Search Results (161)

Non-small-cell lung cancer (NSCLC) constitutes approximately all lung cancers (LCs), and metastasis remains a major challenge in its treatment, thus necessitating the detection of novel molecular players involved in this process. In this study, we performed a comprehensive analysis of microarray and RNA-seq cohorts extracted from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) to identify differentially expressed genes (DEGs) and differentially expressed miRNAs (DEMs) and associated them with metastasis-related genes involved in brain metastasis (BM) in NSCLC. We thus identified differentially expressed metastatic genes (DEMGs) and constructed a protein–protein interaction network (PPIN) using these DEMGs. These DEMGs were further analyzed for associations with patient age, gender, and tumor stage, and the significant impact of specific genes on overall survival (OS) was assessed to determine the prognostic significance of the identified targets. We finally constructed a three-node microRNA (miRNA) feed-forward loop (FFL) involving miR-23b-3p, CD44, and five transcription factors (TFs) [EOMES, FOS, FOSL1, GLIS3, TP63] specific to NSCLC metastasis. Further mutational analysis of these FFL elements revealed that all were altered in the patient samples analyzed. Thus, our study identified potential genomic drivers that may play crucial roles in NSCLC BM. Overall, it provides valuable insights for the discovery of novel therapeutic targets in the management of NSCLC metastasis. However, further in vitro and in vivo experimentations are needed to justify the prognostic role of NSCLC biomarkers in BM pathogenesis. Full article

Background/Objectives: Craniofacial malformations such as orofacial clefts affect ~1 in 700 births; 40–60% lack clear genetic etiology, and many exhibit asymmetry and variable expressivity unexplained by classical Sonic Hedgehog (SHH) morphogen gradient models. We investigated whether integrated molecular modules linking morphogen signaling with metabolic stress responses may better account for craniofacial developmental outcomes. Methods: Sequential UniProt gene set integration identified 186 candidate craniofacial regulators. STRING network analysis revealed modular architecture. Molecular docking profiled 17 compounds against SMO, CK1δ, PINK1, and TIE2 (control). Pathway reconstruction integrated the SHH–CK1δ–HIF1A–HEY1–PINK1 axis with in-silico-predicted CK1δ phosphorylation sites on SMO (S615, T593, S751), HIF1A (Ser247), and GLI1/2/3 transcription factors. A developmental decision tree mapped affinity profiles to node-specific phenotype hypotheses. Results: CK1δ and PINK1 emerged as candidate nodes coupling morphogen signaling with mitochondrial quality control. Cross-docking showed preferential binding to developmental kinases (CK1δ: −8.34 kcal/mol; PINK1: −8.80 kcal/mol) versus TIE2 control (−6.76 kcal/mol; p < 0.001). Pathway reconstruction suggested that CK1δ-mediated Ser247 phosphorylation of HIF1A disrupts ARNT dimerization, redirecting HIF1A toward ARNT-independent HEY1 induction and consequent PINK1 suppression. Based on computed profiles, node-specific associations were proposed as computational hypotheses: SMO perturbation → midline defects; CK1δ → facial asymmetry/clefting; PINK1 → mandibular hypoplasia. Multi-target compounds (e.g., purmorphamine, taladegib) generated composite phenotype predictions consistent with clinical complexity. Conclusions: This strictly in silico study identifies candidate integrated morphogenic modules whose multi-node perturbation may underlie anatomically specific craniofacial malformation patterns. Node–phenotype associations are prioritized computational hypotheses requiring experimental validation; if confirmed, the framework could inform developmental toxicity assessment, therapeutic design, and reclassification of idiopathic craniofacial anomalies. Full article

