JAG1—highlighting their roles in tooth development. Several noncoding RNAs were also identified, sharing promoter methylation patterns with developmental genes and being implicated in regulatory networks associated with stem cell differentiation and tissue-specific function. Altogether, DNA methylation profiling revealed that distinct epigenetic landscapes underlie the developmental identity and differentiation potential of dental-derived mesenchymal stem cells. This integrative analysis highlights the relevance of noncoding RNAs and regulatory networks, suggesting novel biomarkers and potential therapeutic targets in regenerative dentistry and orthodontics. Full article

Basal cell carcinoma (BCC), the most common skin cancer, is primarily driven by Hedgehog (Hh) and TP53 pathway alterations. Although additional pathways were implicated, the mutational landscape in Asian populations, particularly Koreans, remains underexplored. We performed whole-exome sequencing of BCC tumor tissues from Korean patients and analyzed mutations in 11 established BCC driver genes (PTCH1, SMO, GLI1, TP53, CSMD1/2, NOTCH1/2, ITIH2, DPP10, and STEAP4). Mutational profiles were compared with Caucasian cohort profiles to identify ethnicity-specific variants. Ultraviolet (UV)-exposed and non-UV-exposed tumor sites were compared; genes unique to non-UV-exposed tumors were further analyzed with protein–protein interaction analysis. BCCs in Koreans exhibited distinct features, including fewer truncating and more intronic variants compared to Caucasians. Korean-specific mutations in SMO, PTCH1, TP53, and NOTCH2 overlapped with oncogenic gain-of-function/loss-of-function (GOF/LOF) variants annotated in OncoKB, with some occurring at hotspot sites. BCCs in non-exposed areas showed recurrent mutations in CSMD1, PTCH1, and NOTCH1, suggesting a UV-independent mechanism. Novel mutations in TAS1R2 and ADCY10 were exclusive to non-exposed BCCs, with protein–protein interaction analysis linking them to TP53 and NOTCH2. We found unique ethnic-specific and UV-independent mutational profiles of BCCs in Koreans. TAS1R2 and ADCY10 may contribute to tumorigenesis of BCC in non-exposed areas, supporting the need for population-specific precision oncology. Full article

Recently, there has been a gradual increase in the demand for chicken and eggs. The gut, as the vital place of nutrient digestion and absorption, is highly associated with the development of livestock and poultry and the quality of meat, eggs, and milk. Intestinal stem cells, as an important source of intestinal cell proliferation and renewal, exert a vital effect on repairing injured intestinal epithelial cells and keeping homeostasis. Intestinal stem cell-regulated intestinal epithelial balance is closely controlled and modulated by interlinked developmental loops that maintain cell proliferation and differentiation processes in balance. Some conservative signaling pathways, including the Wnt, Notch, hedgehog, and bone morphogenetic protein (BMP) loops, have been proved to modulate intestinal health in poultry. Meanwhile, studies have revealed the importance of the Hippo pathway in gastrointestinal tract physiology by regulating intestinal stem cells. Moreover, crosstalk between Hippo and other signaling pathways provides tight, yet versatile, regulation of tissue homeostasis. In this review, we summarize studies on the role of the Hippo pathway in the intestine in these physiological processes and the underlying mechanisms responsible via interacting with these signaling pathways and discuss future research directions and potential therapeutic strategies targeting Hippo signaling in intestinal disease. A comprehensive understanding of how these signaling pathways regulate stem cell proliferation, differentiation, and self-renewal will help to understand the regulation of intestinal homeostasis. In addition, it has the capacity for creative ways to govern intestinal damage, enteritis, and associated disorders induced by different factors. Full article

