Citations

Summary Long-read nanopore sequencing enables simultaneous detection of germline variation and native DNA base modifications on individual DNA molecules, providing a unique opportunity to investigate allele-specific epigenetic regulation. Here, we performed whole-genome nanopore sequencing on normal and tumor prostate tissues to characterize differential methylation, methylation entropy, and allele-specific methylation (ASM) associated with noncoding genetic variants. Genome-wide analysis identified extensive cancer-associated differentially methylated regions (DMRs), with hypermethylated DMRs significantly enriched near transcription start sites and transcriptional regulatory regions. Integration with transcriptomic datasets revealed strong inverse relationships between promoter methylation and gene expression, while 5-hydroxymethylcytosine (5hmC) levels positively correlated with transcriptional activity across gene bodies. Using fragment-level methylation patterns enabled by long-read sequencing, we further quantified methylation entropy incorporating both 5mCG and 5hmCG states. Cancer-hypermethylated DMRs exhibited markedly reduced entropy, consistent with clonal fixation of methylation states during tumor progression. Entropy profiling across chromatin annotations demonstrated maximal epigenetic heterogeneity at partially modified enhancer-associated regions. To investigate cis-regulatory genetic effects, we developed a simple ASM framework (nanoASM) that can partition sequencing reads by allelic state and identifies allele-specific DMRs directly from long-read data. Compared with conventional population-level mQTL analysis, ASM demonstrated substantially improved statistical efficiency by leveraging within-individual contrasts and reducing sample-level heterogeneity. Although germline single nucleotide polymorphisms (SNPs) were largely shared between normal and tumor tissues, ASM patterns differed substantially, with tumor-associated ASM regions displaying significantly larger genomic span and stronger allelic methylation differences. Comparative analysis with TCGA prostate mQTL and GTEx prostate eQTL datasets demonstrated substantial concordance between ASM directionality and downstream transcriptional effects, particularly for variants located within DMRs and near transcription start sites. At the IRX4 prostate cancer risk locus, ASM identified an androgen-responsive regulatory domain overlapping AR ChIP-seq and H3K27ac peaks, nominating rs6885084 as a candidate functional variant. At the PSCA locus, ASM anchored by rs4736369 was associated with allele-specific methylation, chromatin activation, transcript abundance, and isoform usage. Together, these findings establish nanopore-based ASM analysis as a powerful approach for resolving functional noncoding variants and their regulatory domains they control in prostate cancer.

Abstract Glioblastoma (GBM) is among the most aggressive and lethal primary brain cancers. A major therapeutic challenge is that the standard chemotherapeutic agent temozolomide (TMZ) is associated with drug resistance and lacks tumor-specificity. The development of targeted drug delivery systems encapsulating new chemotherapeutic agents may overcome these limitations. Fucoidan has been reported to exhibit tumor-targeting properties through its high binding affinity for P-selectin overexpressed on both GBM cells and activated brain microvascular endothelial cells (BMECs) within and surrounding tumors. Verteporfin (VP), a benzoporphyrin derivative, has been reported to suppress Yes-associated protein (YAP) activity, inhibit tumor angiogenesis, and exhibit antitumor activity in heterogeneous GBM. However, the hydrophobic nature of VP limits its bioavailability, reducing therapeutic efficacy and necessitating high doses that may increase the risk of adverse effects. To address this challenge, we synthesized VP-laden, fucoidan-coated nanoparticles (VP@NP-F), and VP-laden nanoparticles without fucoidan coating (VP@NP). Their capability of enhancing VP delivery and antitumor efficacy was evaluated using human BMECs and patient-derived primary GBM cells (GBM1a). VP@NP-F exhibits ∼4-fold and ∼1.8-fold greater uptake in BMECs and GBM1a than VP@NP, demonstrating the fucoidan coating enhances targeting and internalization. The half-maximal inhibitory concentration (IC50) value of VP@NP-F is ∼12.3-fold and ∼3-fold lower than that of free VP and VP@NP, respectively. These data suggest the therapeutic advantage of the VP-laden, fucoidan-coated nanoparticles in vitro, which warrants further in vivo investigation in the future.

