Search Results (151)

Background/Objectives: The homeostatic imbalance between tumor metastasis-promoting genes and metastasis-suppressing genes determines the metastatic potential of lung adenocarcinoma (LUAD) cells. However, the post-transcriptional regulation mechanism mediated by RNA-binding proteins (RBPs) in maintaining the expression balance of tumor metastasis-related genes remains unclear. Methods: The expression of MCPIP3 and IGF2BP3 in human lung cancer tissues was analyzed using bioinformatics methods and validated using qRT-PCR, immunohistochemistry, and immunoblotting. In vitro cellular experiments and in vivo animal examinations were used to evaluate the effects of MCPIP3 and IGF2BP3 on metastasis. RNA sequencing, PCRarray, RNA pull-down and mass spectrometry, RNA-EMSA, RNA immunoprecipitation (RIP), mRNA stability, and luciferase assays were performed to elucidate the mechanism. Results: MCPIP3 is expressed at low levels, while IGF2BP3 is highly expressed in LUAD tissues. Lower MCPIP3 expression and higher IGF2BP3 expression in lung cancer tissues were significantly associated with poor prognosis in LUAD patients. MCPIP3 significantly inhibited the metastasis of lung cancer cells both in vitro and in vivo, whereas IGF2BP3 promoted metastasis. Mechanistically, MCPIP3 specifically bound to the stem–loop structure in the 3′UTR (untranslated region) of the METAP2 transcript and degraded its mRNA via its RNase domain. In contrast, by interacting with the common stem–loop structure, IGF2BP3 could stabilize METAP2 mRNA and promote its expression. Notably, inverse correlations were observed between the expression of MCPIP3 and IGF2BP3 and the expression of METAP2 in LUAD tissues. Conclusions: MCPIP3 and IGF2BP3 antagonistically control lung cancer cell metastasis by balancing the expression of metastasis-promoting genes through mediating mRNA stability, thereby providing potential targets for lung cancer treatment. Full article

Ryanodine receptor-like (RyR-like) is a key endoplasmic reticulum (ER) Ca²⁺ release channel governing intracellular Ca²⁺ homeostasis and cellular stress responses in invertebrates. However, its function in bivalves under high-temperature stress remains unclear. In the present study, one RyR-like was identified from Yesso scallop Patinopecten yessoensis (PyRyR-like). Its function in regulating intracellular Ca²⁺, IRE1α-mediated unfolded protein response (UPR) and apoptosis in the mantle after high-temperature (25 °C) treatment was investigated using molecular cloning, qRT-PCR, Western blot, pull-down assay, cellular calcium imaging, TUNEL and histology assays; High temperature treatment significantly increased intracellular Ca²⁺ content at 1 and 6 h (p < 0.05), but decreased it at 3, 12 and 24 h (p < 0.05); meanwhile, the cAMP level, PyPKA activity, mRNA expression level of PyRyR-like, and protein expression levels of PyFKBP12 and PyGRP78 were significantly increased at different times. However, high temperature did not affect the expression level of PyNVL and PyXBP1(S). The SPRY and RYR domains of PyRyR-like separately interacted with PyFKBP12 and PyPKA. Moreover, RyR antagonist Dantrolene reversed high-temperature-induced alterations in Ca concentration, PKA activity, and core UPR- and apoptosis-related molecules, and suppressed Caspase-3 activity. These findings suggest that PyRyR-like plays an important role in the high-temperature response of scallops by regulating intracellular Ca²⁺ homeostasis and mediating UPR activation and apoptosis, providing new insight into the molecular mechanism underlying scallop adaptation to high temperature. Full article