Neonatal Diabetes Mellitus (NDM) is a rare, heterogeneous monogenic disorder typically presenting within the first six months of life. Unlike type 1 or type 2 diabetes, NDM is caused by single-gene mutations that disrupt pancreatic β-cell function or development. With the advent of next-generation sequencing, the genetic spectrum of NDM has expanded significantly, necessitating a shift from symptomatic management to precision medicine. This narrative review summarizes the genetic basis and pathogenic mechanisms of NDM, categorizing them into three major pathways: (1) ATP-sensitive potassium (K_ATP) channelopathies (e.g., ABCC8, KCNJ11), where gain-of-function mutations inhibit insulin secretion; (2) Transcription factor defects (e.g., GLIS3, PAX6, GATA6), which impair pancreatic development and often present with syndromic features; and (3) Endoplasmic reticulum (ER) stress-mediated β-cell apoptosis, exemplified by WFS1 mutations. Furthermore, we highlight the clinical complexity of these mutations, including the “biphasic phenotype” observed in ABCC8 and HNF1A variants. Understanding these molecular mechanisms is critical for clinical decision-making. We discuss the transformative impact of genetic diagnosis in treatment, particularly the successful transition from insulin to oral sulfonylureas in patients with K_ATP channel mutations, and emphasize the importance of early genetic testing to optimize glycemic control and prevent complications. Full article

Glioblastoma (GBM) is the most prevalent and devastating form of primary brain tumors in adults, with dismal survival despite advancements in treatment modalities. The current study sought to develop clinically significant prognostic models for GBM patients by comprehensively profiling MGMT, NUPR1, NDRG2, and GLI1 gene promoter methylation in GBM tissues vs. non-neurooncological disease (NND) and their association with clinical characteristics and therapeutic outcome. This was further evaluated by in silico functional enrichment analysis. NUPR1, NDRG2, and GLI1 gene promoter methylation were significant epigenetic discriminators between GBM and NND. However, NDRG2 methylation was the sole independent predictor for neoplastic lesions (OR = 1.71, 95% CI [1.25–3.57], p = 0.028). Multivariable Cox regression analysis revealed that NUPR1 promoter hypermethylation was significantly correlated with a lower risk of mortality (HR = 0.96, 95% CI [0.96–0.99], p = 0.002), while multiple tumor sites were linked to an increased risk of mortality in the univariate model (HR = 4.44, 95% CI [1.42–13.88], p = 0.01). A heatmap correlation matrix identified a robust positive correlation among the MGMT and NUPR1 methylation status (r = 0.93, p < 0.001). NUPR1 and MGMT promoter hypermethylation was associated with a favorable response to temozolomide therapy. Patients with NUPR1 and MGMT hypermethylation exhibited extended OS and PFS compared to those with hypomethylation levels, whereas GLI1 and NDRG2 hypermethylation were linked to shorter PFS. In conclusion, the multi-faceted epigenetic panel adopted in the current study captures different aspects of GBM biology and moves towards a more comprehensive model that reflects the molecular heterogeneity of GBM as insights for personalized therapy. Full article

The development of RNA-based drugs for MAFLD-related fibrosis is severely hampered by the poor oral bioavailability of nucleic acids. This study employed a novel, patent-protected LNP formulation to orally deliver plant-derived miR-55 and investigate its therapeutic potential, focusing on its novel mechanism of action via the CK2α/SMO interaction. In a rat model established with a methionine-choline-deficient diet, orally administered miR-55 markedly improved liver injury, lipid dysregulation, oxidative stress, and pathological collagen deposition. The anti-fibrotic efficacy was quantitatively confirmed by a significant reduction in hepatic hydroxyproline content and downregulation of key fibrogenic genes (Col1a1, Col3a1, TIMP-1, TGF-β1, CTGF) and pro-inflammatory cytokines (TNF-α, IL-6), achieving effects comparable to the full Ge Xia Zhu Yu Decoction. Mechanistically, both bioinformatic prediction and in vivo validation indicated that miR-55 is predicted to target CK2α. This targeting suppressed CK2α expression and disrupted the endogenous CK2α-SMO complex, thereby promoting the ubiquitin-mediated degradation of SMO—a previously unreported mechanism. This cascade inhibited the downstream Gli1 pathway and downregulated pro-fibrotic and pro-angiogenic factors (VEGF, PDGF), thereby providing a comprehensive mechanistic basis for the therapeutic effects. This study is the first to provide evidence that orally delivered, plant-derived miR-55 may act as a natural modulator that potentially through disrupting the CK2α/SMO interaction via a unique complex disruption-promoted degradation mechanism, attenuating Hedgehog signaling and alleviating liver fibrosis. These findings offer important insights into cross-kingdom regulation and highlight miR-55 as a potential targeted therapeutic candidate. Full article

