PolyAMiner-Bulk is a deep learning-based algorithm that decodes alternative polyadenylation dynamics from bulk RNA-seq data.

Alternative polyadenylation (APA) is a key post-transcriptional regulatory mechanism; yet, its regulation and impact on human diseases remain understudied. Existing bulk RNA sequencing (RNA-seq)-based APA methods predominantly rely on predefined annotations, severely impacting their ability to decode novel tissue- and disease-specific APA changes. Furthermore, they only account for the most proximal and distal cleavage and polyadenylation sites (C/PASs). Deconvoluting overlapping C/PASs and the inherent noisy 3' UTR coverage in bulk RNA-seq data pose additional challenges. To overcome these limitations, we introduce PolyAMiner-Bulk, an attention-based deep learning algorithm that accurately recapitulates C/PAS sequence grammar, resolves overlapping C/PASs, captures non-proximal-to-distal APA changes, and generates visualizations to illustrate APA dynamics. Evaluation on multiple datasets strongly evinces the performance merit of PolyAMiner-Bulk, accurately identifying more APA changes compared with other methods. With the growing importance of APA and the abundance of bulk RNA-seq data, PolyAMiner-Bulk establishes a robust paradigm of APA analysis.

CPSF3 inhibition blocks pancreatic cancer cell proliferation through disruption of core histone mRNA processing.

Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease with limited effective treatment options, potentiating the importance of uncovering novel drug targets. Here, we target cleavage and polyadenylation specificity factor 3 (CPSF3), the 3' endonuclease that catalyzes mRNA cleavage during polyadenylation and histone mRNA processing. We find that CPSF3 is highly expressed in PDAC and is associated with poor prognosis. CPSF3 knockdown blocks PDAC cell proliferation and colony formation in vitro and tumor growth in vivo. Chemical inhibition of CPSF3 by the small molecule JTE-607 also attenuates PDAC cell proliferation and colony formation, while it has no effect on cell proliferation of nontransformed immortalized control pancreatic cells. Mechanistically, JTE-607 induces transcriptional readthrough in replication-dependent histones, reduces core histone expression, destabilizes chromatin structure, and arrests cells in the S-phase of the cell cycle. Therefore, CPSF3 represents a potential therapeutic target for the treatment of PDAC.

NUDT21 alters glioma migration through differential alternative polyadenylation of LAMC1.

PURPOSE: Gliomas and their surrounding microenvironment constantly interact to promote tumorigenicity, yet the underlying posttranscriptional regulatory mechanisms that govern this interplay are poorly understood. METHODS: Utilizing our established PAC-seq approach and PolyAMiner bioinformatic analysis pipeline, we deciphered the NUDT21-mediated differential APA dynamics in glioma cells. RESULTS: We identified LAMC1 as a critical NUDT21 alternative polyadenylation (APA) target, common in several core glioma-driving signaling pathways. qRT-PCR analysis confirmed that NUDT21-knockdown in glioma cells results in the preferred usage of the proximal polyA signal (PAS) of LAMC1. Functional studies revealed that NUDT21-knockdown-induced 3'UTR shortening of LAMC1 is sufficient to cause translational gain, as LAMC1 protein is upregulated in these cells compared to their respective controls. We demonstrate that 3'UTR shortening of LAMC1 after NUDT21 knockdown removes binding sites for miR-124/506, thereby relieving potent miRNA-based repression of LAMC1 expression. Remarkably, we report that the knockdown of NUDT21 significantly promoted glioma cell migration and that co-depletion of LAMC1 with NUDT21 abolished this effect. Lastly, we observed that LAMC1 3'UTR shortening predicts poor prognosis of low-grade glioma patients from The Cancer Genome Atlas. CONCLUSION: This study identifies NUDT21 as a core alternative polyadenylation factor that regulates the tumor microenvironment through differential APA and loss of miR-124/506 inhibition of LAMC1. Knockdown of NUDT21 in GBM cells mediates 3'UTR shortening of LAMC1, contributing to an increase in LAMC1, increased glioma cell migration/invasion, and a poor prognosis.

PolyAMiner-Bulk: A Machine Learning Based Bioinformatics Algorithm to Infer and Decode Alternative Polyadenylation Dynamics from bulk RNA-seq data.