Background: Hydroxysafflor Yellow A (HSYA), the major bioactive component from Carthamus tinctorius L., exerts significant protective effects against myocardial ischemia-reperfusion injury (MIRI). Mitophagy is pivotal in the pathological process of MIRI, yet the specific molecular mechanism underlying HSYA-mediated mitophagy regulation remains unclear. Objective: This study aimed to investigate the association between HSYA treatment and mitochondrial autophagy in murine MIRI and to explore the potential mechanistic role of the SIRT1-FOXO3-BNIP3 signaling pathway using functional loss-of-function and rescue experiments. These findings may provide preliminary evidence supporting the clinical translational potential in MIRI therapy. Methods: Mouse myocardial ischemia-reperfusion injury (MIRI) model and oxygen-glucose deprivation/reoxygenation (OGD/R)-induced AC16 cardiomyocyte injury models were established. Metabolomics, molecular docking, and surface plasmon resonance (SPR) techniques were combined to screen the potential targets of HSYA. The SIRT1 inhibitor EX527 and SIRT1 siRNA were used to verify the underlying mechanism. Cardiac function, myocardial infarct size, mitochondrial function, the expression of autophagy-related proteins, and protein–protein interaction were detected and analyzed. Results: Compared with the MIRI group, HSYA significantly improved cardiac function in mice, as evidenced by increased left ventricular ejection fraction (LVEF) and left ventricular fractional shortening (LVFS) (p < 0.01), attenuated ST-segment elevation, and improved myocardial perfusion. HSYA also markedly reduced myocardial infarct size (p < 0.01) and serum levels of CK-MB, LDH, and cTnI (all p < 0.01) and ameliorated myocardial histopathological damage and mitochondrial ultrastructural integrity. Mechanistic studies revealed that HSYA significantly upregulated the expression of SIRT1, FOXO3, BNIP3, Beclin-1, and the LC3II/I ratio while downregulating p62 expression (p < 0.01), consistent with enhanced mitophagy-related activity. Furthermore, these protective effects were markedly attenuated upon SIRT1 inhibition or siRNA-mediated silencing, whereas HSYA intervention partially reversed these alterations. Additionally, co-immunoprecipitation (Co-IP) and pull-down assays demonstrated that HSYA promoted protein–protein interactions between SIRT1-FOXO3, FOXO3-BNIP3, and BNIP3-LC3B. Conclusions: These findings highlight that HSYA is associated with improved cardiac function, enhanced mitophagy-related activity, and upregulated SIRT1-FOXO3-BNIP3 signaling, providing robust experimental evidence for its clinical translational application in MIRI treatment. Full article

Bax, a key member of the B-cell lymphoma 2 (Bcl-2) protein family, is essential for inducing mitochondrial apoptosis. In this study, we employed yeast two-hybrid screening to identify ubiquitin-specific protease 49 (USP49) as a binding partner of Bax. Subsequent immunoprecipitation and glutathione S-transferase (GST) pull-down assays confirmed their direct interaction. Functional assays showed that USP49 reduces Bax polyubiquitination at multiple lysine residues within ubiquitin, with the strongest effects observed on K11, K29, K33, and K63 linkages. In contrast, its effect on K48-linked ubiquitination was weak and insufficient to influence Bax protein stability, indicating that USP49 does not regulate Bax abundance through proteasomal degradation. Instead, RT-qPCR analysis revealed that USP49 overexpression significantly increased Bax mRNA levels, and this effect was maintained under apoptosis stimuli (UV, H₂O₂, and STS), indicating transcriptional regulation largely independent of stress-induced damage, whereas its effect was modest and not statistically significant under starurosporine treatment. Collectively, these findings demonstrate that USP49 regulates Bax primarily through K29/K33/K63-linked ubiquitination and transcriptional upregulation, highlighting its role as a stress-responsive modulator of apoptosis and a potential therapeutic target in cancer. Moreover, under DNA damage condition (UV), USP49 overexpression marked enhanced apoptosis. Full article

