Search Results (202)

A new series of eight novel etodolac-based 1,3,4-oxadiazoles was synthesized, characterized, and tested in silico in multidimensional routes, starting with etodolac, a well-known nonsteroidal anti-inflammatory medication (NSAID). In silico studies were performed prior to synthesis using the molecular docking technique in CCDC GOLD suite software (2025.3) to assess the interactions with two key targets involved in cancer pathogenesis: the crystal structure of the epidermal growth factor receptor EGFR tyrosine kinase domain (PDB ID: 4HJO) and the matrix metalloproteinase (MMP-9) complex (PDB ID: 5CUH). ADME studies were performed to assess the physicochemical properties of the synthesized molecules. Importantly, biotransformation prediction also indicated that the derivatives possess high metabolic stability, with hydroxylation of the thio-ether group as the primary predicted biotransformation route. All compounds were characterized using melting point, FT-IR, ¹H-NMR, and ¹³C-NMR spectroscopy. In vitro and/or in vivo experiments are needed to confirm this preliminary anticancer study. Full article

Background: Papillary Thyroid Cancer (PTC) harboring CCDC6-RET translocation is typically classified as a differentiated epithelial tumor. Although Selpercatinib, a RET-selective drug, was recently approved for use in advanced PTC, the emergence of drug resistance has already been observed. Tumor plasticity, including non-canonical Epithelial–Mesenchymal Transition (EMT) programs, is recognized as a key mechanism underlying drug resistance. The downregulation of the transcription factor Wilms’ Tumor 1 (WT1) in cancer is associated with increased motility, invasiveness, and metastatic potential. Methods: In this study, we developed a selpercatinib-resistant PTC-derived cell line, TPC-1-SelpR. Bioinformatic analyses were conducted to study the promoter of the CCDC6-RET gene and the transcriptomic landscape of PTC from RNAseq data. Subsequent real-time PCR, Western blot, and imaging techniques, such as confocal microscopy (CM) and fluorescence microscopy (FM), were employed to study the effects of WT1 loss-of-function following RNAi silencing. Results: In TPC-1-SelpR, WT1 expression appears downregulated compared to its counterpart, TPC-1. Crucially, WT1 silencing induced a context-dependent modulation of the CCDC6-RET driver: while WT1 silencing reduced CCDC6-RET expression in TPC-1, in TPC-1-SelpR, a post-transcriptional compensation of CCDC6-RET was observed. The gene expression of several factors involved in EMT, such as Twist, Vimentin, Integrin beta-1, and Profilin, was rewired in TPC-1-SelpR^{WT1-knockdown}. Although the Vimentin protein product decreased, CM and FM analyses confirmed a reorganization of residual protein: the subcellular redistribution was more dispersed in TPC-1-SelpR^{WT1-knockdown}. Further upregulation of the stemness factor Sox2 over the differentiation factor Sox17 occurred. These molecular changes were associated with higher cell motility of TPC-1-SelpR^{WT1-knockdown}. Conclusions: Collectively, these findings suggest that WT1 is a critical regulator involved in tumor plasticity, thereby supporting selpercatinib resistance. Full article

Chronic obstructive pulmonary disease (COPD) is a leading cause of mortality worldwide, yet only a fraction of smokers develops the disease, suggesting protective mechanisms in resilient individuals. Identifying airway-localized molecular signatures may improve our understanding of disease pathomechanisms and support hypothesis generation for biomarker research. In this pilot study, induced sputum from smokers with COPD (n = 28) and smokers without COPD (n = 16; Global Initiative for Chronic Obstructive Lung Disease (GOLD)-defined pre-COPD) was analyzed by untargeted proteomics, metabolomics, and lipidomics. After quality control, 1180 proteins, 187 metabolites, and 1234 lipids were retained. Analyses included univariate models with false discovery rate adjustment and multivariate analyses (PCA, PLS-DA), followed by pathway enrichment and protein interaction network analysis. While few features remained significant after FDR correction, consistent cross-omics patterns were observed. COPD was characterized by ↑ glutathione, creatine, and L-arginine; ↓ CCDC88A and ↑ STAT3 and SYDE2; and broad lipid remodeling involving phosphatidylcholines, sphingolipids, and eicosanoids. Network analysis highlighted STAT3 as a highly connected node linking COPD-related genes. These findings suggest that the multi-omic profiling of induced sputum can capture coherent airway-localized molecular signatures such as oxidative stress, cytoskeletal remodeling, and Rho-family GTPase signaling. However, the results should be interpreted as exploratory and require validation in functional studies. Full article

