Genes & genomics最新文献

Liquid-liquid phase separation (LLPS) segregates the eukaryotic nucleus into membraneless ribonucleoprotein (RNP) condensates that orchestrate multiple stages of gene expression. In contrast to cytoplasmic granules, these nuclear assemblies lie in direct contact with chromatin and nascent pre‑mRNA, granting first‑order control over transcriptional initiation, co‑transcriptional RNA processing, and mRNA export. Consequently, alterations in their biochemical properties can propagate transcriptome‑wide disturbances and increase disease susceptibility. This review synthesizes current knowledge of the molecular composition, architectural scaffolds, and regulatory roles of the four canonical nuclear condensates-nuclear speckles, paraspeckles, Cajal bodies, and histone locus bodies. We discuss how these dynamic hubs accelerate spliceosome assembly, enforce RNA quality control, and reprogram transcription under stress, and we compile evidence that condensate hardening, mislocalization, or compositional rewiring contributes to diverse pathologies. Finally, we evaluate emerging therapeutic strategies that reengineer condensate phase behavior and outline future directions for biophysical and multi-omics approaches needed to translate condensate biology into precision medicine.

Background: Nuclear receptor coactivator 4 (NCOA4) is known to be involved in ferroptosis. However, its expression and function in gliomas are still unclear.

Objective: To assess the expression of NCOA4 in gliomas and explore the mechanisms by which NCOA4 affects glioma progression.

Methods: RNA-seq data for glioma patient tissues and normal brain tissues were obtained from The Cancer Genome Atlas and the Genotype Tissue Expression project. NCOA4 expression was assessed by Western blotting (WB) and immunohistochemistry (IHC). Overexpression and knockdown of NCOA4 were induced in glioma cell lines via transduction of recombinant adenovirus encoding NCOA4 and NCOA4 siRNA, respectively. Cell Counting Kit-8 (CCK-8), Transwell and flow cytometry assays were performed to assess cell proliferation, invasion and apoptosis.

Results: WB and IHC revealed that NCOA4 was markedly downregulated in glioma cell lines and human specimens compared to controls, and high NCOA4 expression was associated with a better glioma prognosis. NCOA4 overexpression inhibited glioma cell growth and invasion and induced apoptosis, whereas NCOA4 knockdown promoted glioma cell growth. PTCH1 was predicted to interact with NCOA4 via bioinformatics analysis. NCOA4 overexpression increased the expression of PTCH1 and suppressed the expression of SMO, Bcl-2 and the nuclear translocation of Gli1, indicating that NCOA4 suppresses the SHH pathway. PTCH1 knockdown reversed the inhibitory effects of NCOA4 on the malignant behaviours of glioma cells.

Conclusions: These results suggest that NCOA4 is downregulated in gliomas and that its overexpression predicts better overall survival in glioma patients. Mechanistically, NCOA4 overexpression inhibits the progression of glioma by suppressing the SHH pathway.

Background: Forkhead box (Fox) proteins belong to a large family of transcription factors characterized by a highly conserved DNA binding domain termed the 'forkhead box'. They are involved in critical functions during early development and in the adult.

Objective: In this work, Foxj3 was found to regulate negatively the transcription of target genes induced by Activin/Nodal or BMP signal in Xenopus embryos. Thus, we sought to investigate the molecular mechanisms underlying this function of Foxj3 as a transcriptional repressor.

Methods: Microinjection of mRNA and anti-sense morpholino oligo was employed to achieve the gain- and loss-of Foxj3 function, respectively. RT-PCR and luciferase assays were performed to investigate the effects of overexpression or knockdown of Foxj3 on TGF-β signals-responsive transcriptions. Animal cap elongation assay was used to check whether Foxj3 would affect the dorsalization of ectodermal tissues induced by Activin signal. Whole-mount in situ hybridization was carried out to analyze the in vivo expression of key marker genes in the embryos overexpressing or depleted of Foxj3.

Results: Overexpression of Foxj3 was found to repress the gene responses activated by Activin/Nodal or BMP4 signals. Its increased levels also caused defective mesodermal and ectodermal specification in embryo. Conversely, knockdown of Foxj3 augmented Nodal-responsive transcription of target genes. In line with this, Foxj3 morphants displayed the malformed phenotypes resembling those of embryos exposed to increased levels of Nodal signal. Furthermore, Foxj3 repression of transcriptional responses was blocked by depletion of RNF152 or co-expression of β-catenin.

Conclusion: Foxj3 functions via the RNF152/β-catenin signaling axis to repress TGF-β-dependent transcriptional responses in Xenopus early development.

Background: Multidrug-resistant (MDR) Acinetobacter baumannii (A. baumannii) poses a pressing threat to global healthcare settings, as most antibiotics are ineffective against this nosocomial pathogen. Vaccines, particularly peptide-based vaccines, offer a promising and effective strategy to deal with these infections.

Objective: This study aimed to evaluate the potential of epitopes derived from the OmpA protein of A. baumannii as vaccine candidates for combating this pathogen.