This study aimed to investigate the molecular mechanisms underlying dopaminergic injury induced by gestational and lactational atrazine (ATR) exposure in rat offspring, with a particular focus on non-coding RNA-mediated regulation. Pregnant rats were exposed to ATR during gestation and lactation. Offspring underwent behavioral testing at postnatal day 21 (PND21) and were sacrificed for midbrain tissue collection at PND28. Behavioral alterations, histopathological changes in the substantia nigra, and dopaminergic marker expression were assessed to evaluate ATR-induced neurotoxicity. Whole-transcriptome sequencing was then performed to identify differentially expressed mRNAs, miRNAs, and lncRNAs, followed by co-expression, protein–protein interaction, and competing endogenous RNA (ceRNA) network analyses. Key targets were validated by qRT-PCR. Candidate molecules identified from transcriptomic and ceRNA analyses were further examined in an ATR-induced neurotoxicity model established in RA-differentiated SK-N-SH cells. Dual-luciferase reporter, Ago2-RNA immunoprecipitation, and biotin-labeled RNA pull-down assays were used to examine putative binding relationships and molecular interactions. In addition, lentivirus-mediated Elavl4 overexpression was performed to further evaluate the role of this candidate regulator in ATR-induced Nurr1 downregulation. Gestational and lactational ATR exposure induced significant behavioral abnormalities in rat offspring. These changes were accompanied by histopathological alterations in the substantia nigra, including reduced TH immunoreactivity, as well as abnormal expression of dopaminergic markers, characterized by decreased TH and Nurr1 levels and increased α-syn expression. Together, these findings indicate the presence of dopaminergic injury. Whole-transcriptome analysis further revealed widespread dysregulation of mRNAs, miRNAs, and lncRNAs in ATR-exposed offspring. Subsequent integrative analysis suggested a potential ceRNA regulatory relationship among Elavl4, miR-301a-5p, and Nurr1, which was further supported by qRT-PCR. Dual-luciferase reporter, RIP, and RNA pull-down assays supported direct interactions between miR-301a-5p and both Elavl4 and Nurr1, as well as their association with the Ago2-containing silencing complex. Moreover, Elavl4 overexpression partially reversed ATR-induced Nurr1 downregulation in vitro. Gestational and lactational ATR exposure induced behavioral abnormalities and dopaminergic injury in rat offspring. Whole-transcriptome analysis combined with experimental validation suggests a potential association between the Elavl4/miR-301a-5p/Nurr1 ceRNA axis and ATR-induced dopaminergic injury, providing insight into the post-transcriptional mechanisms underlying developmental neurotoxicity. Full article

Circular RNAs (circRNAs) exhibit significant sex- and development stage-specific expression patterns in the gonads of various fish species, yet their functions and regulatory mechanisms in male reproductive development remain largely unexplored in crucian carp (Carassius auratus). In this study, we characterized the expression features and biological functions of circSPEF2, a circular RNA derived from the reproduction-related gene spef2. Our results showed that circSPEF2 expression was markedly elevated in mature testes and progressively upregulated during gonadal maturation. Functional studies suggested that circSPEF2 likely does not act through a ceRNA-dependent mechanism. Transcriptome sequencing following circSPEF2 overexpression identified 45 upregulated and 70 downregulated differentially expressed genes, with GO and KEGG enrichment analyses revealing significant alterations in multiple gonadal development-related genes and signaling pathways. Subsequent siRNA-mediated knockdown of circSPEF2, combined with qRT-PCR validation, confirmed that circSPEF2 positively regulates the expression of genes associated with cell maturation and differentiation, including prdm1a, lamc2, and slc25a27, while concurrently suppressing that of proliferation- and apoptosis-related genes such as wnt8b, cpeb3, and bcl2l11. Furthermore, RNA pull-down combined with mass spectrometry identified three candidate circSPEF2-binding proteins, namely, hnRNP A/B, SRSF2, and CFAP263. Collectively, these findings indicate that circSPEF2 plays an important role in male gonadal development in fish and provide new insights into the post-transcriptional regulatory mechanisms underlying vertebrate male reproduction. Full article

Cellular therapy using human cardiac mesenchymal progenitor cells (hMPCs) for regenerative medicine is hindered by poor cell survival and senescence. Long non-coding RNAs (lncRNAs) are critical regulators of cellular processes, yet their role in cardiac aging remains underexplored. Here, lncRNA microarray profiling identified a novel lncRNA, XLOC_002543, upregulated in hMPCs preconditioned with cobalt protoporphyrin (CoPP), which was named CoPP-Induced and SFPQ-Associated RNA Transcript (CISAT) due to its interaction with splicing factor proline and glutamine rich (SFPQ), confirmed via RNA pull-down and immunoprecipitation. CISAT was the only highly expressed transcript among seven lnc-ANKMY1-5 variants in hMPCs, as shown by RT-PCR. Notably, CISAT expression decreased in aging/senescent hMPCs, correlating with elevated p16^INK4A, a senescence marker. Overexpression of CISAT reduced p16^INK4A levels; enhanced hMPC survival, proliferation, and migration; and increased antioxidant and anti-apoptotic protein expression, while CISAT knockdown reduced resistance to H₂O₂-induced oxidative stress. In vivo, intramyocardial transplantation of CISAT-overexpressed hMPCs in an immune-deficient murine myocardial infarction model reduced fibrosis, promoted angiogenesis, and preserved cardiac function. Mechanistically, CISAT interacts with SFPQ to regulate NRF2-mediated redox homeostasis and inhibits p38 MAPK phosphorylation, mitigating senescence and enhancing cell survival. These findings suggest that targeting CISAT to modulate redox signaling and p38 MAPK pathways in aging hMPCs could improve their therapeutic efficacy for myocardial repair in heart disease. Full article

