Search Results (43)

Sepsis-associated acute kidney injury (SA-AKI) is a life-threatening complication of sepsis, characterized by high mortality and prolonged hospitalization. Early diagnosis and effective therapy remain difficult despite extensive investigation. To address this, we developed an AI-driven integrative framework that combines a Transformer-based deep learning model with established machine learning techniques (LASSO, SVM-RFE, Random Forest and neural networks) to uncover complex, nonlinear interactions among gene-expression biomarkers. Analysis of normalized microarray data from GEO (GSE95233 and GSE69063) identified differentially expressed genes (DEGs), and KEGG/GO enrichment via clusterProfiler revealed key pathways in immune response, protein synthesis, and antigen presentation. By integrating multiple transcriptomic cohorts, we pinpointed 617 SA-AKI-associated DEGs—21 of which overlapped between sepsis and AKI datasets. Our Transformer-based classifier ranked five genes (MYL12B, RPL10, PTBP1, PPIA, and TOMM7) as top diagnostic markers, with AUC values ranging from 0.9395 to 0.9996 (MYL12B yielding 0.9996). Drug–gene interaction mining using DGIdb (FDR < 0.05) nominated 19 candidate therapeutics for SA-AKI. Together, these findings demonstrate that melding deep learning with classical machine learning not only sharpens early SA-AKI detection but also systematically uncovers actionable drug targets, laying groundwork for precision intervention in critical care settings. Full article

Transcribed conserved non-coding elements (TCNEs), which are non-coding genomic elements that can regulate vital gene expression, play an unclear role in the development of severe diseases mainly associated with carcinogenesis. Currently, there are no mature tools for the identification of TCNEs. To compensate for the lack of a systematic interpretation of the functional characterization and regulatory mechanisms of TCNE spatiotemporal activities, we developed a flexible pipeline, called captureTCNE, to depict the landscape of TCNEs and applied it to our breast cancer cohort (SEU-BRCA). Meanwhile, we investigated the genome-wide characteristics of TCNEs and unraveled that TCNEs harbor enhancer-like chromatin signatures as well as participate in the transcriptional machinery to regulate essential genes or architect biological regulatory networks of breast cancer. Specifically, the TCNE transcripts could recruit RBPs, such as ENOX1 and PTBP1, which are involved in gene expression regulation, to participate in the formation of regulatory networks and the association with altered splicing patterns. In particular, the presence of a non-classical secondary structure, called RNA G-quadruplex, on TCNE transcripts contributed to the recruitment of RBPs associated with subtype-specific transcriptional processes related to the estrogen response in breast cancer. Ultimately, we also analyzed the mutational signatures of variant-containing TCNEs and discerned twenty-one genes as essential components of the regulatory mechanism of TCNEs in breast cancer. Our study provides an effective TCNE identification pipeline and insights into the regulatory mechanisms of TCNEs in breast cancer, contributing to further knowledge of TCNEs and the emergence of innovative therapeutic strategies for breast cancer. Full article

Background. Skin contact with items containing p-tert-butylphenol-formaldehyde resin (PTBP-FR) may induce sensitization and allergic contact dermatitis (ACD). Methods. This multi-centric cross-sectional study investigated the prevalence of sensitization to PTBP-FR in 30,629 consecutive outpatients patch-tested during 1997–2021 in four research centers from Northern Italy: Padua; Pordenone; Trieste; and Trento/Bolzano/Rovigo. Patch tests were applied on the upper back of patients with suspected ACD. All patches were removed after 48 h and read at 72 or 96 h. Results. The overall prevalence of PTBP-FR sensitization was 1.11% (=341/30,629) of cases, with lower prevalence occurring in the Province of Trento/Bolzano/Rovigo (0.36%). The body area most frequently affected were the hands (36.32%), followed by face (19.52%) and legs (8.09%). During 1997–2004, the prevalence of PTBP-FR positivity was significantly lower in Trento/Bolzano/Rovigo (aOR = 0.19; 95%CI: 0.11; 0.35), whereas it was higher among restaurant workers (aOR = 2.44; 95%CI: 1.44; 4.13). During the entire study period (1997–2021), excluding Trento/Bolzano/Rovigo, PTBP-FR positivity significantly decreased in the period 2011–2021 (aOR = 052; 95%CI: 0.39; 0.69) compared to 1997–2010 in males (OR = 0.69; 95%CI: 0.52; 0.91). Conclusions. Females were likely to react to PTBP-FR at patch tests. Prevalence of PTBP-FR sensitization significantly decreased over time, possibly reflecting reduced occupational and non-occupational exposure due to replacement of the resin with other adhesive products (acrylates or epoxy agents). Full article