Background: Emerging evidence suggests that biological sex shapes glioma biology and therapeutic response. Methods: We performed a sex-stratified analysis of CGGA (Chinese Glioma Genome Atlas) RNA sequencing data comparing low-grade glioma (LGG) with high-grade glioma (HGG) and glioblastoma (GBM). Using the 3PodR framework, we integrated differential expression analysis with Gene Set Enrichment Analysis (GSEA), EnrichR, leading-edge analysis, and iLINCS drug repurposing. Results: These comparisons provide a proxy for biological processes underlying malignant transformation. In LGG vs. HGG, 973 significantly differentially expressed genes (DEGs) were identified in females and 1236 in males, with 15.5% and 33.5% unique to each sex, respectively. In LGG vs. GBM, 2011 DEGs were identified in females and 2537 in males, with 12.6% and 30.7% being unique. Gene-level contrasts included GLI1 upregulation in males and downregulation in females, GCGR upregulation in males, MYOD1 upregulation in females, and HIST1H2BH downregulation in males. Additional top DEGs included PRLHR, DGKK, DNMBP-AS1, HOXA9, CTB-1I21.1, RP11-47I22.1, HPSE2, SAA1, DLK1, H19, PLA2G2A, and PI3. In both sexes, LGG–HGG and LGG–GBM grade comparisons converged on neuronal and synaptic programs, with enrichment of glutamatergic receptor genes and postsynaptic modules, including GRIN2B, GRIN2A, GRIN2C, GRIN1, and CHRNA7. In contrast, collateral pathways diverged by sex: females showed downregulation of mitotic and chromosome-segregation programs, whereas males showed reduction of extracellular matrix and immune-interaction pathways. Perturbagen analysis nominated signature-reversing compounds across sexes, including histone deacetylase inhibitors, Aurora kinase inhibitors, microtubule-targeting agents such as vindesine, and multi-kinase inhibitors targeting VEGFR, PDGFR, FLT3, PI3K, and MTOR. Conclusions: Glioma grade comparisons reveal a shared neuronal–synaptic program accompanied by sex-specific transcriptional remodeling. These findings support sex-aware therapeutic strategies that pair modulation of neuron–glioma coupling with chromatin- or receptor tyrosine kinase/angiogenic-targeted agents, and they nominate biomarkers such as GLI1, MYOD1, GCGR, PRLHR, and HIST1H2BH for near-term validation. Full article

Basal cell carcinoma (BCC) is the most common skin cancer, predominantly affecting sun-exposed areas. It typically grows slowly and rarely metastasizes, though untreated cases can cause significant tissue destruction and morbidity. Its pathogenesis primarily involves dysregulation of the Hedgehog (HH) signaling pathway, mainly through mutations in PTCH1 or SMO genes, leading to chronic activation of downstream GLI transcription factors. Accordingly, current targeted therapies for locally advanced, unresectable, or metastatic BCC focus on SMO inhibition, using orally administered drugs such as vismodegib and sonidegib. Although these therapies have shown success, many patients develop resistance, with about 50% harboring mutated SMO. In numerous cases, genetic determinants (sometimes pre-existing) of resistance remain unidentified, complicating patient management. Here, we report a case of a 58-year-old female with advanced BCC who initially exhibited a favorable response to sonidegib but developed resistance after approximately one year. This resistance was not attributable to the acquired mutations in SMO but rather to intra-tumor heterogeneity and additional mutations in critical driver genes, including TP53, APC, FGFR1 and NOTCH1, which likely enable HH pathway inhibition. To our knowledge, this is the first report documenting a sonidegib resistance mechanism in BCC that is independent of HH pathway mutations. This case highlights the complexity of resistance mechanisms to HH inhibitors and underscores the critical need for comprehensive molecular tumor profiling prior to initiating targeted therapy. Full article

Sesquiterpene lactones (SLs) are plant-derived metabolites with recognized pharmacological properties. Dysfunction of the primary cilium (PC), a solitary sensory organelle essential for development, is associated with disorders such as ciliopathies and tumors. While previous studies have shown that certain SLs can alter PC structure in human retinal cells, their influence on ciliary signaling pathways remains unclear. In this study, we examined the effect of four SLs—grosheimin, costunolide, α-cyclocostunolide (α-C), and β-cyclocostunolide (β-C)—on ciliary function in human primary fibroblasts. Using immunofluorescence and qPCR to assess cilia structure and Hedgehog (Hh) pathway activation, we found that grosheimin enhanced ciliogenesis without affecting Hh signaling. In contrast, costunolide, α-C, and β-C disrupted ciliary structure and suppressed the Hh pathway transcripts Gli1 and Ptch1. RNA sequencing revealed that grosheimin upregulated genes related to microtubule binding and ciliogenesis, whereas α-C downregulated tubulin subunit transcripts. These findings suggest distinct molecular mechanisms through which SLs affect ciliary structure and function. Collectively, this study highlights the potential of specific SLs as modulators of ciliary signaling, offering promising leads for therapeutic strategies targeting ciliopathies and tumors. Full article