Methods: This study employed advanced bioinformatic tools to identify potential epitopes for vaccine candidates against A. baumannii infections. IEDB and SYFPEITHI were used to identify T-cell epitopes of A. baumannii OmpA protein. The epitopes were filtered based on score, clustering, human similarity, immunogenicity, cytokine response, and safety. Epitopes with high scores and both class-I and class-II sites were selected. Three epitopes were chosen for molecular docking and physicochemical evaluation as potential vaccine candidates.

Results: Three epitopes (EP1, EP2, and EP3) derived from A. baumannii OmpA were found to effectively bind with specific human leukocyte antigen (HLA) alleles. These epitopes have shown promising potential to elicit both cellular and humoral immune responses. Their physicochemical and immunological properties were thoroughly evaluated, indicating strong antigenic potential, non-toxicity, lack of allergenic properties, good binding affinity, and wide population coverage. The epitopes' two- and three-dimensional structures were predicted, and they were docked with their respective HLA alleles to assess their ability to stimulate innate immune responses. The predicted epitopes and HLA-allelic complexes exhibited excellent binding affinity, optimal Root Mean Square Deviation (RMSD) values, favorable physicochemical properties, and high-quality structural characteristics.

Conclusions: This study identified epitopes that hold promise as potential solutions for combating multidrug-resistant A. baumannii, pending validation through wet lab experiments and clinical trials.

Background: OTOP3, a proton channel located at 17q25.1, drives colorectal cancer growth by enhancing c-Myc stability and inhibiting ferroptosis through GPX4 regulation. Inhibition of OTOP3 suppresses CRC proliferation via c-Myc destabilization, ROS accumulation, and lipid peroxidation, while modulating metabolic shifts linked to the Warburg effect. These findings position OTOP3 as a novel therapeutic target for CRC by disrupting oncogenic signaling and ferroptosis resistance.

Objective: To investigate OTOP3's role in CRC growth/metastasis and its link to ferroptosis and metabolic reprogramming. To evaluate OTOP3 targeting as a therapeutic strategy.

Methods: Colorectal cancer (CRC) cell lines were transfected with OTOP3 siRNA to suppress gene expression, followed by cell viability assays to assess proliferation changes. Western blotting quantified c-Myc and GPX4 levels, while fluorescent probes measured ROS accumulation and lipid peroxidation. Ferroptosis induction was validated using ferroptosis inhibitors, and glycolytic activity was analyzed via glycolysis-related gene expression and lactate production assays.

Results: OTOP3 inhibition destabilized c-Myc, suppressed proliferation, and induced ferroptosis via GPX4 reduction, ROS accumulation, and lipid peroxidation. Altered glycolysis factors indicated enhanced Warburg effect.

Conclusion: Our study provides compelling evidence that targeting OTOP3 effectively suppresses colorectal cancer proliferation by reducing c-Myc protein stability and inducing ferroptosis. These effects are closely associated with metabolic shifts characteristic of the Warburg effect, emphasizing OTOP3 as a potential therapeutic target in colorectal cancer treatment.

Background: Hereditary hearing loss (HHL) exhibits considerable genetic heterogeneity. Among the known causative genes, MYO7A is frequently linked to autosomal recessive non-syndromic hearing loss (ARNSHL), contributing to auditory dysfunction through impaired inner ear cellular mechanics.

Objective: This study aimed to identify the genetic cause of ARNSHL in a Korean family (SR-323) and to assess the pathogenicity of candidate MYO7A variants.

Methods: Whole-exome sequencing (WES) was performed on five family members (two affected individuals and three unaffected relatives). Variant filtering, co-segregation analysis, and Sanger sequencing validation were conducted to identify candidate mutations. Conservation analysis across vertebrate species and in silico pathogenicity predictions were used to evaluate the biological impact of the variants. Additionally, 100 unrelated normal-hearing Korean individuals were screened to determine the frequency of the variant in the general population.

Results: Two MYO7A variants, c.4501G > A (p.Val1501Met) and c.6070 C > T (p.Arg2024Stop), were identified in affected individuals in a compound heterozygous state. Unaffected family members carried only one heterozygous variant. Both amino acid residues were highly conserved across seven vertebrate species. In silico analyses predicted p.Val1501Met to be pathogenic, while c.6070 C > T was previously classified as likely pathogenic. These variants were absent in the normal-hearing cohort, and only individuals with both variants exhibited hearing loss, supporting a compound heterozygous inheritance.

Conclusion: Compound heterozygosity of the MYO7A variants c.4501G > A and c.6070 C > T likely underlies the ARNSHL phenotype in the SR-323 family. These findings expand the known mutational spectrum of MYO7A and highlight the importance of genetic screening in hereditary hearing loss within the Korean population.

Background: Somatic mosaicism is caused by a postzygotic de novo mutation. It is a very rare genetic event, and mosaic cases have been reported only very limitedly among Korean patients with peripheral neuropathies, including Charcot-Marie-Tooth disease (CMT) so far.

Objective: This study was performed to identify and characterize somatic mosaicism in Korean families with CMT.

