Search Results (302)

Polyglutamine expansion in Ataxin-2 (ATXN2) is responsible for rare, dominantly inherited Spinocerebellar Ataxia type 2 (SCA2). Together with its paralog Ataxin-2-like (ATXN2L), both proteins have received much interest, since the deletion of their yeast and fly orthologs alleviates TDP-43-triggered neurotoxicity in Amyotrophic Lateral Sclerosis models. Their typical structure across evolution combines LSm with LSm-Associated Domains and a PAM2 motif. To understand the physiological regulation and functions of Ataxin-2 homologs, the phylogenesis of sequences was analyzed. Human ATXN2 harbors multiple alternative start codons, e.g., from an intrinsically disordered sequence (IDR) present since armadillo, or from the polyQ sequence that arose since amphibians, or from the LSm domain since primitive eukaryotes. Multiple smaller isoforms also exist across the C-terminus. Therapeutic knockdown of polyQ expansions in human ATXN2 should selectively target exon 1B. PolyQ repeats developed repeatedly, usually framed and often interrupted by (poly)Pro, originally near PAM2. The LSmAD sequence appeared in algae as the characteristic Ataxin-2 feature with strong conservation. Frequently, Ataxin-2 has added domains, likely due to transcriptional readthrough of neighbor genes during cell stress. These chimerisms show enrichment of rRNA processing; nutrient store mobilization; membrane strengthening via lipid, protein, and glycosylated components; and cell protrusions. Thus, any mutation of Ataxin-2 has complex effects, also affecting membrane resilience. Full article

Background/Objectives: The oncoprotein EWS::FLI1 is a chimeric transcription factor that aberrantly brings transcriptional deregulation relevant to Ewing sarcoma. It is also regarded as a therapeutic target for suppressing oncogenic progression, but the inhibition and clearance of the EWS::FLI1 oncoprotein remain a challenge. Methods: We apply a polyglutamine (polyQ) fusion strategy to directly target EWS::FLI1 in suppression of its transcriptional malfunction in A673 cells derived from Ewing sarcoma. Based on the template of the N-terminal fragment of polyQ-expanded ataxin-7 (Atx7_93Q-N172) and the homologous peptides of EWS::FLI1, we have designed and constructed three polyQ fusion proteins, namely Atx7_93Q-N172-SYGQ1, Atx7_93Q-N172-SYGQ2, and Atx7_93Q-N172-LCD. Results: Supernatant/pellet fractionation and immunofluorescence imaging reveal that the polyQ fusion proteins co-precipitate and co-localize with EWS::FLI1 in A673 cells, indicating that the polyQ fusions we have designed can sequester endogenous EWS::FLI1 into insoluble aggregates and reduce its cellular availability. Moreover, these polyQ fusions, especially Atx7_93Q-N172-LCD, alter the expression of EWS::FLI1 downstream genes, with an increase in P21 (CDKN1A) and a decrease in c-Myc. Conclusions: These results demonstrate that the engineered polyQ fusions entrap endogenous EWS::FLI1 protein into aggregates and reduce its soluble fraction in Ewing sarcoma cells. This study provides an alternative potential for treating Ewing sarcoma and other tumors by directly targeting the oncogenic proteins in the future. Full article

Mechanical stimulation critically regulates mesenchymal stem cell (MSC) differentiation, yet its effects in three-dimensional (3D) environments remain poorly defined. Here, we developed a custom dynamic stretcher integrating poly(dimethylsiloxane) (PDMS) chambers to apply cyclic strain to human MSCs encapsulated in Fmoc-diphenylalanine (Fmoc-FF) peptide hydrogels—a fully synthetic, tunable extracellular matrix mimic. Finite element modeling verified uniform strain transmission across the hydrogel. Dynamic stretching at 0.5 Hz and 10% strain induced pronounced cytoskeletal alignment, enhanced actin stress fiber formation (coherency index $\approx 0.85$), and significantly increased proliferation compared to static or high-frequency (2.5 Hz, 1%) conditions (coherency index $\approx 0.6$). Quantitative image analysis confirmed strain-dependent increases in coherency index and F-actin intensity, indicating enhanced mechanotransductive remodeling. Biochemical assays and qRT–PCR revealed 2–3-fold upregulation of osteogenic markers—RUNX2, ALP, COL1A1, OSX, BMP, ON, and IBSP—under optimal strain. These results demonstrate that low-frequency, high-strain mechanical loading in 3D peptide hydrogels activates RhoA/ROCK and YAP/TAZ pathways, driving osteogenic differentiation. The integrated experimental–computational approach provides a robust platform for studying mechanobiological regulation and advancing mechanically tunable biomaterials for bone tissue engineering. Full article

Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disease characterized by cerebellar ataxia and retinal degeneration, caused by an abnormal expansion of CAG repeats at the ATXN7 gene. Disease onset and progression vary among patients, underscoring the need for novel tools to improve disease monitoring. Circulating miRNAs represent a promising prognostic tool, due to their minimally invasive sampling and high stability. The aim of this study was to assess the expression of twelve circulating miRNAs associated with neurodegeneration in plasma samples from SCA7 patients and in an inducible SCA7 glial cell model. A comparison of SCA7 patients and controls revealed that nine miRNAs exhibited significantly higher expression. Furthermore, comparison of patients with different SCA7 phenotypes to controls revealed that most miRNAs were overexpressed in plasma from early-onset patients corresponding to the clinically more severe phenotype. Regarding the cell model, we identified three miRNAs that were dysregulated; however, only hsa-miR-342-5p displayed a pattern consistent with that observed in the plasma of patient. Our findings indicate that hsa-miR-342-5p is differentially expressed in the plasma of patients and the SCA7 cellular model, implying that it can serve as a biomarker and facilitate the identification of novel processes involved in SCA7. Full article

RhoA (Ras homolog A) is a prominent member of the Rho GTPase family, playing a key role in various cellular processes such as cytoskeletal dynamics, cell migration, and immune responses. However, its function in red swamp crayfish remains unclear. In this study, it is proposed that RhoA may regulate the innate immune response in P. clarkii. The gene was fully characterized as PcRhoA in P. clarkii. The results showed that the open reading frame (ORF) of PcRhoA is 663 bp, encoding a 220-amino acid protein with a conserved Rho domain of 174 amino acids. Phylogenetic analysis placed PcRhoA close to Cherax quadricarinatus RhoA. RT-qPCR analysis revealed high expression levels of the PcRhoA gene in the hepatopancreas, muscle, heart, ovary, and stomach, with lower expression in the blood, intestine, gills, and tentacle gland. Furthermore, PcRhoA mRNA transcript was significantly upregulated in the intestine following LPS and Poly I:C challenges. Knockdown of PcRhoA suppressed the expression of downstream genes in the immune signaling pathway. These results indicate that PcRhoA appears to play a pivotal role in regulating the immune response of crayfish. Full article

Background: Atherosclerosis is the pathological basis for lethal cardio-cerebral vascular diseases, such as coronary artery disease and stroke. Fructus Choerospondiatis (FC) has demonstrated cardiac protective effects in multiple ethnomedicine. Whether these protective effects are attributed to the prevention of vascular atherosclerosis, however, remains unknown. We aim to examine the anti-atherosclerotic effect of FC aqueous extract and elucidate the underlying mechanism. Methods: FC was separated into peel and pulp, and the aqueous extract was obtained separately by boiling in water to mimic decocting. Atherosclerosis model was established in ApoE^−/− mice fed with a high-fat diet, and histological analysis were utilized to evaluate the development of atherosclerosis. Various inflammatory models were constructed in mice to evaluate the anti-inflammatory effect of FC extract systemically, including acute local inflammation induced by traumatic injury (ear/foot swelling), acute systemic inflammation triggered by pathogenic infection (LPS- and POLY (I:C)-induced), as well as chronic inflammatory conditions associated with oxidative stress (D-galactose-induced), metabolic disorder (db/db mice), and aging. LC-MS and network pharmacology identified bioactive components and targets. Western blotting, ELISA, qPCR, and immunofluorescence were utilized to analyze the key genes involved in the mechanisms. Results: FC peel extract reduced serum IL-6 level, atherosclerotic plaque area, and macrophage content in the plaque, while pulp extract showed no protective effects. Peel extract exhibits anti-inflammatory effects in all models. The integrative application of LC-MS and network pharmacology identified ellagic acid as the major bioactive component and AKT as its target protein. Mechanistically, FC peel extract inhibits AKT phosphorylation, suppresses c-FOS expression and nuclear translocation, reduces IL-6 transcription and inflammation, and thus alleviates atherosclerosis. Conclusions: FC peel aqueous extract exerts anti-atherosclerotic effect by inhibiting inflammation through AKT/c-FOS/IL-6 axis. This study provides novel insights into the protective effects against atherosclerosis of FC peel and highlights its potential application in the prevention and treatment of coronary artery diseases. Full article