The transcription factor c-Myc is known to regulate DNA replication via a non-transcriptional mechanism by interacting with proteins of the pre-replicative complex. In addition, c-Myc localizes to DNA replication foci, similarly to Proliferating Cell Nuclear Antigen (PCNA); however, the significance of this localization remains unclear. Here, we investigated whether c-Myc interacts with PCNA and analyzed the possible function of this association. We found a conserved interaction motif, the PCNA-interacting protein (PIP) box, in the N-terminal region of c-Myc. Confocal microscopy analysis showed co-localization with PCNA in early S-phase, but not in late S-phase cells. Co-immunoprecipitation from cell extracts and pull-down of recombinant proteins indicated a direct physical association between c-Myc and PCNA, which was confirmed in situ by the Proximity Ligation Assay (PLA). Further experiments demonstrated that c-Myc interacts with CUL4A and DDB1, components of the Cullin Ring E3 ubiquitin ligase 4 (CRL4) complex, in which PCNA functions as a cofactor. Mutations in the PIP box of c-Myc, as well as depletion of CUL4A by RNA interference, resulted in an increased stability of c-Myc protein. These results suggest that the interaction with PCNA functionally contributes to the regulation of c-Myc stability in early S phase via the CRL4 complex. Full article

We have previously identified MACC1 and IER2 as functional biomarkers in the context of colorectal cancer. In silico correlation analysis suggested a possible functional connection between the expressions of these biomarkers, given that a significant positive correlation between IER2 and MACC1 RNA was observed. In loss- and gain-of-function experiments, we found that MACC1 positively regulates the expression of IER2. Furthermore, pulldown experiments provided evidence for MACC1-IER2 protein–protein interactions. Functionally, MACC1 enhanced proliferation of HCT116 cells overexpressing IER2 but not of HCT116 cells with knockdown of IER2 expression. Patients with high expressions of both biomarkers lived significantly shorter, whereas those with low concentrations of both markers showed the longest survival. Taken together, these findings show a functional interplay between the colorectal biomarkers MACC1 and IER2, which, in turn, has an impact on the survival of colorectal cancer patients. Full article

Long non-coding RNAs (lncRNAs) encoded by viruses play crucial roles in viral infection, pathogenesis processes, the interaction between viruses and hosts, and immune escape. Herein, by employing RNA pull-down, mass spectrometry technology, and RNA immunoprecipitation, we identified a host protein (G3BP2) that specifically interacts with the lncRNA encoded by the infectious bronchitis virus (IBV). Additionally, we identified a novel host miRNA (novel-340) in IBV-infected H1299 cells and further verified that novel-340 can target the 3′-UTR (untranslated region) of G3BP2 and downregulate its expression in a dose-dependent manner. We discovered that IBV-lncRNA may facilitate IBV replication in H1299 cells through direct interaction with G3BP2 and/or the regulation of the IBV-lncRNA/novel-340/G3BP2 interactive regulatory network. This work deepens the understanding of the biological function of IBV-lncRNA. Full article