More than half of human genes exercise alternative polyadenylation (APA) and generate mRNA transcripts with varying 3' untranslated regions (UTR). However, current computational approaches for identifying cleavage and polyadenylation sites (C/PASs) and quantifying 3'UTR length changes from bulk RNA-seq data fail to unravel tissue- and disease-specific APA dynamics. Here, we developed a next-generation bioinformatics algorithm and application, PolyAMiner-Bulk, that utilizes an attention-based machine learning architecture and an improved vector projection-based engine to infer differential APA dynamics accurately. When applied to earlier studies, PolyAMiner-Bulk accurately identified more than twice the number of APA changes in an RBM17 knockdown bulk RNA-seq dataset compared to current generation tools. Moreover, on a separate dataset, PolyAMiner-Bulk revealed novel APA dynamics and pathways in scleroderma pathology and identified differential APA in a gene that was identified as being involved in scleroderma pathogenesis in an independent study. Lastly, we used PolyAMiner-Bulk to analyze the RNA-seq data of post-mortem prefrontal cortexes from the ROSMAP data consortium and unraveled novel APA dynamics in Alzheimer's Disease. Our method, PolyAMiner-Bulk, creates a paradigm for future alternative polyadenylation analysis from bulk RNA-seq data.

Alternative polyadenylation alters protein dosage by switching between intronic and 3'UTR sites.

Alternative polyadenylation (APA) creates distinct transcripts from the same gene by cleaving the pre-mRNA at poly(A) sites that can lie within the 3' untranslated region (3'UTR), introns, or exons. Most studies focus on APA within the 3'UTR; however, here, we show that CPSF6 insufficiency alters protein levels and causes a developmental syndrome by deregulating APA throughout the transcript. In neonatal humans and zebrafish larvae, CPSF6 insufficiency shifts poly(A) site usage between the 3'UTR and internal sites in a pathway-specific manner. Genes associated with neuronal function undergo mostly intronic APA, reducing their expression, while genes associated with heart and skeletal function mostly undergo 3'UTR APA and are up-regulated. This suggests that, under healthy conditions, cells toggle between internal and 3'UTR APA to modulate protein expression.

Assessing the effects of body weight on subchondral bone formation with quantitative 18F-sodium fluoride PET.

OBJECTIVES: The aim of this study was to quantify subchondral bone remodeling in the elbows, hands, knees, and feet using volumetric and metabolic parameters derived from 18F-sodium fluoride positron emission tomography (NaF-PET) and to assess the convergent validity of these parameters as an index of joint degeneration and preclinical osteoarthritis. METHODS: A retrospective analysis was conducted in 34 subjects (32 males, 2 females) with metastatic bone disease who underwent full-body NaF-PET/CT scans. An adaptive contrast-oriented thresholding algorithm was applied to segment NaF-avid regions in the bilateral elbows, hands, knees, and feet of each subject, and metabolically active volume (MAV), maximum standardized uptake value (SUVmax), mean metabolic volumetric product (MVPmean), and partial volume-corrected MVPmean (cMVPmean) of the segmented regions were calculated. Global parameters for MAV, SUVmax, MVPmean, and cMVPmean were defined as the sum of the corresponding values in all the joints of a subject. Inter-rater reliability was determined with Lin's concordance correlation, and associations of global values with subject body weight and age were assessed with Pearson correlation and Spearman correlation analyses. RESULTS: Inter-rater reliability was observed to be the highest in SUVmax (ρc = 0.99), followed by MVPmean (ρc = 0.96), cMVPmean (ρc = 0.93), and MAV (ρc = 0.93). MAV, MVPmean, and cMVPmean were observed to significantly increase with weight (all p < 0.0001) determined by Pearson correlation. In addition, Spearman rank-order analysis demonstrated a significant correlation between SUVmax and weight in addition to MAV, MVPmean, and cMVPmean and weight (all p < 0.01). No significant association between age and any PET parameter was observed. CONCLUSIONS: These preliminary data demonstrate the feasibility and reliability of assessing bone turnover at the joints using quantitative NaF-PET. Our findings corroborate the fact that biomechanical factors including mechanical loading and weight-bearing are contributors to osteoarthritis disease progression.

Comparison of methods of quantifying global synovial metabolic activity with FDG-PET/CT in rheumatoid arthritis.

AIM: 2-deoxy-2-[18 F]fluoro-d-glucose positron emission tomography/computed tomography (FDG-PET/CT) can portray increased glycolysis due to inflammation in rheumatoid arthritis (RA). The aim of this study was to evaluate and compare the reliability and construct validity of two methods of quantifying RA disease activity using FDG-PET/CT. METHOD: Nineteen RA patients and 19 healthy controls matched to sex and age underwent prospective FDG-PET/CT imaging. Metabolic and volumetric metrics were calculated using fixed and adaptive thresholding techniques and partial volume correction. Fixed thresholds segmented regions above average maximum physiological uptake in controls. Differences of means between RA and controls were assessed using t tests, and discrimination was assessed using receiver operating characteristics. Spearman correlation analysis was used to assess associations between FDG-PET/CT measures and clinical assessments of disease activity. RESULTS: All FDG-PET/CT measures were substantially different and nearly non-overlapping between RA and controls (all P < .001). Area under the curve (AUC) for adaptive threshold parameters ranged from 0.986 to 0.997, and AUC for fixed threshold parameters ranged from 0.898 to 0.945. PET parameters were found to correlate positively with various clinical features, namely C-reactive protein, erythrocyte sedimentation rate, interleukin (IL)-6, IL-1, and swollen joint count. CONCLUSION: All FDG-PET/CT parameters reflecting global RA disease activity differentiated between RA and controls, indicating high clinical utility to diagnose and assess RA. Adaptive thresholds can be used in a wider setting without control data, but methods utilizing fixed thresholds were more reproducible and more closely associated with indications of inflammation.