Background: Breast cancer remains the most common malignancy among women worldwide. Current systemic treatment strategies include chemotherapy, immunotherapy, bone-stabilizing agents, endocrine therapy for hormone receptor-positive disease, anti-HER2 therapy for HER2-positive disease, and poly (ADP-ribose) polymerase (PARP) inhibitors for BRCA mutation cases. However, effectively overcoming drug resistance and reducing recurrence and metastasis rates remain major therapeutic challenges. Methods: To investigate the underlying mechanism of RSL3 in PARPi-resistant breast cancer cells, we treated several PARPi-resistant breast cancer cells with varying doses of RSL3. The regulatory proteins of STAT3 were analyzed using real-time quantitative polymerase chain reaction (RT-qPCR) and Western blot analysis. Immunoprecipitation and ubiquitination assay were performed to identify the STAT3 ubiquitination levels. Results: Recently, we identified that RSL3, a ferroptosis activator, exhibits potent antitumor activity against PARPi-resistant breast cancer. Yet, its underlying mechanism remains unclear. Here, we demonstrate that RSL3 directly targets STAT3 and promotes its degradation via the ubiquitination pathway, leading to increased LC3-II levels and decreased p62 expression. These changes ultimately enhance autophagy, which at least partially contributes to elevated apoptosis. Rescue experiments confirmed that STAT3 overexpression reverses RSL3-induced autophagy and apoptosis. Conclusions: Our findings highlight RSL3 as a promising therapeutic agent and STAT3 as a potential target for treating PARPi-resistant breast cancer. Full article

Background: Biliary tract cancer (BTC) is an aggressive malignancy with poor prognosis and limited therapeutic options. Poly(ADP-ribose) polymerase (PARP) inhibitors have demonstrated efficacy in tumors with homologous recombination repair (HRR) deficiency. However, actionable BRCA1/2 mutations are rare in BTC. Epigenetic modulation via DNA methyltransferase (DNMT) inhibition is a proposed strategy for inducing an HR-deficient (“BRCAness”) phenotype and thereby enhancing therapeutic response to PARP inhibitors. This study aimed to determine whether the DNMT inhibitor azacitidine (AZA) enhances the antitumor effects of the PARP inhibitor niraparib (NIR) and to identify molecular mechanisms underlying this interaction. Methods: Two BTC cell lines, TFK-1 and RBE, were treated with AZA and/or NIR or subjected to siRNA-mediated DNMT1, DNMT3A, or DNMT3B knockdown. Functional analyses included homologous recombination (HR) assays, flow cytometric evaluation of cell-cycle distribution and apoptosis, proliferation and survival assays, and IC₅₀ determination. Whole-transcriptome RNA sequencing was performed to identify differentially expressed genes after AZA treatment or DNMT3B knockdown, followed by validation via qPCR and Western blotting. To explore epigenetic regulation, whole-genome bisulfite sequencing was performed on TFK-1 cells following DNMT3B knockdown. Results: AZA treatment decreased HR frequency in a dose-dependent manner and enhanced the sensitivity of BTC cells to NIR, as evidenced by increased apoptosis, suppressed proliferation, and reduced IC₅₀ values. DNMT3B knockdown recapitulated these effects, establishing a causal relationship between DNMT3B suppression and disrupted HR repair. RNA sequencing identified opioid growth factor receptor (OGFR) as a commonly upregulated gene after DNMT3B knockdown. Functional validation showed that OGFR overexpression reduced HR activity, increased apoptosis, and enhanced NIR sensitivity. Contrarily, OGFR knockdown conferred relative resistance. Whole-genome bisulfite sequencing showed no significant CpG methylation changes at the OGFR promoter region, indicating that OGFR induction is mediated through DNMT3B-dependent transcriptional regulation rather than direct promoter demethylation. Conclusions: DNMT3B inhibition sensitizes BTC cells to PARP inhibitors by disrupting HR repair. OGFR was identified as a novel regulator of HR and PARP inhibitor sensitivity, controlled via noncanonical DNMT3B-dependent transcriptional mechanisms that operate independently of CpG methylation. These findings provide new mechanistic insights into the epigenetic control of DNA repair and support the rationale for combining DNMT and PARP inhibitors as a promising therapeutic strategy for BTC beyond genetically HR-deficient cases. Full article