The Krüppel-like transcription factor GLIS3 plays an important regulatory role in the development of various tissues, both in mice and humans. Loss-of-function mutations in GLIS3 are implicated in several pathologies, including polycystic kidney disease, diabetes, and hypothyroidism. Previous studies have reported that the mouse Glis3 gene generates a 7524 bp mRNA encoding a 935 amino acid (aa) protein, with a homologous human protein of 930 aa. Here, we identify a shorter mouse mRNA lacking the third exon, producing a shorter 659 aa GLIS3 protein. This shorter transcript is expressed at a higher level than the longer transcript in all mouse tissues tested and produces a protein that is more stable and exhibits a greater transactivation potential. This suggests that the 276 aa N-terminus in the longer mouse GLIS3 protein encompasses important regulatory domain(s). Mass spectrometry identified several phosphorylation sites that may contribute to the post-translational regulation of GLIS3 activity and function and several known members of co-activator and co-repressor complexes, consistent with the concept that GLIS3 can act both as a transcriptional repressor and activator. These data offer important insights into how GLIS3 activity is regulated and offer potential mechanisms for its control during tissue development and disease. Full article

Morphoeic basal cell carcinoma (mBCC) has a higher risk of local recurrence than the more indolent nodular (nodBCC) subtype. Little is known about the genetic and molecular makeup of mBCC that determines its invasive behaviour: a comparison of mBCC with nodBCC was carried out. Whole-exome sequencing (WES) of 20 BCC tumours (10 eyelid morphoeic and 10 nodular) underwent driver gene detection using OncodriveFM and MutSigCV, followed by a randomisation analysis procedure. Samples underwent RNA sequencing, gene-set enrichment analysis and candidates verified by RT-PCR. PTCH1, FLNB, and double-knockdown human keratinocyte models were used to validate phenotype and gene expression. Hedgehog pathway analysis of 20 additional BCCs underwent immunostaining verification. Our analysis revealed FLNB as a potential driver with a mutational cluster in FLNB Filamin domain 24 and a 4-fold reduction in expression compared to normal eyelids in mBCC only. FLNB knockdown demonstrated an mBCC phenotype. Aberrant Gli2 dominant hedgehog (Hh) signalling was seen in mBCC on three molecular levels: mutational significance, transcriptome profile, and protein expression. Gli2-dominant Hh overexpression was seen in the tumour plus stroma of eyelid morphoeic but not nodular BCC. FLNB is a potential tumour suppressor, with its loss producing a morphoeic phenotype in vitro. Full article

Congenital hypothyroidism (CH) is one of the most common endocrine disorders of childhood. The primary form of CH is attributable to thyroid dysgenesis (agenesis, hypoplasia, or ectopy) in 65–85% of cases, with the remaining cases being attributed to dyshormogenesis. Thyroid dysgenesis was considered a sporadic disease. However, the recent advantages of molecular techniques have significantly contributed to the understanding of the pathogenesis of the disease. The higher prevalence of congenital malformations and syndromes in patients with CH compared to the general population supports the genetic basis. This narrative review aims to provide an overview of the identified and potential genetic causes of thyroid dysgenesis. Mutations in ten genes involved in thyroid gland development during embryogenesis, TSHR, PAX8, NKX2-1, NKX2-5, FOXE1, JAG1, NTN1, GLIS3, CDC8A, and TUBB1, have been identified in cohorts of patients with thyroid dysgenesis. However, most cases remain unexplained. Novel candidate genes have been proposed. The extant evidence suggests that the pathogenesis of thyroid dysgenesis involves a spectrum of genetic etiologies, ranging from monogenic to multigenic, and that epigenetic or environmental factors may also contribute. As molecular techniques are continuously refined, future studies are expected to elucidate the complex genetic background of thyroid dysgenesis. 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