While chronic alcohol consumption is an established risk factor for lipid metabolic dysregulation, the underlying genetic mediators remain largely elusive. This study investigated the synergistic impact of CCDC63 (coiled-coil domain containing 63) polymorphisms and alcohol intake on dyslipidemia risk within a Korean cohort. Leveraging data from the KARE study (N = 6655; 4327 dyslipidemia cases vs. 2328 controls), we analyzed SNPs across the CCDC63 locus via Affymetrix SNP Array 5.0. Logistic regression, adjusted for age and sex, was performed to evaluate genotype–phenotype association and gene–environment interactions induced by alcohol exposure duration. Three intronic variants (rs10849915, rs11065756, and rs2238149) were significantly associated with dyslipidemia (OR ≥ 1.15, p < 0.005). Notably, stratified analysis revealed a clear gene–environment interaction. In ever-drinkers, the G-allele of rs10849915 was significantly associated with a higher risk of dyslipidemia (OR = 1.23, p < 0.05), significantly lower γ-GTP levels (β = −8.08), and reduced HDL (β = −1.42). However, no such genetic associations were observed in the non-drinking group (p > 0.05 for all traits). Our findings demonstrate that CCDC63 variants specifically modulate lipid metabolism and hepatic enzyme levels in an alcohol-dependent manner. The paradoxical association—lower γ-GTP yet higher dyslipidemia risk in drinkers—suggests that CCDC63 plays a critical role in the complex interplay between alcohol exposure and systemic lipid homeostasis. Full article

Background: Visceral fat plays a central role in cardiometabolic risk among people with type 2 diabetes mellitus (T2DM), yet its assessment in routine clinical practice remains largely dependent on imaging techniques or indirect anthropometric measures. Identifying accessible blood-based markers that reflect visceral adiposity may facilitate improved phenotyping in this population. This study aimed to investigate whether circulating coiled-coil domain–containing protein 3 (CCDC3) reflects visceral fat accumulation in adults with T2DM. Methods: Public RNA-sequencing datasets and human adipose tissue samples were analyzed to identify CCDC3 as a visceral fat–enriched secretory gene. In this cross-sectional study of 160 adults with T2DM undergoing dual-energy X-ray absorptiometry, plasma CCDC3 was measured by ELISA. Associations between plasma CCDC3 and visceral fat area (VFA) were examined using multivariable regression. Logistic regression models for abdominal obesity (VFA ≥ 100 cm²), with and without CCDC3, were evaluated using receiver operating characteristic (ROC) analysis, calibration curves, decision curve analysis (DCA), and Shapley additive explanations (SHAP). Results: Circulating CCDC3 levels were positively associated with VFA (β = 3.11, p < 0.001), independent of demographic and metabolic factors. Incorporating CCDC3 into the baseline model significantly improved discrimination of abdominal obesity (AUC 0.820 vs. 0.663; p = 0.009). Calibration curves and DCA supported better model fit and higher net clinical benefit with CCDC3. SHAP analysis showed that CCDC3 contributed the greatest incremental importance beyond waist circumference, sex, and age. Conclusions: Circulating CCDC3 may serve as a blood-based biomarker reflecting visceral adiposity in adults with T2DM and provides complementary information beyond traditional anthropometric measures. Full article

Background/Objectives: Consanguine families are helpful to identify recessive candidate genes for inherited diseases, but can also show an unusual inheritance pattern of pathogenic mutations. In this case series, we demonstrate this in five consanguine families with epilepsy from Pakistan. Methods: We performed whole exome sequencing of respective index patients, analyzed the data using two different models for inheritance of mutations and determined the segregation pattern of relevant mutations in the families by bi-directional Sanger sequencing. Results: Apart from mutations in classical dominant epilepsy genes (TSC2, DEPDC5, and CACNA1I), pathogenic mutations in rare recessive epilepsy-related genes (PGAP2, NOVA2, and CCDC88C) were also identified. Interestingly, we were able to provide evidence that GALR2 is potentially an additional gene associated with a recessive form of epilepsy. In one family, a homozygous ‘pathogenic’ TRAF3IP1 p. Gly387* nonsense mutation was identified, which, most probably due to stop-codon read-through, did not contribute to the phenotype. Conclusions: Our case series of consanguine families with epilepsy exemplifies the inheritance pattern of mutations in rare recessive epilepsy genes, and shows that mutations in classical epilepsy genes showing dominant or sporadic inheritance can also be relevant. That requires the analysis of whole exome data on the basis of different inheritance models. Full article

