Search Results (332)

Plant homeodomain (PHD) finger protein 20-like 1 (PHF20L1) is a novel epigenetic “reader” that specifically recognises histone post-translational modifications (PTMs) via its Tudor and PHD finger domains, thereby regulating chromatin remodelling, DNA damage repair, and oncogene transcriptional activation. This review comprehensively summarises the role of PHF20L1 in various cancers, including breast, ovarian, and colorectal cancers, as well as retinoblastomas, and elucidates its molecular mechanisms of action in cancer pathogenesis. Accumulating evidence indicates that PHF20L1 is upregulated in these malignancies and drives tumour progression by promoting proliferation, metastasis, and immune evasion. Furthermore, PHF20L1 orchestrates tumour-related gene expression by interacting with key epigenetic complexes. Given its unique structural features, we propose novel strategies for developing small-molecule inhibitors and combinatorial therapies, providing a theoretical basis for targeted epigenetic regulation for precision treatment. Future research should further investigate the molecular regulatory networks of PHF20L1 in different cancers and other human diseases and focus on developing specific small-molecule inhibitors to enable precision-targeted therapies. Full article

Skeletal muscle is the largest heterogeneous organ in the body, and multiple factors in intrinsic genetic and epigenetic regulation influence its growth. The N⁶-methyladenosine ed(m⁶A) modification is a conserved and most prevalent RNA modification, whose function is dependent on m⁶A writers, erasers, and m⁶A readers, such as the YTH protein family. YTHDC1 is the only member of the YTH protein family member that exists in the cell nucleus, which plays an important role in mRNA alternative polyadenylation and alternative splicing processes. However, the function of YTHDC1 in regulating myoblast proliferation, differentiation, and in vivo skeletal muscle development remains unclear. Therefore, in this study, we studied the function of YTHDC1 in C2C12 cell line and mouse. Our results showed that YTHDC1 significantly promoted myogenic differentiation while inhibiting myoblast proliferation in C2C12 cells, and the results of our in vivo experiment showed that interfering with YTHDC1 led to a significant enhancement of muscle growth in mice. Furthermore, the transcriptome sequencing analysis revealed that YTHDC1 might modulate skeletal muscle development by regulating alternative splicing of genes, including Akap13, Smarca2, Tnnt3, and Neb. Our study shed light on understanding the function and molecular mechanisms of YTHDC1 in regulating skeletal muscle development, highlighting the critical contribution of m⁶A-mediated RNA splicing in muscle growth. These results indicated that YTHDC1 could be a potential breeding target gene to enhance meat quality in livestock. Full article

Background: N6-methyladenosine (m6A) is the most prevalent chemical modification of eukaryotic RNA, playing a crucial role in regulating plant growth and development, stress responses, and other essential biological processes. The enzymes involved in m6A modification—methyltransferases (writers), demethylases (erasers), and recognition proteins (readers)—have been identified in various plant species; however, their roles in the economically significant tree species Populus deltoides × P. euramericana (NL895) remain underexplored. Results: In this study, we identified 39 m6A-related genes in the NL895 genome, comprising 8 writers, 13 erasers, and 18 readers. Evolutionary analysis indicated that the expansion of writers and readers primarily resulted from whole-genome duplication events. Purifying selection pressures were observed on all duplicated gene pairs, suggesting their essential roles in functional differentiation. Phylogenetic analysis revealed that writers, erasers, and readers are categorized into six, four, and two groups, respectively, with these genes being more conserved among dicotyledonous plants. Gene structure, protein domains, and motifs exhibited greater conservation within the same group. Promoter analysis of m6A-related genes showed enrichment of cis-acting elements associated with responses to light, phytohormones, and stress, indicating their potential involvement in gene expression regulation. Under cadmium treatment, the expression of all writers was significantly upregulated in both the aboveground and root tissues of NL895. Conclusions: This study systematically identified m6A-related gene families in Populus deltoides × P. euramericana (NL895), elucidating their evolutionary patterns and expression regulation characteristics. These findings provide a theoretical foundation for analyzing the molecular mechanisms of m6A modification in poplar growth, development, and stress adaptation, and offered candidate genes for molecular breeding in forest trees. Full article