The red swamp crayfish (Procambarus clarkii) is a globally important freshwater crustacean that exhibits pronounced sexual dimorphism, with males growing faster than females. However, the molecular mechanisms underlying sex differentiation in crustaceans remain poorly understood. In this study, Oxford Nanopore-based Direct RNA Sequencing (DRS) was employed to analyze the gonadal transcriptomes of male and female P. clarkii, identifying 20,001 previously unannotated genes and revealing extensive sex-specific differences in transcript structure, alternative splicing, and RNA modifications. Ovarian transcripts had shorter poly(A) tails and more frequent alternative splicing, while male gonads showed greater enrichment of m⁶A and psU modifications in the 3′ UTRs. qPCR validation confirmed the sex-biased expression of key candidate genes, including Dmrt7, FR, Fruitless, IAGBP, RDH, and Vtg. Collectively, these findings provide the first comprehensive epitranscriptomic landscape of P. clarkii gonads, underscoring the pivotal role of post-transcriptional regulation in sex determination and offering valuable insights for mono-sex breeding strategies in aquaculture. Full article

Polyelectrolyte-based complexes have attracted attention, as the interaction of the oppositely charged components results in nanoparticle formation through an easy but highly efficient method, avoiding the use of strong solvents, extreme temperatures, and toxic chemicals. Sodium oleate (NaOL) is a widely used surfactant in the pharmaceutical industry due to its availability, eco-friendliness, and low cost. In the present study, the neutral-cationic block copolymer poly(oligo(ethylene glycol) methyl ether methacrylate)–b–quaternized poly(2-(dimethylamino) ethyl methacrylate) (POEGMA-b-Q(PDMAEMA)) is mixed with the anionic surfactant sodium oleate for the formation of nanoscale polyelectrolyte complexes through electrostatic interactions. Different weight ratios of copolymer to surfactant are studied. Then, the co-solvent protocol was implemented, and curcumin is successfully loaded in the formed particles for drug delivery applications. The size and morphology of the macromolecular complexes are examined via Dynamic Light Scattering (DLS) and Cryogenic Transmission Electron Microscopy (cryo-TEM). The methods that we have used have indicated that the polymer–surfactant complexes form spherical complexes, worm-like and vesicle-like structures. When curcumin was introduced, encapsulation was effectively achieved into micelles, giving rise to vesicle-like shapes. The success of curcumin encapsulation is confirmed by Ultraviolet–Visible absorption (UV–Vis) and fluorescence (FS) spectroscopy. POEGMA-b-Q(PDMAEMA)–sodium oleate polyelectrolyte complexes revealed promising attributes as efficient drug carrier systems for pharmaceutical formulations. Full article

