Search Results (1,204)

Methacrylyl-CoA is a key metabolic intermediate in the valine catabolic pathway. Its accumulation has been found to be cytotoxic and associated with pathological conditions. Nevertheless, detailed biological effects of methacrylyl-CoA and methacrylate in human physiology and pathology are poorly understood. We propose that the electrophilicity of the alkene bond in the methacrylyl group can react with the cysteine residues in proteins resulting in an unexplored protein post-translational modification (PTM), cysteine S-2-carboxypropylation (C2cp). To test and validate this mechanistic hypothesis, we experimentally detected and profiled S-2-carboxypropylated proteins from the complex cellular proteome with the design and application of a bioorthogonal chemical probe, N-propargyl methacrylamide. We tested the probe in different mammalian cell models and demonstrated its versatility and sensitivity to protein cysteine S-2-carboxypropylation. We established quantitative chemical proteomics for global and site-specific profiling of protein S-2-carboxypropylation, which successfully identified 403 S-2-carboxypropylated proteins and 120 cysteine modification sites from HEK293T cells. Through bioinformatic analysis, we found that C2cp-modified proteins were involved in a variety of critical cellular functions including translation, RNA splicing, and protein folding. Our chemoproteomic studies demonstrating the proteome-wide distribution of cysteine S-2-carboxypropylation provide a new biochemical mechanism for the functional investigation of methacrylyl-CoA and understanding valine-related metabolic disorders. Full article

The rapid evolution of sequencing technologies has profoundly advanced precision oncology. Whole-exome sequencing (WES), whole-genome sequencing (WGS), and whole-transcriptome sequencing (RNA-Seq) enable comprehensive characterization of tumor biology by detecting actionable mutations, gene fusions, splice variants, copy number alterations, and pathway dysregulation. These approaches also provide critical insights into biomarkers such as homologous recombination deficiency (HRD), tumor mutational burden (TMB), and microsatellite instability (MSI), which are increasingly essential for guiding therapeutic decisions. Importantly, comprehensive genomic profiling not only refines patient stratification for targeted therapies but also sheds light on tumor–immune interactions and the tumor microenvironment, paving the way for more effective immunotherapeutic combinations. WGS is considered the gold standard for detecting germline mutations and complex structural variants, while WES remains central for detecting somatic driver mutations that guide targeted therapies. RNA-Seq complements these methods by capturing gene expression dynamics, identifying clinically relevant fusions, and revealing mechanisms of resistance. Together with advances in bioinformatics and artificial intelligence, these tools translate molecular data into actionable strategies for patient care. This review integrates insights from WGS, WES, and RNA-Seq with an overview of FDA- and EMA-approved targeted therapies, organized by tumor type, and highlights the molecular signaling pathways that drive cancer development and treatment. By bridging genomic profiling with regulatory-approved therapies, we outline current advances and future perspectives in delivering personalized cancer care. Full article

RNA maturation, particularly splicing, depends on coordinated actions of RNA-binding proteins through post-transcriptional processing and constitutes a central mechanism of gene regulation. Aberrant splicing is associated with various diseases, including cancer. Here, we show that the CoREST complex, in coordination with c-MYC, transcriptionally regulates a subset of RNA processing genes, including those encoding essential small nuclear ribonucleoproteins (snRNPs) required for proper spliceosome function. Genetic depletion or the pharmacological inhibition of the CoREST complex in melanoma cells disrupted spliceosome activity, leading to widespread changes in alternative mRNA isoform expression and reduced cell viability. These splicing alterations were associated with changes in the 2′-O-methylation (Nm) of U1 snRNA, a modification critical for spliceosomal function. The ectopic expression of the nucleolar protein NOLC1, a downstream target of the CoREST complex and known for its role in ribosomal RNA processing, partially rescued viability, splicing patterns, and U1 snRNA methylation in CoREST-deficient melanoma cells. Conversely, NOLC1 depletion sensitized melanoma cells to the MEK inhibitor trametinib, a clinical drug approved for treating advanced melanoma. Together, these findings uncover a novel CoREST-NOLC1 axis which is a transcriptional regulatory mechanism playing a significant role in RNA splicing, highlighting that NOLC1 is a downstream effector of the CoREST complex and a potential therapeutic target for melanoma treatment. Full article