Methods: Genetic causes were identified by whole exome sequencing (WES) and a subsequent filtering process of the variants. The level of mosaicism for the de novo somatic mutations was determined by counting altered sequences from approximately 100 colonies/mutation and the ratio of altered sequences per total reads at the mutation site using the WES data.

Results: We observed two cases of somatic mosaicism in different families with CMT: p.Cys104Tyr in INF2 (male with CMT1) and p.Ser729Arg in TRPV4 (female with CMT2). The approximate levels of mosaicism were determined to be 24% and 30% in the blood, respectively. A man with the INF2 mutation showed very mild symptoms, while a woman with the TRPV4 mutation showed severe clinical phenotypes. The INF2 mutation is specifically considered a case of gonadal mosaicism. In addition, we confirmed that the p.Cys104Tyr in INF2 is associated with the CMT1 phenotype without focal segmental glomerulosclerosis (FSGS).

Conclusion: This study may be the first or second report for the INF2 and TRPV4 mosaicism. The degrees of the phenotypic severity for the mosaic mutations probably depend on the mutation sites and the levels of mosaicism in the affected tissues. This study suggests that somatic mosaicism may contribute to inter- or intra-familial phenotypic heterogeneity.

Background: Ovarian cancer is among the most lethal malignancies affecting women, largely due to its asymptomatic progression in early stages, rapid advancement, and high mortality rate. Tight junction protein 1 (TJP1), also known as Zonula occludens-1 (ZO-1), plays a critical role in epithelial and endothelial cell integrity by regulating paracellular permeability. Additionally, ZO-1 is involved in cell-cell communication networks, influencing cellular proliferation, differentiation, and metastasis. While previous studies have demonstrated the significance of ZO-1 in tumorigenesis and cancer progression, its precise mechanistic role remains to be fully elucidated.

Objective: This study aims to investigate the functional role of ZO-1 in human ovarian cancer cells to provide a molecular perspective on its impact on tumor progression.

Methods: Human ovarian cancer cell lines SNU119 and SKOV3 were utilized. ZO-1 knockout (KO) was achieved using the Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR-associated protein 9 (CRISPR-Cas9) system in combination with single-guide RNA (sgRNA) targeting ZO-1. Hygromycin B selection was employed to establish stable ZO-1 KO SNU119 and ZO-1 KO SKOV3 cell lines. The successful knockout of ZO-1 was confirmed at both the transcript and protein levels via real-time quantitative PCR (RT-qPCR) and Western blotting. Functional assays, including cell proliferation, migration, and invasion assays, were conducted to assess the effects of ZO-1 KO on key tumor-associated characteristics.

Results: CRISPR-Cas9-mediated ZO-1 KO in SNU119 and SKOV3 ovarian cancer cell lines resulted in a significant reduction of ZO-1 expression at both the transcript and protein levels. The loss of ZO-1 led to a disruption of cell-cell junctions. Functionally, ZO-1 KO cells exhibited reduced proliferation, whereas cell migration and invasion were significantly enhanced, suggesting a shift toward a more aggressive phenotype.

Conclusion: The findings indicate that ZO-1 KO in ovarian cancer cells suppresses cell proliferation while promoting migratory and invasive properties, hallmarks of tumor progression. These results underscore the complex role of ZO-1 in ovarian cancer and highlight the need for further investigation into its broader regulatory impact on oncogenic pathways.

Background: Intelectin (ITLN) plays a pivotal role in innate immunity, inflammatory responses, and tumor progression. However, its physiological roles in caudate amphibians, such as Andrias davidianus, remain elusive.

Objective: A proto-type of intelectin (AdITLN1) from A. davidianus was characterized, following which an AdITLN1 homology model was generated to analyze its expression profiles and functional characterizations.

Methods: The intelectin1 gene (AdITLN1) was cloned, and its evolutionary relationship with ITLN1 from other species was explored. Additionally, a homology model was generated using Molecular Operating Environment (MOE) software, and the active binding pocket of AdITLN1 was identified. Infections with Aeromonas hydrophila were conducted to analyze changes in ITLN1 transcript levels in liver tissue. Finally, recombinant A. davidianus ITLN1 protein (rAdITLN1) was synthesized using prokaryotic expression, and its bacterial agglutination activity and impact on macrophage phagocytosis were examined.

Results: Multiple sequence alignment and phylogenetic analysis indicated that AdITLN1 shared the closest evolutionary relationship with amphibians, with its structure being similar to that of human intelectin1 and Xenopus Embryonic Epidermal Lectin. Moreover, AdITLN1 mRNA was expressed in a wide range of tissues and was significantly up-regulated post-A. hydrophila infection. Meanwhile, the AdITLN1 protein was successfully expressed and purified in Escherichia coli (E. coli) BL21 (DE3). The recombinant AdITLN1 (rAdITLN1) displayed strong agglutination activity against different Gram-negative and Gram-positive bacteria. Lastly, The phagocytosis of rAdITLN1-treated E. coli by macrophages was significantly enhanced.

Conclusion: The results of the present study demonstrated that AdITLN1 was a multifunctional immune protein with potent immunomodulatory activity. This study offers valuable insights into disease control in giant salamanders and the conservation of natural resources.