Aptamers are powerful tools for detecting and analyzing biomolecules that consist of proteins or nucleic acids. However, their application to aptamers against viroids—highly structured self-replicating RNAs—has not yet been explored. In this study, a magnetic bead- and high-throughput sequencing-based SELEX (MB-HTS-SELEX) protocol for selecting potential aptamers against potato spindle tuber viroid (PSTVd) is presented. Full-length biotinylated-PSTVd RNA was transcribed in vitro, immobilized on streptavidin-coated magnetic beads, and incubated with a library of ~3.32 × 10¹⁴ molecules of random single-stranded oligo-DNAs (oligo-ssDNAs) of 20, 30, or 40 nucleotides (L20, L30, or L40, respectively) flanked by primer binding sites for downstream PCR amplification. Simultaneous biotin labeling of the anti-aptamer strand of the resulting double-stranded DNA (dsDNA) amplicons facilitated strand separation using streptavidin-coated magnetic beads. After 10 selection rounds, high-throughput sequencing, followed by bioinformatics analysis of the generated sequences, allowed for the detection of several enriched sequences, representing putative PSTVd-binding aptamers. Subsequent pull-down assays showed that the most abundant oligo-ssDNA in L30 was docked on PSTVd molecules. This combination method may ameliorate the selection of high-affinity aptamers against PSTVd, reduce the number of selection cycles, time, and other costs of aptamer production, thereby promoting future massive and cost-effective viroid detection and characterization. Full article

Metastatic breast cancer (BC) remains a major clinical challenge, and identifying molecular mechanisms driving tumor cell migration and invasion is critical to develop effective therapeutic strategies. Clusterin (CLU), a secreted chaperone-like protein, is upregulated in BC and metastatic tissue; however, its functional contribution to tumor aggressiveness remains unclear. Here, we silenced CLU by siRNA in two BC cell lines with distinct aggressiveness and examined its impact on migration, invasion, and associated signaling pathways. Following CLU silencing, cell migration and invasion were assessed using transwell assays. Cytoskeletal organization was evaluated by F-actin staining, while downstream signaling pathways were analyzed by RT-PCR, Western blotting, and Rho GTPase pull-down. A comparative proteomic analysis was performed in CLU-expressing and CLU-silenced MDA-MB-231 cells. CLU knockdown significantly reduced migration and invasion in MDA-MB-231, concomitantly with loss of F-actin-rich membrane protrusions, reduced expression of MMP9, COL1A1, and COL4A1, and decreased activation of Akt, NF-κB, and RhoA. Proteomic profiling revealed extensive remodeling of pathways involved in cell adhesion, cytoskeletal dynamics, and extracellular matrix interactions. Differently, no or very mild effects were observed in CLU-silenced MCF-7 cells. These findings identify CLU as an upstream regulator of a pro-metastatic adhesion–cytoskeleton signaling in BC, selectively operative in EMT-engaged, basal-like cells, highlighting the importance of patient stratification for CLU-targeted therapeutic strategies. Full article

The circadian clock genes in tomato are key regulators of cold stress adaptation. However, the low-temperature regulatory mechanism of the circadian clock gene SlPCL1 remains unclear. In this study, we evaluated the role of SlPCL1 in cold tolerance through low-temperature treatment of transgenic plants. Downstream target genes were identified using RNA-seq, RT-qPCR, yeast-one-hybrid (Y1H), dual-luciferase assays, and electrophoretic mobility shift assay (EMSA), while interacting proteins were characterized using yeast-two-hybrid (Y2H), luciferase complementation imaging (LCI), and pull-down assays, thereby elucidating the molecular mechanism underlying SlPCL1-mediated low-temperature regulation. We identified SlPCL1 as a nuclear-localized circadian clock gene with transcriptional repressor activity. Overexpression of SlPCL1 resulted in a cold-sensitive phenotype, whereas virus-induced gene silencing (VIGS)-mediated silencing of SlPCL1 enhanced cold tolerance. SlNPF4.6 functions as an abscisic acid (ABA) transporter involved in ABA transport. RNA-seq and RT-qPCR identified the ABA transporter SlNPF4.6 as a downstream target. Functional assays confirmed that SlPCL1 binds to the MYB element in the SlNPF4.6 promoter to repress its expression. Meanwhile, VIGS-mediated silencing of SlNPF4.6 decreased cold tolerance. Furthermore, the expression levels of the ABA receptor SlPYLs in the silenced lines were significantly reduced, confirming the decrease in intracellular ABA content. SlSUMO1, a ubiquitin-like protein, can influence gene transcription through noncovalent interactions. In addition, SlSUMO1 was found to interact with the SlPCL1 protein, attenuating SlPCL1 transcriptional repression activity. Together, these findings establish an SlSUMO1-mediated fine control mechanism of the SlPCL1-SlNPF4.6 regulatory module. This integration of circadian clock regulation uncovers new molecular mechanisms of cold tolerance and supports the development of cold-resistant breeding materials. Full article