Insulin-like growth factors (IGFs) play crucial roles in the regulation of animal growth and reproduction. However, the functional and regulatory mechanisms underlying ovarian growth and oocyte maturation in teleosts remain unclear. In this study, the expression profiles of lncRNAs and mRNAs were analyzed in the ovaries of golden pompano (Trachinotus ovatus) treated with IGF1 and IGF2 proteins to gain insights into the role of these two IGF ligands in the regulation of ovarian development and maturation. A total of 1494 lncRNAs and 8728 mRNAs were differentially expressed following IGF1 treatment compared with the control group. A total of 101 lncRNAs and 377 mRNAs were differentially expressed after IGF2 treatment compared to those in the control group. The results revealed that KEGG pathways enriched by target genes of the DE lncRNAs overlapped significantly with those enriched by the DE mRNAs in both the IGF1 and IGF2 groups. The key overlapping enriched pathways included ECM receptor interaction, gap junction, Hedgehog signaling pathway, Ras signaling pathway, Rap1 signaling pathway, TGF beta signaling pathway, Wnt signaling pathway, GnRH signaling pathway, progesterone-mediated oocyte maturation, oocyte meiosis, cell cycle, and MAPK signaling pathway. The differentially expressed genes (DEGs) involved in ovarian development and oocyte maturation were cyp17a1, cyp19a1, star, hsd17b3, hsd17b7, adam23, slc26a6, htr2b, h2ax, nanos3, krt18, pgr, and inhbb, following IGF1 and IGF2 treatment. Furthermore, four lncRNAs (MSTRG.66521.1, MSTRG.49969.1, MSTRG.59923.1, and MSTRG.13767.1) for IGF1 and two (MSTRG.20896.2 and MSTRG.58123.2) for IGF2 within the lncRNA–mRNA network were found to target DEGs related to ovarian development and maturation. This suggests that IGFs may affect reproductive processes by regulating the expression of lncRNAs and mRNAs. RT-qPCR analysis revealed that these six lncRNAs showed high expression levels in the brain, pituitary, liver, and gonad tissues, indicating their potential involvement in regulating ovarian growth and development. This study elucidates the lncRNA–mRNA regulatory mechanism in response to IGF1 and IGF2 treatment during stage III of ovarian development in golden pompano, thereby deepening our understanding of its functional role. Full article

Background: The rising rates of gallstones and cholecystectomy in pediatric populations underscore the increasing concern regarding chronic cholecystitis. However, the morphopathogenesis of pediatric calculous cholecystitis is still not well understood. This study aimed to determine the expression and distribution of immunomodulatory factors interleukin-12 (IL-12), interleukin-13 (IL-13), interleukin-1β (IL-1β), sonic hedgehog protein (SHH), nuclear factor NF-kappa-B p65 subunit (NFkBp65), and heat shock protein 60 (HSP60) in the gallbladder walls of pediatric patients with chronic calculous cholecystitis. Methods: In total, 11 gallbladder samples were collected from pediatric patients with calculous cholecystitis during cholecystectomy, while 5 healthy gallbladder samples served as controls. IL-12, IL-13, IL-1β, SHH, NFkBp65, and HSP60 were detected by immunohistochemistry. The number of positive structures in gallbladder wall epithelium, vasculature, and inflammatory infiltrate was assessed semi-quantitatively by microscopy. A Mann–Whitney U test and Spearman’s rank-order correlation coefficient were calculated. Results: Statistically significant differences were observed between patient and control samples in the expression of IL-1β, SHH, and NFkBp65 in the epithelium, as well as in the expression of IL-12, SHH, and HSP60 in the blood vessels. The expression of IL-1β was stronger in the epithelium of controls, while other markers were more prominent in patient samples. Conclusions: An increased number of NFkBp65, IL-12, and HSP60 positive cells in patient gallbladder tissue suggests a significant role of these tissue factors in driving immune modulation and sustaining the inflammation in pediatric chronic calculous cholecystitis. The noticeable expression of SHH in patient gallbladder tissue indicates its part in tissue regeneration and repair processes, as well as in modulating inflammation and vascular responses in calculous cholecystitis. The significant positive correlations between the factors studied highlight the importance of their coordinated interaction and intricate crosstalk in the morphopathogenesis of calculous cholecystitis. Full article