Ataxin-2 (Atx2) is a general RNA-binding protein involved in processes such as RNA processing and metabolism in cells. Atx2 is also a polyglutamine (polyQ) tract-containing protein; its abnormal expansion can lead to protein aggregation associated with neurodegenerative diseases. Previous studies have shown that the C-terminal intrinsically disordered regions (c-IDRs) of Atx2 participate in its condensation and aggregation processes. To elucidate the role of polyQ expansion in biomolecular condensation and aggregation, we studied the N-terminal fragments of Atx2 (namely, Atx2-N317 and Atx2-N81) that preserve a polyQ tract and compared their molecular behaviors in cells to those of the full-length Atx2. We found that the molecular mobility of the N-terminal fragments decreases with the increasing length of polyQ, indicating that polyQ expansion promotes a gradual phase transition to an irreversible and insoluble state. Moreover, the molecular state and mobility of Atx2-N317 are not distinct from those of Atx2-N81, regardless of the presence of other domains, demonstrating that the polyQ tract is a direct and sufficient element for protein condensation and aggregation, while the Like Sm (LSm) and LSm-associated (LSmAD) domains and their interactions with RNA are not necessary for these processes. This result is also validated through the in vitro investigation of Atx2-N81 with different polyQ expansions. This study reveals that polyQ expansion controls the biomolecular condensation and aggregation of the N-terminal fragments of Atx2 and is thus thought to modulate the dynamic behaviors of the full-length protein as well, which is implicated in the pathological accumulation of Atx2 in cells. Full article

Background: Rabies virus (RABV) causes approximately 59,000 human deaths annually. Current pre- and post-exposure vaccination relies on inactivated vaccines (INVs) with limited yield and immunogenicity. We engineered a dual-cationic LNP-based nucleocapsid-like nanostructure (NLS) that co-encapsulates RABV G-mRNA and recombinant RABV-N to engage MHC-I/II pathways and enhance protection. Methods: A pVAX-RABV-G plasmid containing 5′/3′UTRs, Kozak, and poly(A) was transcribed in vitro. RABV-N with an N-terminal 6× His tag was expressed in E. coli BL21(DE3) and purified by Ni-Sepharose affinity chromatography. Dual-cationic LNPs (DHA, DOTAP Cl, mPEG-DTA2K, DOPC) were formulated by microfluidics at a 4:1 (G-mRNA:RABV-N) mass ratio. Vaccine quality was assessed by encapsulation efficiency, DLS, PDI, zeta potential, and TEM. Mice received empty LNPs, INV, G-mRNA, or NLS under varied schedules and doses. ELISA measured RABV-G/N-IgG; RFFIT determined neutralizing antibody (nAb) titers; ELISPOT quantified CTL response; qPCR assessed T-cell activation genes. On day 35 after the first immunization of vaccines, mice were challenged intramuscularly with 25 LD₅₀ of CVS-24. Results: G-mRNA purity was >95% and drove strong RABV-G expression in 293T cells. Purified RABV-N was approximately 52 kDa, >90% pure, and reactive to anti-His and anti-N antibodies. NLS achieved >95% encapsulation, a diameter of 136.9 nm, PDI 0.09, and a +18.7 mV zeta potential. A single dose yielded approximately 10 IU mL⁻¹ nAb by day 7; two doses peaked at approximately 1000 IU mL⁻¹. Mice showed 100% survival and no viral rebound in brain, spinal cord, and sciatic nerve. NLS induced stronger MHC-I/II-linked cellular immunity and higher RABV G/N-specific IFN-γ spot frequencies than G-mRNA or INV. Conclusions: The dual-antigen NLS vaccine co-delivering G-mRNA and RABV-N via dual-cationic LNPs robustly activates MHC-I/II, rapidly generates high-titer nAb (≥10 IU mL⁻¹ within 1 week), and sustains potent CD8⁺ CTL and CD4⁺ Th responses. A two-dose regimen (days 0 and 21) conferred complete protection, supporting the NLS platform as a next-generation rabies vaccine candidate. Full article