In mammals, because cardiomyocytes withdraw from cell-cycle activities shortly after birth, the heart cannot repair the damage caused by a myocardial injury; thus, understanding how cardiomyocytes proliferate is among the most important topics in cardiovascular sciences. In newborn neonatal mammals, when a left ventricular injury is applied in hearts earlier than postnatal day 7, the cardiomyocytes actively proliferate and regenerate lost myocardium in the following weeks. The regulators promoting cardiomyocyte proliferation were discovered by analyzing transcriptomic data generated from models. Most of these regulators support the mRNA production of cell-cycle machinery, yet the mRNA requires translation into functional proteins under the regulation of RNA-binding proteins (RBPs). In this work, we performed a meta-analysis to study the relationship between RBP expression and cardiomyocyte proliferation. To identify RBPs associated with mouse and pig cardiomyocyte proliferation, the single-nuclei RNA sequencing (snRNA-seq) data from regenerating mouse and pig hearts were reanalyzed via an Autoencoder focusing on RBP expression. We also generated and analyzed new bulk RNA-seq from two human-induced pluripotent stem cell-derived (hiPSC) cardiomyocyte (hiPSC-CM) cell lines; the first cell line was harvested sixteen days after differentiation, when the cells still actively proliferated, and the second cell line was harvested one hundred and forty days after differentiation, when the cells ceased cell cycle activity. Then, the RBP associated with mouse, pig, and hiPSC-CM were compared across species. Twenty-one RBPs were found to be consistently upregulated, and six RBPs were downregulated in proliferating mouse, pig, and hiPSC-derived cardiomyocytes. Among upregulated RBPs across species, an immunofluorescence-based imaging analysis validated the significant increase in the proteins of DHX9, PTBP3, HNRNPUL1, and DDX6 in pig hearts with proliferating CMs. This meta-analysis in all species demonstrated a strong relationship between RBP expression and cardiomyocyte proliferation. Full article

Background/Objectives: Mesenchymal stem cells (MSCs) possess the remarkable ability to differentiate into various cell types, including osteoblasts. Understanding the molecular mechanisms governing MSC osteogenic differentiation is crucial for advancing clinical applications and our comprehension of complex disease processes. However, the key biological molecules regulating this process remain incompletely understood. Methods: In this study, we conducted systematic re-analyses of published high-throughput transcriptomic datasets to identify and validate key biological molecules that dynamically regulate MSC osteogenic differentiation. Our approach involved a comprehensive analysis of gene expression patterns across human tissues, followed by the rigorous experimental validation of the identified candidates. Results: Through integrated analytical and experimental approaches, we utilized high-throughput transcriptomics to identify four critical regulators of MSC osteogenic differentiation: PTBP1, H2AFZ, BCL6, and TTPAL (C20ORF121). Among these, PTBP1 and H2AFZ functioned as positive regulators, while BCL6 and TTPAL acted as negative regulators in osteogenesis. The regulatory roles of these genes in osteogenesis were further validated via overexpression experiments. Conclusions: Our findings advance our understanding of MSC differentiation fate determination and open new therapeutic possibilities for bone-related disorders. The identification of these regulators provides a foundation for developing targeted interventions in regenerative medicine. Full article

Alternative splicing allows a single gene to produce a variety of protein isoforms. Changes in splicing isoform usage characterize virtually every stage of the differentiation process and define the physiological differences between cardiomyocytes with different function, at different stages of development, and pathological function. Recent identification of cardiac splicing factors provided insights into the mechanisms underlying alternative splicing and revealed how these splicing factors impact functional properties of the heart. Alterations of the splicing of sarcomeric genes, cell signaling proteins, and ion channels have been associated with the development of pathological conditions such as cardiomyopathy and arrhythmia. RBM20, RBM24, PTBP1, RBFOX, and QKI play key roles in cardiac development and pathology. A better understanding of their regulation will yield insights into healthy cardiac development and inform the development of molecular therapeutics. Full article