Abstract Myelodysplastic syndromes (MDS) are clinically and biologically diverse disorders, emphasizing the need for personalized treatment approaches. The International Working Group for Prognostication of MDS (IWG_PM) recently introduced a molecular classification, referred to as the MDS taxonomy, that categorizes patients into 16 subgroups based on 21 gene mutations, 6 cytogenetic abnormalities, and loss of heterozygosity (LOH) at TP53 and TET2 loci. This study sought to validate and enhance the clinical relevance of the MDS taxonomy by analyzing a large retrospective cohort ( n = 5136) and transcriptomic data from a prospective cohort ( n = 477). The taxonomy successfully identified subgroups with distinct clinical characteristics and disease progression patterns. However, incorporating gene interactions from taxonomy subgroups did not improve the prognostic performance of the Molecular International Prognostic Scoring System (IPSS‐M). We further assessed whether the taxonomy could guide management in patients receiving disease‐modifying therapies. Except for the “ TP53 ‐complex” subgroup, taxonomy classifications were not predictive of hypomethylating agent response or transplant outcomes. Nonetheless, they correlated with overall survival, suggesting that while both IPSS‐M and the taxonomy capture disease biology, other non‐genetic factors may influence treatment response. RNA sequencing confirmed the biological distinctiveness of the taxonomy groups. Transcriptomic profiling of CD34+ bone marrow cells revealed unique, homogeneous gene expression patterns, particularly within the AML‐like, bi TET2 , SF3B1 , and TP53 ‐complex subgroups. Further integration of multi‐omics data may refine MDS classification, improving clinical decision‐making and guiding the development of targeted therapies.

Key Points Alanyl-transfer RNA synthetase 1 (AARS1) was upregulated and promoted cyst growth in autosomal dominant polycystic kidney disease. AARS1 promoted lysine lactylation of signal transducer and activator of transcription 3 (K140) and NF-κB p65 (K310), enhancing their phosphorylation, interaction, and transcriptional activity. AARS1 transcriptionally repressed its novel targets, Atg5 and Dusp4, to impair autophagy but activate polycystic kidney disease signaling pathways. Background Autosomal dominant polycystic kidney disease (ADPKD) is the most common inherited kidney disorder, characterized by metabolic reprogramming with enhanced glycolysis and lactate accumulation. However, the enzyme that senses lactate and uses it as a substrate for protein lactylation in ADPKD remains unknown. Alanyl-transfer RNA synthetase 1 (AARS1) is a lactate-responsive enzyme with lactyltransferase activity, while its role and mechanisms in ADPKD have not been defined. Methods To investigate the role of AARS1, we generated Pkd1 and Aars1 double conditional knockout Pkd1 fl/fl :Aars1 fl/fl :Ksp-Cre mice and evaluated the effect of AARS1 inhibitor β -alanine in two ADPKD mouse models. Coimmunoprecipitation and Cleavage Under Targets and Tagmentation analyses were performed to identify novel AARS1 substrates and downstream target genes involved in cystogenesis. Results AARS1 was elevated in Pkd1 mutant renal epithelial cells and kidneys, and genetic deletion of Aars1 significantly delayed cyst growth, preserved kidney function, and reduced renal lactylation in Pkd1 mutant mice. Mechanistically, AARS1 promoted lactylation-dependent activation of signal transducer and activator of transcription 3 (STAT3) and NF-κB (p65), specifically at STAT3 K140 and p65 K310, thereby amplifying pro-proliferative and proinflammatory transcriptional programs. AARS1 also associated with promoter regions and mediated histone H3 lysine 14 lactylation, thereby repressing the transcription of Atg5 to impair autophagy and suppressing the transcription of Dusp4 to sustain phosphorylation of cAMP response element–binding protein and retinoblastoma protein. Cytokine signaling through IL-6 and TNF- α further reinforced AARS1 expression through STAT3- and NF-κB–dependent feed-forward loops. Importantly, inhibition of AARS1 with β -alanine markedly slowed cyst progression in Pkd1 mutant mouse models. Conclusions Our study identified AARS1 as a central metabolic sensor linking lactate-driven lysine lactylation to transcriptional, epigenetic, and signaling pathways that drive ADPKD progression.