Carbonic anhydrase 3 (CA3) exhibits low enzymatic activity compared to other CA isoforms but contains two surface-exposed cysteine residues that undergo glutathionylation under oxidative stress. Highly expressed in muscle tissue, CA3 has been implicated in cellular protection, particularly through interactions with Bcl2-Associated Athanogene 3 (BAG3), modulating autophagy, while CA3 overexpression decreased hypoxia-induced apoptosis in cardiomyocytes. In this study, we investigated the impact of CA3 overexpression on cellular pathways in HEK293T, MDA-MB-231, and SVCT cells using RNA sequencing and proteomics. Gene Set Enrichment Analysis (GSEA) in HEK293T cells revealed the down-regulation of pathways related to protein synthesis, RNA processing, Roundabout signalling, selenocysteine-metabolism, and suppression of neurodegenerative disease-associated pathways. Human breast epithelial cell lines under normoxia and hypoxia showed down-regulation of similar pathways, although notably, hypoxic conditions also suppressed interferon α/β signalling. Proteomic analysis in HEK293T cells using HaloTag pull-down experiments identified putative novel CA3 binding partners, including heat shock 70 kDa proteins 1 and 8, and ribosomal protein S2 (RPS2). RANBP2 protein was consistently up-regulated after CA3 overexpression, irrespective of the presence of CA3 surface-exposed cysteines and HaloTag orientation. These findings suggest that CA3 modulates key cellular processes beyond its enzymatic role, contributing to stress resilience through pathway-level regulation and protein interactions, potentially impacting autophagy and neurodegenerative disease. Full article

Background/Objectives: Atherosclerosis (AS)-related cardiovascular diseases are a major global health threat, with vascular smooth muscle cells (VSMCs) phenotypic switching, abnormal proliferation, and migration as key progression drivers. Nuclear receptor coactivator 4 (NCOA4), a core ferritinophagy mediator overexpressed in AS plaques, may promote VSMCs ferroptosis by perturbing mitochondrial iron metabolism and ROS homeostasis, but precise mechanisms remain unclear. The classic Chinese herbal combination “Gualou-Xiebai” (GLXB) has anti-AS effects, yet how it modulates NCOA4-mediated ferroptosis to inhibit VSMCs’ functions is unknown. This study addresses this gap to advance GLXB’s therapeutic potential and identify AS targets. Methods: An AS model was established in ApoE^−/− mice by 12-week high-fat diet feeding, with model validation confirmed via ultrasound monitoring and H&E staining. NCOA4 was genetically modulated (knockdown and overexpression) to assess its role in plaque formation and lipid deposition using H&E staining, aortic imaging, immunofluorescence, and Western blotting. In vitro, VSMCs were stimulated with ox-LDL to induce proliferation and migration. NCOA4 was silenced using siRNA to examine associated ferroptosis levels and molecular mechanisms. Protein interactions between NCOA4 and the mitochondrial iron storage protein FTMT were evaluated by Co-IP and GST pull-down assays, while mitochondrial ROS (mitoROS) levels were measured to explore functional relationships. The extent of ferroptosis and the underlying regulatory mechanisms were assessed following treatment with GLXB-containing serum or transfection with small interfering RNA targeting LOX-1 (si-LOX-1). Results: NCOA4 knockdown reduced aortic lipid deposition, plaque burden, VSMC proliferation/migration, and mitochondrial ferroptosis. NCOA4 bound and suppressed FTMT, inducing mitochondrial iron overload, ROS accumulation, membrane depolarization, and ferroptosis. Combining NCOA4 silencing with FTMT inhibition elevated mitoROS, confirming the axis’s role in iron homeostasis. GLXB attenuated VSMCs dysregulation in vivo and in vitro, an effect abrogated by LOX-1 overexpression. Conclusions: NCOA4 promotes AS by binding FTMT, disrupting mitochondrial iron homeostasis, and triggering VSMCs ferroptosis. GLXB inhibits LOX-1-mediated NCOA4 expression, mitigating ferroptosis and VSMCs dysregulation, supporting its potential as a targeted anti-AS therapy. Full article