Alternative splicing (AS) is a widely recognized post-transcriptional regulatory mechanism that plays a crucial role in plant evolution and environmental adaptation. In this study, five representative Panax species were systematically analyzed to examine the evolutionary conservation and functional characteristics of AS events. Results revealed an expansion in the number of AS events and associated genes across the Panax species, accompanied by a genome-wide shift in splicing types from a dominance of intron retention (IR) to an increase in exon skipping (ES), alternative donor (A5), and alternative acceptor (A3) events. Splicing preferences were also found to diverge among allotetraploid species, which exhibited more complex AS patterns. The genomic features of IR and ES events, such as GC content and length of the sequence involved in AS, were highly conserved among Panax species of different ploidy levels (diploid vs. allotetraploid). Genes harboring conserved IR events across all five species were identified, and functional annotation indicated that these genes are primarily involved in chromatin modification and RNA splicing-related processes. This study elucidates the dynamic remodeling of AS during the evolution of Panax and provides important insights into the evolutionary adaptive mechanisms of AS in plants. Full article

Treatment paradigms for B-cell lymphomas have evolved significantly in the last decades. Nevertheless, the widespread clinical use of immunotherapy has demonstrated that it invariably leads to the development of resistance. This review outlines the underlying molecular mechanisms of resistance associated with emerging immunotherapeutic strategies, including Chimeric Antigen Receptor (CAR) T cell therapy and bispecific antibodies (BsAbs). In high-grade B-cell lymphomas, nearly 50% of patients progress following CAR T treatment due to host-related factors affecting CAR T cell proliferation and persistence, as well as tumor-intrinsic factors, such as loss of CD19 epitope expression, trogocytosis, and other genomic alterations (e.g., CD19 mutations, chromothripsis, APOBEC mutational activity, and deletions of RHOA). Additional genomic and epigenetic events, including mutations, alternative splicing of CD19, and aberrant promoter methylation, further contribute to resistance. BsAbs, representing an off-the-shelf T-cell-redirecting strategy, have recently shown promising single-agent efficacy with a manageable toxicity profile, predominantly characterized by T cell overactivation syndromes. Similarly to CAR T cell therapy, BsAb resistance arises through diverse mechanisms, such as antigen loss, T cell dysfunction (exhaustion and regulatory T cell activation), tumor-intrinsic alterations (e.g., TP53 mutations and MYC amplifications), and immunosuppressive influences from the tumor microenvironment. These findings underscore the complexity of immune evasion in B-cell lymphomas and highlight the ongoing need to optimize immunotherapeutic strategies and develop combination approaches to overcome resistance. Full article

Chronic pain is a serious health issue, often irrationally managed by conventional analgesics. Duloxetine, a serotonin–norepinephrine reuptake inhibitor (SNRI), also effective in neuropathic and musculoskeletal pain, but the molecular mechanism of its analgesic action is still unclear. Here, we examined whether Duloxetine exerts pleiotropic effects by directly targeting phosphorylated STAT3 (pSTAT3), a key regulator of neuroinflammation and pain sensitization. Molecular docking showed that Duloxetine binds with pSTAT3 with binding energy −5.83 kcal/mol. Ruxolitinib, a JAK/STAT inhibitor used as reference, showed binding energy of −6.19 kcal/mol. Molecular dynamics (MD) simulations confirmed stable Duloxetine–pSTAT3 complexes, while MM-PBSA free energy analysis revealed more favorable binding for Duloxetine (ΔG = −15.17 kJ·mol⁻¹) than Ruxolitinib (ΔG = −12.98 kJ·mol⁻¹) for pSTAT3. In-vitro analyses, Western blot showed that Duloxetine significantly reduced IL-6–induced STAT3 and pSTAT3 expression in C2C12 cells in a dose-dependent manner (6.4 and 12.8 μM, *** p < 0.0001), although Ruxolitinib produced a stronger suppression. Transcriptomic analysis revealed Duloxetine-specific enrichment of mitochondrial, oxidative phosphorylation, and synaptic pathways, distinct from the immune-suppressive influence of Ruxolitinib. RNA-seq further revealed that STAT3 transcript abundance remains constant under all treatment conditions, indicating that post-transcriptional or post-translational mechanisms, such as phosphorylation-dependent activation, may be involved rather than transcriptional modulation of STAT3 in action of Ruxolitinib and Duloxetine and the formation of novel STAT3 indicating enhanced transcript diversity. The rMATS splicing analysis confirmed dose-dependent modulation, with Duloxetine promoting mild exon skipping at 6.4 μM (IncLevel 0.90 → 0.80) and recovery at 12.8 μM (0.85 → 0.86), while Ruxolitinib induced stronger exon inclusion (0.85 → 1.00,0.94), with broader transcript suppression at 6.4 μM and 12.8 μM, respectively. These findings establish Duloxetine as a dual-action therapeutic that combines neurotransmitter reuptake inhibition with pSTAT3 suppression and isoform-level transcriptomic modulation. This pleiotropic mechanism provides a rationale for its durable analgesic effects and supports repurposing in STAT3-associated disorders. Full article