The Hedgehog (HH) signaling pathway is an evolutionarily conserved, multi-component signaling pathway. Its activation is initiated by the Hh protein, which signals upstream regulators PATCH and SMO to activate the transcription factor GLI. Upon activation, GLI translocates to the nucleus to induce the transcription of Hh/GLI target genes. Under normal conditions, the HH pathway plays a crucial role in embryogenesis, development, tissue patterning, and stem cell maintenance. Deregulation of the HH signaling pathway leads to various diseases, including cancer. However, in many human cancers, GLI1 is upregulated through a non-canonical pathway (independent of the HH pathway). This aberrant regulation of GLI1 via a non-canonical pathway is linked to the increased expression of various oncogenes. Aberrant expression of GLI not only affects the genes of several DNA repair pathways but also cancer stem cell pathways, which can contribute to genome instability and ultimately lead to cancer. The ineffectiveness of current HH pathway inhibitors in clinical trials necessitates the discovery of new HH pathway inhibitors. In this review, we will discuss our current understanding of the aberrant signaling of the HH-GLI pathway and focus on GLI1-mediated HH signaling in cancers, cancer stem cells, and carcinogenesis. We will also discuss the effectiveness of current HH inhibitors/drugs and combination therapies based on recent advances in this field. Furthermore, we will also review the role of HH-GLI in cancer stem cell markers, DNA damage response, gene regulation, tumor initiation, metastasis, cancer pathogenesis, and the role of drugs/inhibitors on this pathway. Full article

Overcoming drug resistance and targeting cancer stem cells remain challenges for curative cancer treatment. In particular, patients with chronic myeloid leukemia (CML) often require lifelong therapy with ABL1 tyrosine kinase inhibitors (TKIs), partly due to a persistent population of TKI-resistant leukemic stem cells (LSCs). Therefore, identifying specific pathways crucial for LSC maintenance is necessary. The Hedgehog (HH) pathway, especially the protein Smoothened (SMO), has been found to be essential for CML LSCs, but its role in TKI resistance is still largely unknown. We have now demonstrated that the expression of HH pathway genes SMO and GLI2 is increased in CD34⁺ CML stem/progenitor cells compared to healthy counterparts, and is higher in TKI-nonresponders than in responders by transcriptome profiling and qRT-PCR analysis. Interestingly, they are most highly expressed in LSCs compared to progenitors and mature cells in TKI-nonresponders. Inhibition of SMO through genetic knockdown or with a potent, selective SMO inhibitor, Glasdegib, reduces the survival of cells from nonresponder patients. Notably, SMO inhibition also sensitizes TKI-nonresponder stem/progenitor cells to Bostutinib, a second-generation TKI, both in vitro and in a patient-derived xenotransplantation (PDX) model. These findings present a promising therapeutic target and a model for curative combination therapies in stem-cell-driven cancers. Full article

A class of retinal dystrophies known as retinitis pigmentosa (RP) is caused by the loss of photoreceptor cells. RP can be genetically transmitted as an autosomal dominant, autosomal recessive, or X-linked trait. About one-third of genes implicated in retinal degeneration encode for proteins whose functional dysregulation affects the “connecting cilium” in photoreceptors, altering its structure and function. Here we report on a 33-year-old woman who was referred for clinical genetic testing following a previous diagnosis of degenerative retinopathy, which was not informative. She was enrolled in a research program dedicated to undiagnosed retinal disorders, where a whole genome sequencing approach was employed to understand the underlying genetic basis. The genomic analysis documented the occurrence of compound heterozygosity for two functionally relevant missense variants in BAIAP3, which encodes a protein with a well-documented role in SNARE-mediated trafficking and ciliogenesis. Confocal microscopy analysis showed elongated cilia in patient-derived and BAIAP3-depleted fibroblasts compared to control cells. Real-time PCR analyses showed a consistent significant reduction of GLI1 mRNA levels in patient-derived and BAIAP3-depleted cells, both in basal conditions and after treatment with Smoothened agonist, SAG, indicating Sonic hedgehog signaling dysregulation. Collectively, these data suggest that biallelic loss-of-function variants of BAIAP3 may cause photoreceptor degeneration and underlie isolated RP. Full article