Purpose: Collagen membranes are widely used biomaterials in periodontal and implant dentistry and can be combined with hyaluronic acid (HA). Although collagen membranes are expected to exhibit bioactive properties and support fibroblast infiltration, their specific impact on fibroblast behavior remains unclear. Methods: To investigate this, human gingival fibroblasts were seeded on collagen matrices—mucoderm^®, a collagen fleece derived from dermis, and Jason^® membrane derived from pericardium—with or without lyophilized HA. Subsequent bulk RNA sequencing was used to assess transcriptional responses. Results: Both mucoderm^® and the collagen fleece caused significant transcriptional changes compared with fibroblasts grown on standard tissue culture surfaces and Jason^® membrane. These changes included upregulation of CEMIP, STC1, and TM4SF1, and downregulation of ADM2, PSAT1, and GPR1. Notably, the collagen fleece increased expression of extracellular matrix-related genes including CCN1, CCN2, COL1A1, POSTN, SPARC, TAGLN, FBN2, CCDC80, and CREB3L1 relative to mucoderm^®. Additionally, the expression of proteases MMP3 and MMP10, along with detoxification-related genes MT1E, MT2A, HMOX1, and NQO1, was relatively decreased. HA coating elevated IL24 expression in mucoderm^®, but no similar effect was observed in the collagen fleece. Conclusions: These findings demonstrate that collagen membranes can influence the transcriptome of gingival fibroblasts and suggest that collagen fleece has a stronger effect on extracellular matrix formation than mucoderm^®. Furthermore, HA coating does not consistently alter fibroblast responses. Full article

Background: Interstitial deletions of the short arm of chromosome 12 are rare, and very little is known about the potential genetic basis of the most common phenotypic presentations to date described in the literature. Methods: In the present study, we present a new patient carrying a heterozygous de novo 12p deletion, identified by a-CGH. Results: Comparison between the new case with phenotypically similar 12p-deleted patients drawn from the literature and from the DECIPHER (the DatabasE of Chromosomal Imbalances and Phenotypes using Ensembl Resources) database allowed us to analyze 22 cases and to define a revised minimal critical region not previously considered. Discussion: Within the new minimal critical region, we identified genes intolerant to haploinsufficiency, highlighting the involvement of PTHLH and CCDC91 in the onset of skeletal abnormalities and proposing the involvement of PPFIBP1 in neurodevelopmental disorders (although it has previously been associated only with autosomal recessive conditions). Conclusions: We suggest that clinical severity in cases with 12p deletions varies depending on the cytobands involved, being more moderate when they occur at 12p11—where the gene DENND5B (12p11.23) has recently been associated with a dominant neurodevelopmental disorder—than at 12p12. Full article

One group of human proteins found in the cytoplasm, but not in the nucleus, is characterized by the presence of short (6–9 aa), specific amino acid sequences thought to be involved in retaining proteins in the cytoplasm (cytoplasmic retention sequences). While strong evidence supports the ability of some peptides to act in this way, the number of such supported cases is small. We have taken the view that the situation would be improved by enhancing the methods available to identify cytoplasmic retention (CR) sequences. Here, we describe an appropriate bioinformatic method to identify CR peptides using information about their location at the ends of cytoplasmic proteins. The method was then used to link seven different human cytoplasmic proteins with sequences suggested to have cytoplasmic retention activity. Further bioinformatic analysis was carried out with isoforms of the cytoplasmic proteins identified. Amino acid sequence information showed that while the proposed CR amino acid sequences can be the same or distinct in different protein isoforms, they are always located at the same site in the protein. For instance, while the proposed retention sequence of CCDC57 isoform X18 is MLARLVSNS, in isoform 7 it is SEPALNEL, yet the two sequences are each located between amino acids 5 and 13 in the CCDC57 sequence. The results support the view that the protein isoform is involved in determining the location of the CR sequence in a protein, while the amino acid sequence itself affects other variables such as the sub-region of the cytoplasm the protein needs to occupy. Overall, the study yielded identification of 15 candidate CR peptides in which 10 of the 15 have unrelated amino acid sequences. Full article