Calcium/calmodulin-dependent protein kinase II (CaMKII) comprises multiple isoforms with distinct nuclear variants that exert transcriptional control in a context-dependent manner. Among them, CaMKIIδB and δ9 in the heart, and CaMKIIγ in the nervous system, have emerged as regulators of chromatin dynamics, transcription factor activity, and developmental gene programs. Nuclear localization is driven by splice-dependent nuclear localization sequences, with phosphorylation at defined serine residues modulating import and retention. Evidence supports CaMKII-dependent phosphorylation of class IIa HDACs (Ser467/Ser632 in HDAC4), linking CaMKII to MEF2 activation in cardiac hypertrophy, and interactions with NF-κB and HSF1 further expand its nuclear repertoire. In the nervous system, CaMKIIγ contributes to kinase-dependent gene expression, potentially influencing plasticity and disease susceptibility. While these mechanisms highlight nuclear CaMKII as an isoform-specific regulator of transcription, direct evidence remains elusive, and several CaMKII putative substrates require further validation. This review synthesizes current knowledge on nuclear CaMKII isoforms, emphasizes established mechanistic pathways, and outlines unsolved questions critical for understanding their roles in development, disease progression, and therapeutic targeting. Full article

Background: Medulloblastoma is an aggressive pediatric brain tumor characterized by marked molecular heterogeneity, which significantly impacts prognosis. The low frequency of genomic mutations in medulloblastoma suggests that alternative mechanisms, such as epigenetic regulation, may play a critical role in its pathogenesis. Methods: Using the EpiFactors database, we investigated the expression of epigenetic regulators in two independent RNA sequencing cohorts [Pediatric Brain Tumor Atlas (PBTA) and Williamson], stratified by molecular subgroups and clinical outcomes. We further analyzed expression heterogeneity at the single-cell level in malignant medulloblastoma cells using single-cell RNA sequencing. Results: Members of the SWI/SNF superfamily were dysregulated across all four molecular subtypes of medulloblastoma. Subtype-specific alterations were also observed: the acetyltransferase complex was shared between Group 3 (with SMARCD3 as a potential marker) and Group 4 (with RBM24 as a potential marker); SWR1, β-catenin/TCF, and protein–DNA complexes were specifically enriched in SHH-MB (with EYA1 and SATB2 as SHH markers); and RSC-type, PRC1, DNA polymerase complexes, and X-chromosome-related factors were enriched in WNT-MB (with FOXA1 and PIWIL4 as WNT markers). An epigenetic score (epi-score), linked to RNA metabolism and S-adenosyl-L-methionine pathways, was developed and identified as an independent adverse prognostic factor. High epi-scores were associated with proliferative, stem-like SHH malignant cells (characterized by G2/M phase, low pseudotime, and high entropy), exhibiting alterations in RNA splicing, DNA recombination, and nuclear division. Conclusions: Expression heterogeneity of epigenetic regulators is closely associated with molecular subgroups and clinical outcomes in medulloblastoma. These findings highlight the role of epigenetic dysregulation in RNA metabolism and tumor progression, particularly in SHH-driven proliferative cells. Full article

Rubisco activase (RCA) is an ATP-dependent enzyme that plays a crucial role in plant stress responses by regulating the catalytic activity of Rubisco. However, the alternative splicing and functional characteristics of the RCA gene exhibit notable species-specific diversity. The variable splice forms and functions of the RCA gene in mangrove plants remain poorly understood. Herein, we cloned the RCA cDNA in the leaves of mangrove plant Kandelia candel (L.) in response to combined flooding and salinity stress, and performed systematic expression analysis and functional validation. Our results demonstrated that the RCA gene undergoes alternative splicing to produce two isoforms, designated as KcRCA_l (GenBank accession: MG492021) and KcRCA_s (GenBank accession: MG492022), respectively. The KcRCA_l encodes a 440-amino acid protein (42.49 kDa) belonging to the β-isoforms, while KcRCA_s encodes a 474-amino acid protein (46.10 kDa) classified as the α-isoforms. Moreover, protein structure analysis revealed that both isoforms contain phosphorylation and lysine acetylation modification sites. Phylogenetic analysis indicated that KcRCA shares the closest evolutionary relationship with RCA from Cicer arietinum (chickpea) and Durio zibethinus (durian). Furthermore, RT-qPCR analysis revealed that the expression levels of KcRCA_l and KcRCA_s were significantly upregulated in K. Candel leaves under the combined stress condition. The following functional validation studies in transgenic Arabidopsis demonstrated that overexpression of the KcRCA cDNA enhances the plant’s tolerance to resist flooding and salinity stress while improving antioxidant capacity and increasing RCA and Rubisco activity, thereby maintaining photosynthetic efficiency under combined flooding and salinity stress. Our study not only provides new experimental evidence for understanding the molecular mechanisms of plant flooding and salinity stress, but also offers theoretical foundations for breeding flooding- and salinity-tolerant crops. Full article