Since the advent of recombinant DNA technologies and leading up to the clinical approval of T cell engager blinatumomab, the modular design of therapeutic antibodies has enabled the fusion of antibody fragments with proteins of various functionalities. This has resulted in an expansive array of possible mechanisms of action and has given birth to fragment-based antibodies (fbAbs) with immune cell engager modalities. In searchable databases, the preclinical development of these antibodies has shown promise; however, clinical outcomes and restructuring efforts involving these agents have produced mixed results and uncertainties. Amid budgetary cuts in both academia and industry, critical planning and evaluation of drug R&D would be more essential than ever before. While many reviews have provided outstanding summaries of preclinical phase fbAbs and cataloged relevant clinical trials, to date, very few of the articles in searchable databases have comprehensively reviewed the details of clinical outcomes along with the underlying reasons or potential explanations for the success and failures of these fbAb drug products. To fill the gap, in this review, we seek to provide the readers with clinically driven insights, accompanied by translational and mechanistic studies, on the current landscape of fragment-based immune cell engager antibodies in treating cancer, infectious, and autoimmune diseases. Full article

R-loops, three-stranded RNA-DNA hybrid nucleic acid structures, are recognized for their roles in both physiological and pathological processes. Regulation of R-loops is critical for genome stability as disruption of R-loop homeostasis can lead to aberrant gene expression, replication stress, and DNA damage. Recent studies suggest that the RNA modification, N6-methyladenosine (m6A), can modify R-loops and the writers, erasers, and readers of m6A are involved in the dynamic regulation of R-loops. Here, we discuss the reported functions of various m6A regulatory proteins in relation to R-loops, highlighting their distinct roles in recognizing and modulating the formation, stability, and resolution of these structures. We further examine the functional implications of m6A and R-loop interaction in human diseases, with a particular emphasis on their roles in cancer. Full article

Nipah virus (NiV), a highly lethal zoonotic paramyxovirus, displays strain-specific pathogenicity, yet the molecular basis for this divergence remains elusive. Here, we identify N6-methyladenosine (m6A) modification as a pivotal regulator of NiV replication. Higher m6A methylation levels on viral genomic RNA and mRNAs are associated with the increased virulence observed in the NiV-Malaysia (NiV-M) strain compared to NiV-Bangladesh (NiV-B). Underlying this phenomenon, NiV infection orchestrates a reprogramming of the host m6A machinery by downregulating the methyltransferase METTL3 and the demethylase ALKBH5, while concurrently upregulating m6A reader proteins YTHDF1-3. Both METTL3 and ALKBH5 bind directly to NiV RNA, with METTL3 installing m6A to promote viral replication and ALKBH5 removing them to inhibit it. Strikingly, pharmacological inhibition of m6A modification markedly attenuates NiV replication in vitro and in vivo, underscoring the therapeutic potential of targeting the m6A pathway. Our study establishes m6A as a key determinant of NiV pathogenicity and provides a paradigm for host-directed antiviral strategies against high-risk RNA viruses. Full article

Human respiratory syncytial virus (RSV) causes acute respiratory illness, attributing to deaths among young children and older adults worldwide. RSV neutralization assay is an important tool to measure RSV neutralization antibody that can prevent infection and severe complication of RSV. Conventional RSV neutralization assays have some limitations of speed and cost, especially for expensive kits, reagents or instruments required for detection. To solve this problem, this paper describes an improved simple and economical RSV neutralization assay protocol using recombinant RSV (rRSV) expressing reporter fluorescent protein to measure RSV growth as reporter activity with plate reader. The condition of 3 days culture demonstrated sufficient fluorescent activity even when small amounts of rRSV were used to inoculate Hep-2 cells. In addition, white 96-well cell culture plate showed better stable reporter activities than black plate. Furthermore, RSV neutralization assay protocol using rRSV-reporter fluorescent protein demonstrated similar signal detection capacity for RSV antibody titer detection compared to other protocols, such as rRSV-Luciferase and ELISA assay. The new RSV neutralization assay protocol can be applied to RSV antibody titration of numerous samples necessary for RSV surveillance or antiviral testing. Full article

Facioscapulohumeral muscular dystrophy (FSHD) is caused by the aberrant expression of the double homeobox 4 (DUX4) gene. In this study, an analysis of human FSHD muscle biopsies revealed differential expressions of six m6A regulators, including writers, readers and eraser proteins. In immortalized human FSHD myoblasts, we found higher levels of mRNA and protein expression of a major m6A regulator, methyltransferase-like protein 3 (METTL3), in comparison with myoblasts from unaffected siblings (UASbs). Quantification of the overall RNA m6A levels in the FSHD myoblasts revealed significant elevation compared with their UASb, which was reversed to UASb levels following treatment with an antisense oligonucleotide targeting the DUX4 mRNA. Using Oxford Nanopore direct-RNA sequencing, we mapped m6A across the transcriptome and identified genes harboring differential methylated m6A sites, including several involved in iron homeostasis. Western blot protein quantification showed that FSHD myoblasts had higher levels of ferritin-heavy chain-207 isoform and mitoferrin-1. In addition, our data showed elevation in mitochondrial ferrous iron in FSHD myoblasts. Our findings suggest that m6A RNA modifications play a pivotal role in FSHD pathophysiology and may serve as biomarker for this disease. Full article