Myeloproliferative neoplasms (MPNs) are a heterogeneous group of diseases originating from hematopoietic stem cell transformation, characterized by the clonal proliferation of hematopoietic progenitors. A specific subset includes myeloid/lymphoid neoplasms with eosinophilia and tyrosine kinase (TK) gene fusions, particularly involving PDGFR A or B, which are sensitive to TK inhibitor treatment. We report a case of a 21-year-old patient with a myeloproliferative/myelodysplastic neoplasm, presenting with hyperleukocytosis, anemia, thrombocytopenia, and elevated LDH. The peripheral blood smear showed hypogranular neutrophils, eosinophils, basophils, and myeloid precursors. The absence of BCR::ABL1 and mutations in JAK2, CALR, and MPL excluded common MPNs. Cytogenetic analysis revealed a rearrangement between chromosomes 5 and 14. FISH analysis confirmed an inverted insertion from chromosome 5 to chromosome 14, involving the PDGFRB gene. WGS and RNAseq identified a fusion between PDGFRB and CCDC88C, causing the constitutive activation of PDGFRB. The fusion gene was confirmed by sequencing. This allowed for targeted therapy with a tyrosine kinase inhibitor (TKI), leading to molecular remission monitored by RT-qPCR. This case highlights how a multidisciplinary approach can identify atypical transcripts in MPN, guiding targeted therapy with TK inhibitors, thus resulting in effective treatment and molecular remission. Full article

Background: Osteoporosis is highly prevalent in postmenopausal women, yet genome-wide association studies often miss disease-relevant variants because of incomplete single nucleotide polymorphism (SNP) coverage and platform-specific limitations. We aimed to identify genetic contributors to osteoporosis risk by integrating two exome-based genotyping platforms with multilayer analytic approaches. Methods: We analyzed extreme osteoporosis phenotypes in Korean postmenopausal women from the Korean Genome and Epidemiology Study (KoGES) Ansan–Anseong cohorts using the Illumina Infinium HumanExome BeadChip and the Affymetrix Axiom Exome Array. After standard quality control, single-SNP logistic regression, cross-platform overlap analysis, and three machine-learning models were applied. Predicted functional impact was evaluated using multiple in silico algorithms and conservation scores. Finally, datasets from both platforms were merged, and cross-platform linkage disequilibrium (LD) blocks were defined to identify loci containing SNPs with p < 1 × 10⁻⁴. Results: No overlapped SNP reached genome-wide significance, but rs2076212 in PNPLA3 achieved suggestive significance (p < 1 × 10⁻⁵) only on the Illumina array. Cross-platform analysis identified 111 overlapping SNPs in 70 genes. Integrated machine-learning, in silico, and conservation evidence prioritized ARMS2, CCDC92, NQO1, ZNF510, PTPRB, and DYNC2H1 as candidate genes. LD-block analysis revealed 10 blocks with at least one SNP at p < 1 × 10⁻⁴, including four chromosome 12 loci (NAV2, BICD1, CCDC92, ZNF664) that became apparent only when LD patterns were evaluated jointly across platforms. Conclusions: Combining dual exome arrays with LD-block analysis, machine learning, and functional prediction improved sensitivity for detecting low bone mineral density-related loci and highlighted CCDC92, DYNC2H1, NQO1, and related genes as biologically plausible candidates for future validation. Full article

Lion-head goose is a large-sized breed native to Guangdong Province, China, exhibits remarkable capacity for fatty liver production under overfeeding conditions and is highly valued by local farmers and consumers. However, the molecular mechanisms driving fatty liver development in this breed are still unknown. In this study, we evaluated liver weight differences between normally fed and overfed Lion-head geese and further examined sex-specific differences following overfeeding. Overfeeding significantly increased liver weight more than 340%, and males possess a stronger capacity for lipid deposition under the same feeding regimen compared with females. RNA-Seq analysis identified 1476 differentially expressed genes (DEGs) shared by both sexes, which were mainly enriched in lipid and energy metabolism, oxidative stress, and mitochondrial pathways. In addition, 627 male-specific and 420 female-specific DEGs revealed sex-dependent differences, with males showing stronger transcriptional regulation and females exhibiting enhanced antioxidant and detoxification responses. Weighted gene co-expression network analysis (WGCNA) revealed 320 co-hub genes enriched in lipid and energy metabolism in overfeeding-induced fatty liver, along with 9 co-hub genes related to sex differences. Alternative splicing (AS) analysis detected 131 differentially spliced genes (DSGs). Integration of both approaches identified 7 overlapping genes, HYCC2 (Hyccin PI4KA lipid kinase complex subunit 2), AGL (Amylo-Alpha-1,6-Glucosidase and 4-Alpha-Glucanotransferase), CCDC62 (Coiled-coil domain containing 62), IGSF5 (Immunoglobulin superfamily member 5), MGARP (Mitochondria-localized glutamic acid-rich protein), CD80 (Cluster of Differentiation 80), and FPGS (Folylpolyglutamate synthase), as potential key regulators. These findings provide new insights into transcriptional and post-transcriptional regulation of overfeeding-induced fatty liver in geese. Full article