Acute leukemias are highly aggressive hematologic malignancies that demand intensive chemotherapy regimens. However, drug toxicity remains a major barrier to treatment success and patient survival. In this context, pharmacogenomics offers a promising strategy by identifying single-nucleotide variants (SNVs) that influence drug metabolism, efficacy, and toxicity, ultimately impacting treatment outcomes. This study analyzed data from the ClinPGx/PharmGKB database to identify clinically annotated variants related to chemotherapy response in Acute Myeloid Leukemia (AML) and Acute Lymphoblastic Leukemia (ALL). A total of 24 variants were curated for AML and 57 for ALL. Among these, nonsynonymous variants were most frequent in ALL (31.6%), while synonymous variants predominated in AML (33.3%). Although traditionally considered neutral, synonymous and intronic variants may influence gene expression through regulatory or splicing mechanisms. The analysis revealed clinically significant variants associated with chemotherapy response, particularly in the ABCB1 gene, observed in 12.5% of AML and 10.5% of ALL cases. Several variants, particularly TPMT, NUDT15, ABCC1, SLC28A3, and RARG, were associated with severe adverse effects such as myelotoxicity, mucositis, cardiotoxicity, and hepatotoxicity. This study reinforces the importance of genetic variants in modulating the therapeutic response and toxicity to chemotherapy drugs in acute leukemias. Analysis of ClinPGx/PharmGKB data emphasizes ABCB1 as a potential resistance marker and supports pre-treatment genotyping of genes like TPMT and NUDT15 to prevent severe toxicities. Future advances should include the expansion of pharmacogenetic studies in underrepresented populations and the clinical validation of new markers in prospective trials, aiming to consolidate precision medicine as a routine part of the therapeutic management of acute leukemias. Full article

The double-sex and mab-3-related transcription factors (Dmrt) are widely distributed in the animal kingdom and play a crucial role in sex determination and differentiation. In this study, we identified eight Dmrt transcription factors in the genome of the centipede Scolopendra mutilans, including five Dsx-related genes (as Dsx1, Dsx2 (five splice variants), Dsx3, Dsx4 and Dsx5) and three Dmrt-related genes (as Dmrt11E, Dmrt99B, and Dmrt93B). Phylogenetic analysis revealed evolutionary conservation across arthropods, with Dsx genes clustered into class-specific clades (Chilopoda, Insecta, Crustacea, Arachnida). Structural analysis confirmed conserved DM domains and sex-specific motifs, with tandem duplication of Dsx2 on chromosome 4. Expression profiling demonstrated significant sexual dimorphism: Dsx5 was female-biased, whereas Dsx2, Dsx3, and Dsx4 were male-biased, suggesting their functional divergence in sexual differentiation. Correlation analysis linked the expression of Sxl and Fem-1C to the regulation of Dsx isoforms, suggesting the presence of a conserved upstream regulatory cascade for sex-specific splicing. These findings elucidate the structural and functional landscape of Dmrts in S. mutilans, and provide insights into how sex-determination mechanisms evolved in Myriapoda. Full article

Alternative splicing (AS) is a crucial post-transcriptional regulatory mechanism that enhances transcriptomic and proteomic diversity by generating multiple mRNA isoforms from a single gene. In plants, AS plays a central role in modulating growth, development, and stress responses. We summarize the prevalence and functional roles of AS in plant development and stress adaptation, highlighting mechanisms that link AS to hormone signaling, RNA surveillance, and epigenetic regulation. Polyploid crops, with their duplicated genomes, exhibit expanded AS complexity, contributing to phenotypic plasticity, stress tolerance, and adaptive evolution. Thus, this review synthesizes current knowledge on AS in plants, with a focus on three economically important polyploid crops—Brassica napus, Gossypium hirsutum, and Triticum aestivum. We also discuss how subgenome interactions shape diversity in polyploids and influence trait variation. Despite significant advances enabled by high-throughput sequencing, mechanistic studies that directly link specific AS events to phenotypic outcomes remain limited. Understanding how polyploidy reprograms AS and how isoform variation contributes to stress adaptation will be critical for harnessing AS in crop improvement. Full article