YTH domain-containing proteins act as the primary readers of N⁶-methyladenosine (m⁶A), playing an important role in plant development and stress responses. However, little is known about the YTH proteins in medicinal plants. Genome-wide identification of the YTH gene family in the medicinal model plant, Salvia miltiorrhiza Bunge, identified a total of nineteen SmYTH genes from five chromosomes, with SmYTH8–SmYTH19 clustered on chromosome 8. Phylogenetic analysis showed that SmYTH proteins belong to the YTHDF category. No YTHDC members were identified. Conserved domain identification, amino acid sequence alignment, and phase separation prediction revealed that SmYTH1–SmYTH4 exhibited the characteristic m⁶A reader protein feature, containing conserved aromatic cages (WWW) capable of binding m⁶A residues. SmYTH5–SmYTH19 proteins contain a unique conserved F-box protein interaction domain that has not been reported previously. qRT-PCR analysis revealed tissue-specific patterns, with SmYTH1–SmYTH4 genes highly expressed in roots and leaves, whereas SmYTH8–SmYTH19 were mainly expressed in leaves. The results were consistent with RNA-seq data. The expression of various SmYTHs and the content of phenolic acid active ingredients were significantly altered under MeJA and SA treatments. The results provide useful information for further studies on the biological functions of m⁶A and YTH proteins in S. miltiorrhiza. Full article

Background/Objectives: PARP inhibitors (PARPi) are pivotal to treating homologous recombination repair-deficient (HRD) cancers, particularly BRCA1/2-mutated ovarian and breast cancers. However, most ovarian and breast cancers harbor wild-type (WT) BRCA1/2, limiting PARPi eligibility. This study aims to identify an approved drug that could induce a BRCAness phenotype, thereby sensitizing WT BRCA cancers to PARPi. Methods: Ovarian and breast cancer cell lines with WT BRCA1/2 were treated with ivosidenib. HR repair efficiency was assessed via RAD51 foci formation and reporter assays. Synthetic lethality with PARPi was evaluated using viability and colony formation assays. Mechanistic studies included RNA-binding protein pulldown, co-immunoprecipitation, and functional analyses of DNA repair pathways. YTHDC2′s role in HR was investigated through siRNA knockdown and rescue experiments. Results: Ivosidenib significantly reduced HR repair efficiency and sensitized cells to PARPi, inducing synthetic lethality. Mechanistically, ivosidenib directly bound YTHDC2, an m6A reader critical for HR. This interaction disrupted YTHDC2′s ability to promote DNA double-strand break repair via HR, evidenced by impaired recruitment of repair proteins (e.g., BRCA1, RAD51) and accumulation of DNA damage (γH2AX foci). YTHDC2 knockdown phenocopied ivosidenib effects, while overexpression rescued HR defects. Conclusions: Ivosidenib induces BRCAness in WT BRCA ovarian and breast cancers by targeting YTHDC2, thereby suppressing HR repair and enhancing PARPi sensitivity. This uncovers a novel, metabolism-independent mechanism of ivosidenib, repositioning it as a therapeutic agent for HRD tumors. These findings propose a strategy to expand PARPi eligibility to WT BRCA cancers, addressing a critical unmet need in oncology. Full article

The first demonstration of wheat germ extract (WGE)-based in vitro translation synthesising a protein from exogenously introduced messenger ribonucleic acid (mRNA) was published approximately fifty years ago. Since then, there have been numerous crucial improvements to the WGE-based in vitro translation, resulting in a significant increase in yield and the development of high-throughput protein-producing platforms. These developments have transformed the original setup into a versatile eukaryotic protein production method with broad applications. The present review explores the theoretical background of the implemented modifications and brings a panel of examples for WGE applications in high-throughput protein studies and synthesis of challenging-to-produce proteins such as protein complexes, extracellular proteins, and membrane proteins. It also highlights the unique advantages of in vitro translation as an open system for synthesising radioactively labelled proteins, as illustrated by numerous publications using WGE to meet the protein demands of these studies. This review aims to orientate readers in finding the most appropriate WGE arrangement for their specific needs and demonstrate that a deeper understanding of the system modifications will help them make further adjustments to the reaction conditions for synthesising difficult-to-express proteins. Full article