Dextran-Coated Iron Oxide Nanoparticles as Biomimetic Catalysts for Localized and pH-Activated Biofilm Disruption.

Biofilms are surface-attached bacterial communities embedded within an extracellular matrix that create localized and protected microenvironments. Acidogenic oral biofilms can demineralize the enamel-apatite on teeth, causing dental caries (tooth decay). Current antimicrobials have low efficacy and do not target the protective matrix and acidic pH within the biofilm. Recently, catalytic nanoparticles were shown to disrupt biofilms but lacked a stabilizing coating required for clinical applications. Here, we report dextran-coated iron oxide nanoparticles termed nanozymes (Dex-NZM) that display strong catalytic (peroxidase-like) activity at acidic pH values, target biofilms with high specificity, and prevent severe caries without impacting surrounding oral tissues in vivo. Nanoparticle formulations were synthesized with dextran coatings (molecular weights from 1.5 to 40 kDa were used), and their catalytic performance and bioactivity were assessed. We found that 10 kDa dextran coating provided maximal catalytic activity, biofilm uptake, and antibiofilm properties. Mechanistic studies indicated that iron oxide cores are the source of catalytic activity, whereas dextran on the nanoparticle surface provided stability without blocking catalysis. Dextran-coating facilitated NZM incorporation into exopolysaccharides (EPS) structure and binding within biofilms, which activated hydrogen peroxide (H2O2) for localized bacterial killing and EPS-matrix breakdown. Surprisingly, dextran coating enhanced selectivity toward biofilms while avoiding binding to gingival cells. Furthermore, Dex-NZM/H2O2 treatment significantly reduced the onset and severity of caries lesions (vs control or either Dex-NZM or H2O2 alone) without adverse effects on gingival tissues or oral microbiota diversity in vivo. Therefore, dextran-coated nanozymes have potential as an alternative treatment to control tooth decay and possibly other biofilm-associated diseases.

Evolving Role of PET/CT-MRI in Assessing Muscle Disorders.

2-Deoxy-2-[18F]fluoroglucose (FDG) uptake in muscle is influenced by many normal physiologic processes and can also indicate pathology. Variability in physiologic uptake can be reduced with proper patient preparation, allowing for a better determination of abnormal activity. Although malignant diseases, such as rhabdomyosarcoma and skeletal muscle metastasis, are clear applications of FDG-PET/CT, there may be additional applications in infection and benign inflammatory disorders that warrant further research.

A novel method to assess subchondral bone formation using [18F]NaF-PET in the evaluation of knee degeneration.

PURPOSE: Fluorine-18-sodium fluoride-PET ([F]NaF-PET) facilitates direct assessment of subchondral bone formation to evaluate degeneration in articulating joints. No standards exist for the quantification of joint activity using [F]NaF-PET, and many techniques rely on focal uptake to characterize an entire region of interest. This study proposes a novel method of quantitative global knee analysis to assess regions of expected bone remodeling in the evaluation of knee degeneration. PATIENTS AND METHODS: The study population consisted of 18 patients with rheumatoid arthritis who underwent [F]NaF-PET/computed tomography imaging. The maximum standardized uptake value (knee SUVmax) in addition to a target-to-background ratio (TBR) that represents global knee activity adjusted for systemic bone formation measured at the lateral femoral neck (global knee TBR) were calculated. A radiologist scored standard radiographs of the knee in nine patients using the Kellgren-Lawrence grading system. RESULTS: Patients with greater [F]NaF uptake demonstrated greater knee deterioration, which was corroborated by the radiograph findings. Average Kellgren-Lawrence grading was strongly associated with both global knee TBR (Spearman ρ=0.69, P=0.04) and knee SUVmax scores (Spearman ρ=0.93, P=0.0003). CONCLUSION: Assessment of global activity within the joint is a feasible and clinically useful technique for characterizing disease activity with a single value. Furthermore, a ratio based on systemic bone turnover in a nonarticulating, weight-bearing site adjusts for differences in bone formation related to bodyweight or metabolic bone diseases. We hypothesize that a global knee TBR score may be more sensitive at detecting changes in disease progression, as new spatially distinct lesions with a lower SUV that develop within an region of interest would not be detected by the SUVmax methodology. Longitudinal studies assessing sensitivity with larger patient cohorts are needed to further validate this methodology.