Mycobacterium tuberculosis (M. tuberculosis) has developed some strategies to evade host immune responses through ubiquitination, thereby facilitating persistent mycobacterial infection. The Rv3717 protein has been identified as a peptidoglycan (PG) amidase that contributes to mycobacterial survival, but its exact mechanism is still unclear. The findings of this study indicate that Rv3717 inhibits mycobacterial clearance within pulmonary epithelial cells. To elucidate the molecular mechanisms by which Rv3717 facilitates persistent infection, we identified intracellular candidates interacting with Rv3717 using co-immunoprecipitation (Co-IP) combined with liquid chromatography–mass spectrometry (LC-MS/MS). The unique proteins are categorized into three functional networks: mRNA splicing, the immune system process, and the translation process through Protein–Protein Interaction (PPI) analysis. The candidate interacting proteins of Rv3717 are involved in interleukin-2 enhancer-binding factor 2 (ILF2) and TAF15, as well as the polyubiquitin chain (UBC) and E3 ubiquitin ligase TRIM21. Our results suggest that intracellular Rv3717 is likely to influence biological processes through the potential interacting proteins. Our findings confirmed that Rv3717 interacted with interleukin enhancer-binding factor 2 (ILF2) through Co-IP and immunofluorescence assays. Furthermore, Rv3717 was verified to bind with ubiquitin and be degraded through the proteasome system. More importantly, the ubiquitination of Rv3717 accelerated the proteasomal degradation of ILF2 and downregulated the expression of IL-2. This study is the first to propose that the ubiquitination of the mycobacterial membrane vesicle-associated protein Rv3717 facilitates the proteasomal degradation of ILF2, resulting in the downregulation of IL-2 expression. Overall, the role of intracellular Rv3717 in promoting mycobacterial survival is associated with its ubiquitination and the proteasomal degradation of ILF2. Full article

The search for novel tumor-specific markers and therapeutic targets is driving the development of more effective and personalized treatment strategies for cancer patients. This article focuses on investigating a promising new source of biomarkers—readthrough transcripts, or downstream-of-gene (DoG) transcripts. These transcripts are extended products of gene transcription that continue into intergenic regions and can overlap neighboring genes, sometimes giving rise to cis-splicing of adjacent gene (cis-SAGe) transcripts. Recent studies suggest that besides frequently being a “transcriptional noise”, DoG transcripts can perform regulatory functions, serve as a source of novel protein products, and act as prognostic markers of patient survival across various cancers. This article aims to investigate the regulatory mechanisms and functional significance of readthrough transcripts in tumors, to identify currently known tumor-specific variants with potential utility as cancer biomarkers or therapeutic targets, and to evaluate the most suitable approaches for their detection. The knowledge gained through this research may provide a foundation for the development of diagnostic test systems and the design of new anticancer drugs. Full article

To evaluate the creep and fatigue fracture lives of structural acrylic spliced components fabricated via bulk polymerization, and to elucidate the associated fracture mechanisms, this study conducted creep and fatigue tests on spliced coupons annealed at 85 °C and 65 °C, as well as base material coupons. The experimental life data were fitted using log-log linear regression models. Based on statistical analysis, a simple yet robust statistical framework was established for life prediction, featuring three design curves: 97.7% survival curves, improved 95% confidence interval lower bounds, and one-sided tolerance curves. Fractographic examination using scanning electron microscopy (SEM) was performed to characterize macroscopic failure modes. The results indicate distinct threshold behavior between stress levels and both creep and fatigue life. The creep threshold stresses are 25 MPa for the base material, 29 MPa for the spliced coupons annealed at 85 °C, and 17 MPa for the spliced coupons annealed at 65 °C. Corresponding fatigue threshold stress amplitudes are 21 MPa, 22 MPa, and 31 MPa, respectively. Failure in the base material is primarily initiated by randomly distributed internal defects, whereas failure in the spliced coupons is mainly caused by defects within the seam or interfacial tearing. Full article