Benzo[a]pyrene, as the primary component of air pollutants, has been implicated in the pathogenesis of non-small-cell lung cancer (NSCLC). As an m6A reader that facilitates mRNA translation, YTHDF1 serves as a crucial regulator in tumor progression. Therefore, we established Benzo[a]pyrene(B[a]P)-induced bronchial epithelial malignant transformed cells (HBE-P35) to simulate the precancerous lesions of NSCLC and investigated the regulatory axis of YTHDF1 in both HBE-P35 and A549 lung cancer cells. A high level of m6A expression was detected in both HBE-P35 and A549 cells. Over-expression of YTHDF1 was observed in NSCLC tissues and correlated with poor overall survival in NSCLC patients. TMT labeling-based proteomic analysis and clinical lung tissue microarray assays demonstrated that CDK6 and MAP3K6 were positively correlated with YTHDF1 expression. MeRIP and RIP analyses revealed that YTHDF1 mediates the m6A-dependent regulation of CDK6 and MAP3K6 protein expression. The acquisition and deletion of miR-139/145-5p, along with luciferase reporter gene assays, demonstrated that miR-139-5p can target YTHDF1. Therefore, we conclude that YTHDF1 regulates CDK6 and MAP3K6 through m6A in B[a]P-induced HBE-P35 and A549 cells, providing a potential target for lung cancer treatment. Full article

Rapid and cost-effective measurements of the autofluorescence of wine can provide valuable information on the brand, origin, age, and composition of wine and may be helpful for the authentication of wine and detection of forgery. The list of fluorescent components of wines includes flavonoids, phenolic acids, stilbenes, some vitamins, aromatic amino acids, NADH, and Maillard reaction products. Distinguishing between various fluorophores is not simple, and chemometrics are usually employed to analyze the fluorescence spectra of wines. Front-face fluorescence is especially useful in the analysis of wine, obviating the need for sample dilution. Front-face measurements are possible using most plate readers, so they are commonly available. Additionally, the use of fluorescent probes allows for the detection and quantification of specific wine components, such as resveratrol, oxygen, total iron, copper, hydrogen sulfite, and haze-forming proteins. Fluorescence measurements can thus be useful for at least a preliminary rapid evaluation of wine properties. Full article

Nipah virus (NiV) is a severe zoonotic pathogen that substantially threatens public health. Pigs are the natural hosts of NiV and can potentially transmit this disease to humans. Establishing a rapid, sensitive, and accurate point-of-care detection method is critical in the timely identification of infected pig herds. In this study, we developed an NiV detection method based on reverse transcription–recombinase polymerase amplification (RT-RAA) and the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 13a (Cas13a) system for the precise detection of NiV. The highly conserved region of the NiV gene was selected as the detection target. We first designed eleven pairs of RT-RAA primers, and the optimal primer combination and reaction temperature were identified on the basis of RT-RAA efficiency. Additionally, the most efficient crRNA sequence was selected on the basis of the fluorescence signal intensity. The results revealed that the optimal reaction temperature for the developed method was 37 °C. The detection limit was as low as 1.565 copies/μL. Specificity testing revealed no cross-reactivity with nucleic acids from six common swine viruses, including Seneca virus A (SVA), foot-and-mouth disease virus (FMDV), classical swine fever virus (CSFV), porcine epidemic diarrhea virus (PEDV), African swine fever virus (ASFV), and pseudorabies virus (PRV). A validation test using simulated clinical samples revealed a 100% concordance rate. The detection results can be visualized via a fluorescence reader or lateral flow strips (LFSs). Compared with conventional detection methods, this RT-RAA-CRISPR/Cas13a-based method is rapid and simple and does not require scientific instruments. Moreover, the reagents can be freeze-dried for storage, eliminating the need for cold-chain transportation. This detection technology provides a convenient and efficient new tool for the point-of-care diagnosis of NiV and for preventing and controlling outbreaks. Full article

Thyroid Cancer (TC) is the most common endocrine cancer, of which papillary thyroid cancer (PTC), a well-differentiated type of TC, accounts for 80–90%. Long non-coding RNAs (lncRNAs), which comprise non-protein-coding segments of the genome, have been found to play a crucial role in various biological processes, including cancer development. The activity of lncRNAs is modified through epigenetic modifications, with N6-Methyladenosine (m6A) modifications implicated in the progression of several malignancies. The activity of m6A is further regulated by modifying enzymes classified as “readers”, writers”, and “erasers”, of which specific enzymes have been found to play a role in various aspects of PTC. Recent research has highlighted the significance of m6A modification in regulating the expression and function of lncRNAs associated with PTC pathogenesis. Dysregulation of this process implicates tumor proliferation, invasion, and metastasis, with subsequent impact on prognosis. Therefore, understanding the interplay between m6A modification and lncRNAs provides valuable insights into the molecular mechanisms underlying PTC progression. This narrative review aims to explore the established role of several prominent m6A modifying enzymes and lncRNAs on cancer pathogenesis and seeks to clarify the function of these enzymes in PTC pathogenesis. Full article