The popular method of micro-respirometry (μR) for measuring total viable (aerobic) count (TVC) utilises luminescence-based O₂ sensors that are difficult to fabricate and therefore expensive. A simple method is described for making inexpensive, ink-based potential substitutes that utilise the same O₂-sensitive dyes. The sensitivity of such inks is readily increased by using dyes with a long lifetime in the absence of O₂, τ_o, and/or an ink resin/polymer with a high O₂ permeability, P_m(O₂). Response modelling of the μR-based TVC system and subsequent testing using a range of O₂ sensors of different sensitivity show that there is little to be gained by making the O₂ sensor either very sensitive or insensitive, and that the best O₂ sensors are dyes such as Pt(II) tetraphenyltetrabenzoporphyrin (PtBP), with τ_o = ca. 40–50 μs. Further work shows that a simple-to-make PtBP ink can be used as a direct replacement for the expensive O₂ sensor used in commercial instruments for measuring TVC based on μR. In addition, the PtBP can be replaced by an even less expensive O₂-sensitive dye, Pt(II) meso-tetra(pentafluorophenyl)porphyrin (PtTFPP). The potential use of inexpensive O₂-sensitive inks as an alternative to any expensive commercial counterpart based on the same O₂-sensitive dye is discussed briefly. Full article

Polypyrimidine tract-binding protein 1 (PTBP1) plays an essential role in splicing and post-transcriptional regulation. Moreover, PTBP1 has been implicated as a causal factor in tumorigenesis. However, the involvement of PTBP1 in cellular senescence, a key biological process in aging and cancer suppression, remains to be clarified. Here, it is shown that PTBP1 is associated with the facilitation of tumor growth and the prognosis in lung adenocarcinoma (LUAD). PTBP1 exhibited significantly increased expression in various cancer types including LUAD and showed consistently decreased expression in multiple cellular senescence models. Suppression of PTBP1 induced cellular senescence in LUAD cells. In terms of molecular mechanisms, the silencing of PTBP1 enhanced the skipping of exon 3 in F-box protein 5 (FBXO5), resulting in the generation of a less stable RNA splice variant, FBXO5-S, which subsequently reduces the overall FBXO5 expression. Additionally, downregulation of FBXO5 was found to induce senescence in LUAD. Collectively, these findings illustrate that PTBP1 possesses an oncogenic function in LUAD through inhibiting senescence, and that targeting aberrant splicing mediated by PTBP1 has therapeutic potential in cancer treatment. Full article

Gastric cancer (GC) is the most common type of malignant tumor within the gastrointestinal tract, and GC metastasis is associated with poor prognosis. Polypyrimidine tract binding protein 1 (PTBP1) is an RNA-binding protein implicated in various types of tumor development and metastasis. However, the role of PTBP1 in GC metastasis remains elusive. In this study, we verified that PTBP1 was upregulated in GC tissues and cell lines, and higher PTBP1 level was associated with poorer prognosis. It was shown that PTBP1 knockdown in vitro inhibited GC cell migration, whereas PTBP1 overexpression promoted the migration of GC cells. In vivo, the knockdown of PTBP1 notably reduced both the size and occurrence of metastatic nodules in a nude mice liver metastasis model. We identified phosphoglycerate kinase 1 (PGK1) as a downstream target of PTBP1 and found that PTBP1 increased the stability of PGK1 by directly binding to its mRNA. Furthermore, the PGK1/SNAIL axis could be required for PTBP1’s function in the promotion of GC cell migration. These discoveries suggest that PTBP1 could be a promising therapeutic target for GC. Full article

In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica. Full article

The goal of our study was to identify signatures of selection in the Turopolje pigs and other commercial pig breeds. We conducted a comprehensive analysis of five datasets, including one local pig breed (Turopolje) and four commercial pig breeds (Large White, Landrace, Pietrain, and Duroc), using strict quality control measures. Our final dataset consisted of 485 individuals and 54,075 single nucleotide polymorphisms (SNPs). To detect selection signatures within these pig breeds, we utilized the XP-EHH and XP-nSL methodologies, which allowed us to identify candidate genes that have been subject to positive selection. Our analysis consistently highlighted the PTBP2 and DPYD genes as commonly targeted by selection in the Turopolje breed. DPYD is associated with muscular development in pigs and other species and PTBP2 emerges as one of the potential genes linked to seminal characteristics. Furthermore, in the Large White breed, a number of genes were detected with the two methods, such as ATP1A1, CASQ2, CD2, IGSF3, MAB21L3, NHLH2, SLC22A15, VANGL1. In the Duroc breed, a different set of genes was detected, such as ARSB, BHMT, BHMT2, DMGDH, JMY. The function of these genes was related to body weight, production efficiency and meat quality, average daily gain, and other similar traits. Overall, our results have identified a number of genomic regions that are under selective pressure between local and commercial pig breeds. This information can help to improve our understanding of the mechanisms underlying pig breeding, and ultimately contribute to the development of more efficient and sustainable pig production practices. Our study highlights the power of using multiple genomic methodologies to detect genetic signatures of selection, and provides important insights into the genetic diversity of pig breeds. Full article