Background/Objectives: Pancreatic adenocarcinoma (PDAC) remains one of the most lethal cancers, with limited advancements in treatment efficacy due to high rates of chemoresistance. Circulating tumor cells (CTCs) derived from liquid biopsies offer a non-invasive approach to monitoring tumor evolution and identifying molecular mechanisms of resistance. This study aims to longitudinally collect, culture, and characterize CTCs from PDAC patients to elucidate resistance mechanisms and tumor-specific gene expression profiles. Methods: Blood samples from 10 PDAC patients were collected across different treatment stages, yielding 16 CTC cultures. Differential gene expression, pathway dysregulation, and protein–protein interaction studies were utilized, highlighting patient-specific and disease progression-associated changes. Longitudinal comparisons within five patients provided further insights into dynamic molecular changes associated with therapeutic resistance. Results: CTC cultures exhibited the activation of key pathways implicated in PDAC progression and resistance, including TNFα/NF-kB, hedgehog signaling, and the epithelial-to-mesenchymal transition. Longitudinal samples revealed dynamic changes in signaling pathways, highlighting upregulated mechanisms of chemoresistance, including PI3K/Akt/mTOR and TGF-β pathways. Additionally, protein–protein interaction analysis emphasized the role of the immune system in PDAC progression and therapy response. Patient-specific gene expression patterns therefore suggest potential applications for precision medicine. Conclusions: This proof-of-concept study demonstrates the feasibility of longitudinally capturing and analyzing CTCs from PDAC patients. The findings provide critical insights into molecular drivers of chemoresistance and highlight the potential of CTC profiling to inform personalized therapeutic strategies. Future large-scale studies are warranted to validate these findings and further explore CTC-based approaches in PDAC management. Full article

Myeloproliferative neoplasms (MPNs) are characterized by increased proliferation of myeloid lineages in the bone marrow. Calreticulin (CALR) 52 bp deletion and CALR 5 bp insertion have been identified in essential thrombocythemia (ET) and primary myelofibrosis (PMF). There is not much data on the crosstalk between mutated CALR and MPN-related signaling pathways, such as JAK/STAT, PI3K/Akt/mTOR, and Hedgehog. Calreticulin, a multifunctional protein, takes part in many cellular processes. Nevertheless, there is little data on how mutated CALR affects the oxidative stress response and oxidative stress-induced DNA damage, apoptosis, and cell cycle progression. We aimed to investigate the role of the CALR 52 bp deletion and 5 bp insertion in the pathogenesis of MPN, including signaling pathway activation and functional analysis in CALR-mutated cells. Our data indicate that the JAK/STAT and PI3K/Akt/mTOR pathways are activated in CALR-mutated cells, and this activation does not necessarily depend on the CALR and MPL interaction. Moreover, it was found that CALR mutations impair calreticulin function, leading to reduced responses to oxidative stress and DNA damage. It was revealed that the accumulation of G2/M-CALR-mutated cells indicates that oxidative stress-induced DNA damage is difficult to repair. Taken together, this study contributes to a deeper understanding of the specific molecular mechanisms underlying CALR-mutated MPNs. Full article

Mutations in human CILK1 (ciliogenesis associated kinase 1) are linked to ciliopathies and epilepsy. Homozygous point and nonsense mutations that extinguish kinase activity impair primary cilia function, whereas mutations outside the kinase domain are not well understood. Here, we produced a knock-in mouse equivalent to the human CILK1 A615T variant identified in juvenile myoclonic epilepsy (JME). This residue is in the intrinsically disordered C-terminal region of CILK1 separate from the kinase domain. Mouse embryo fibroblasts (MEFs) with either heterozygous or homozygous A612T mutant alleles exhibited a higher ciliation rate, shorter individual cilia, and upregulation of ciliary Hedgehog signaling. Thus, a single A612T mutant allele was sufficient to impair primary cilia and ciliary signaling in MEFs. Gene expression profiles of wild-type versus mutant MEFs revealed profound changes in cilia-related molecular functions and biological processes. The CILK1 A615T mutant protein was not increased to the same level as the wild-type protein when co-expressed with scaffold protein KATNIP (katanin-interacting protein). Our data show that KATNIP regulation of a JME-associated single-residue variant of CILK1 is compromised, and this impairs the maintenance of primary cilia and Hedgehog signaling. Full article