Background/Objectives: Despite extensive research on hepatitis B virus (HBV), its post-transcriptional regulatory mechanisms remain incompletely characterized, particularly regarding epitranscriptomic modifications. This study aims to systematically profile the transcriptomic complexity and RNA modification landscape of HBV in hepatocellular carcinoma models. Methods: We transfected PLC/PRF/5 and Huh7 cells with the HBV 1.3-mer WT replicon plasmid, followed by qPCR measurement of viral load. Total nucleic acids extracted from transfected cells underwent nanopore direct RNA sequencing. The complete HBV transcriptome was then analyzed in two established hepatocellular carcinoma cell lines (PLC/PRF/5 and Huh7), with alternative splicing, polyadenylation, and RNA modifications identified through comprehensive bioinformatics analysis. Results: Our analysis revealed substantial transcriptomic diversity, identifying 34 distinct splice variants—including 14 previously unreported isoforms—with cell-type-specific expression patterns. Additionally, we detected 30 high-confidence RNA modification sites across HBV transcripts, with 93% (28 sites) conserved between both cellular environments. Notably, we observed significant intercellular heterogeneity in poly(A) tail length distributions. Conclusions: A comparison of the post-transcriptional processing modifications of HBV in PLC/PRF/5 and Huh7 cells reveals that the former may be better able to mimic the immune evasion mechanisms of chronic HBV infection. In contrast, the longer poly(A) tails present in Huh7 cells facilitate efficient replication, rendering these cells more amenable to the study of HBV transcription and replication mechanisms. These findings comprehensively elucidate the post-transcriptional regulatory mechanisms of hepatitis B virus in different hepatocellular carcinoma cell lines, establishing a critical benchmark for selecting appropriate experimental models in virology research. The identified transcriptomic features may provide new insights for developing antiviral strategies targeting the viral epigenome. Full article

Chromophore domains were proposed in a previous work as the mediators of self-healing of optical properties in dye-doped polymers. A statistical mechanical model based on domains matches all observed self-healing dynamics as a function of dye concentration, temperature and light intensity. This suggests that domains are responsible. However, there is no direct observation of domains, nor has their physical morphology been determined. This work reports the first observation of domains in a self-healing polymer using resonant soft X-ray scattering (RSoXS), which gives a domain size in the range of 39.3 Å to 62.8 Å. This range includes the domain model’s prediction of an average domain size of roughly 30 molecules, which is about 56 Å, if the molecules form a loosely packed ball. X-ray scattering of samples of concentration spanning from neat polymer to the saturation limit of disperse orange 11 (DO11) dye in poly(methyl methacrylate) (PMMA) polymer shows domains in the expected size scales, with the mode of the effective scattering width varying little with concentration. However, for constant domain shape, the mode peak would decrease in q with increasing concentration, according to the domain model. This work suggests that the domain shape might change with concentration, which warrants further investigations of domain topology and geometry. The important evidence presented in this work is the direct experimental observation of domains, which is central to self-healing models. Full article

Huntingtin (HTT) is a large, ubiquitously expressed scaffold protein that participates in multiple cellular processes, including vesicular transport, transcriptional regulation, and energy metabolism. The mutant form of HTT (mHTT), characterized by an abnormal polyglutamine (polyQ) expansion in its N-terminal region, is the causative agent of Huntington’s disease (HD), a progressive neurodegenerative disorder. Current therapeutic efforts for HD have primarily focused on lowering HTT levels through gene silencing or promoting mHTT degradation. However, accumulating evidence suggests that post-translational modifications (PTMs) of HTT—such as phosphorylation, ubiquitination, acetylation, and SUMOylation—play pivotal roles in modulating HTT’s conformation, aggregation propensity, subcellular localization, and degradation pathways. These modifications regulate the balance between HTT’s physiological functions and pathological toxicity. Importantly, dysregulation of PTMs has been linked to mHTT accumulation and selective neuronal vulnerability, highlighting their relevance as potential therapeutic targets. A deeper understanding of how individual PTMs and their crosstalk regulate HTT homeostasis may not only provide mechanistic insights into HD pathogenesis but also uncover novel, more specific strategies for intervention. In this review, we summarize recent understanding on HTT PTMs, discuss their implications for disease modification, and outline critical knowledge gaps that remain to be addressed. Full article