Hydrophobic deep eutectic solvents (HDES) are widely used as extractants. Usually, when preparing HDES, only the extraction ability of one component is taken into account, with the second serving as an “inert” component, whose effect on the extraction process is not taken into account. The present study demonstrates the possibility of controlling the selectivity of a hydrophobic deep eutectic solvent based on trioctylphosphine oxide (TOPO) by varying the substance that acts as a hydrogen bond donor, but which does not have an extractive ability. In the course of the work, the influence of the “inert” component on the physicochemical and extraction properties of HDES was confirmed by experimental, spectroscopic, and also calculation methods. A number of phenols with different structural features were chosen as the HDES’ hydrogen bond donors to modify: phenol (Ph), para-tert-butylphenol (PTBP) and thymol (Th). Using the example of separation of the Sm/Co pair, the influence of the structure of a hydrogen bond donor on the extraction ability of a hydrophobic deep eutectic solvent was established, where the degree of extraction of Sm (III) increased in the series Th:TOPO < PTBP:TOPO < Ph:TOPO. HDES based on TOPO and phenols can potentially be used to separate Sm and Co from the process leach solutions generated during the hydrometallurgical processing of waste SmCo magnets. Full article

Polypyrimidine tract binding protein 1 (PTBP1) is one of the most well-described RNA binding proteins, known initially for its role as a splicing repressor before later studies revealed its numerous roles in RNA maturation, stability, and translation. While PTBP1’s various biological roles have been well-described, it remains unclear how its four RNA recognition motif (RRM) domains coordinate these functions. The early PTBP1 literature saw extensive effort placed in detailing structures of each of PTBP1’s RRMs, as well as their individual RNA sequence and structure preferences. However, limitations in high-throughput and high-resolution genomic approaches (i.e., next-generation sequencing had not yet been developed) precluded the functional translation of these findings into a mechanistic understanding of each RRM’s contribution to overall PTBP1 function. With the emergence of new technologies, it is now feasible to begin elucidating the individual contributions of each RRM to PTBP1 biological functions. Here, we review all the known literature describing the apo and RNA bound structures of each of PTBP1’s RRMs, as well as the emerging literature describing the dependence of specific RNA processing events on individual RRM domains. Our goal is to provide a framework of the structure–function context upon which to facilitate the interpretation of future studies interrogating the dynamics of PTBP1 function. Full article

Agrin is a heparan sulfate proteoglycan essential for the clustering of acetylcholine receptors at the neuromuscular junction. Neuron−specific isoforms of agrin are generated by alternative inclusion of three exons, called Y, Z8, and Z11 exons, although their processing mechanisms remain elusive. We found, by inspection of splicing cis−elements into the human AGRN gene, that binding sites for polypyrimidine tract binding protein 1 (PTBP1) were extensively enriched around Y and Z exons. PTBP1−silencing enhanced the coordinated inclusion of Y and Z exons in human SH−SY5Y neuronal cells, even though three constitutive exons are flanked by these alternative exons. Deletion analysis using minigenes identified five PTBP1−binding sites with remarkable splicing repression activities around Y and Z exons. Furthermore, artificial tethering experiments indicated that binding of a single PTBP1 molecule to any of these sites represses nearby Y or Z exons as well as the other distal exons. The RRM4 domain of PTBP1, which is required for looping out a target RNA segment, was likely to play a crucial role in the repression. Neuronal differentiation downregulates PTBP1 expression and promotes the coordinated inclusion of Y and Z exons. We propose that the reduction in the PTPB1−RNA network spanning these alternative exons is essential for the generation of the neuron−specific agrin isoforms. Full article