Upon transcription, most mRNAs associate with the small ribosomal subunit, after which a fully translating ribosome assembles. Under starvation or stress, however, mRNA–ribosome associations are blocked and many mRNAs are instead sequestered with specific RNA-binding proteins into stress granules or other subcellular condensates, a process that has been extensively studied. In contrast, much less attention has been paid to the fate of ribosomes under these same conditions. Ribosomes can remain fully assembled but unbound to mRNA, entering an inactive, dormant state. Dormancy is often supported by specific protein factors which protect ribosomes from degradation and facilitate reactivation once growth conditions improve. In this review, we highlight that dormant ribosome states are well defined in prokaryotes, in part because they possess distinct and experimentally tractable features, such as stable vacant 100S dimers. In eukaryotes, by contrast, analogous disomes are largely absent, making their discovery more indirect and method-dependent. We therefore focus on how evidence for eukaryotic dormant ribosomes has been assembled through multiple independent findings and how their interpretation depends critically on the experimental approaches used to study them. Finally, we consider atypical ribosomal states, such as translationally inactive polysomes in neurons, which underscore the context-dependent nature of ribosome activity. Full article

Spermiogenesis requires extensive molecular and structural remodeling to produce motile sperm. Mutations in the testis-specific RNA methyltransferase NSUN7 are associated with defective fibrous sheath, impaired sperm motility, and male infertility. However, the underlying molecular mechanisms remain poorly understood. Here, we performed proteomic profiling of sorted, elongated, and round spermatids, as well as mature spermatozoa from Nsun7 knockout mice. We showed that NSUN7 is present at all stages of spermiogenesis and is most abundant in round spermatids, which corresponds to the formation of the flagellum and fibrous sheath assembly. Loss of NSUN7 altered the abundance of proteins essential for dynein arm assembly (PIH1D3, CCDC103, CCDC40), intraflagellar transport (IFT122), and fibrous sheath organization (AKAP3, AKAP4, ROPN1L). We also showed that the previously detected impaired retention of cytoplasm in elongated spermatids may be caused by plectin accumulation. Interestingly, no statistically significant changes were found in mature sperm proteomes upon Nsun7 inactivation. Our findings support a model in which NSUN7 primarily stabilizes protein complexes and coordinates flagellar assembly. This indicates that NSUN7 is a critical regulator of spermiogenesis, and its malfunction is a contributing factor to male infertility. Full article

Primary ciliary dyskinesia (PCD) is a rare hereditary disorder belonging to the group of ciliopathies, with autosomal recessive, autosomal dominant, and, less frequently, X-linked inheritance patterns. The aim of this study was to investigate the genetic heterogeneity of the Russian population of PCD patients based on national registry data. The study included patients with PCD confirmed by molecular genetic testing. Quantitative data were analyzed using non-parametric statistical methods. Differences were considered statistically significant at p < 0.05. The study included 109 patients with PCD. Molecular genetic testing identified pathogenic variants in 29 autosomal recessive genes. The analysis of pathogenic variant distribution in the Russian PCD cohort revealed the highest number of changes in the DNAH5 and DNAH11 genes. 26 genetic variants in 13 genes were identified for the first time in the Russian population. Variants in the DNAH5 gene were significantly more frequent in Kartagener’s syndrome (KS) patients (32/55%) compared to those without KS (11/21.5%) (χ² = 12.8; p = 0.0004; OR = 4.48). Preliminary data indicate that the frequency spectrum of DNAH5 and DNAH11 genes in Russian patients is similar to international trends. Additionally, there is an accumulation of pathogenic variants in the DNAH5, DNAH11, CCDC39, and CFAP300 genes. Full article