Abstract Rationale The impacts of COVID-19 vaccination and SAR-CoV-2 infection on brain tissues and structures remain controversial. This study examines whether COVID-19-related exposures are associated with measurable changes in structural magnetic resonance imaging (MRI) using data from the US general population-based Collaborative Cohort of Cohorts for COVID-19 Research (C4R) Study. Methods The C4R study is an observational meta-cohort study of 14 NIH-funded population-based cohorts, with directly measured data on COVID-19-related exposures, including vaccination and infection. For this analysis, we included participants with C4R data and paired brain MRI scans from both before and after the onset of the COVID-19 pandemic (defined as March 1, 2020) from two cohorts: the Atherosclerosis Risk in Communities study (ARIC) and Framingham Heart Study (FHS). MRI features examined as outcomes were white matter volume (WMV), gray matter volume (GMV), total brain volume (BV), hippocampal volume (HV), and white matter hyperintensity volume (WMH), a marker of microvascular disease. Exposures included SARS-CoV-2 infections identified via questionnaires, serosurveys, and medical record reviews from 2020-2025. Infections resulting in hospitalization were classified as severe. Time-to-recovery, symptoms of long COVID, and vaccination status were self-reported by questionnaire. Analysis of covariance (ANCOVA) estimated associations between COVID-19-related exposures and pandemic MRI-measured outcomes, with adjustment for: the corresponding pre-pandemic MRI measure, the time between the two MRI scans, age, sex, systolic blood pressure, diabetes, and cardiovascular disease. Results Of 270 participants with available data, mean (SD) age was 80.6 years (10.6); 43.0% were male; and the mean (SD) interval between paired MRI scans was 4.2 (2.0) years. Most (90%) were vaccinated (of whom 6.7% vaccinated before infection) and 7.9% reported SARS-CoV-2 infection (of which 13.6% were severe infections) prior to their pandemic MRI (conducted March 2020 - June 2022). In fully adjusted models, there was no statistically significant association for change in WMV, GMV, BV, HV, or WMH with SAR-CoV2 infection status, infection severity, vaccination status, or vaccination timing (Table, P > 0.05 for all comparisons). Self-reported symptoms of long COVID and vaccine manufacturer were also not associated with MRI outcomes. Conclusions Based on repeated (pre-pandemic and pandemic era) structural MRI scans, we found no evidence that SARS-CoV-2 infection or COVID-19 vaccination were associated with changes in brain structure or brain microvascular disease. These findings are consistent with prior data supporting COVID-19 vaccine safety and suggest resilience of brain structures following SARS-CoV-2 exposures. Nonetheless, further research is warranted using more sensitive measures and assessing longer term effects. This abstract is funded by: OT2HL156812

This study investigates how word-initial /l/ and /n/ are phonetically realized in Mandarin Chinese as produced by speakers from three regions: Beijing (close to Standard Mandarin), Changsha (where Xiang, which contains /l/ but not /n/, is also spoken locally), and Meizhou (where Hakka, which contains both /l/ and /n/, is also spoken locally), focusing on acoustic cue use and phonological context effects. Using acoustic analysis and random forest classification, we analyzed five acoustic measures (F2–F1 spacing, F3 frequency, BW1, ΔA1, and A1–P0) and evaluated their contribution to distinguishing the two sounds. Results showed that speakers from different regions used distinct cue weighting strategies: Beijing Mandarin speakers relied more on spectral cues, Meizhou Mandarin speakers showed greater reliance on nasality-related cues, and Changsha Mandarin speakers combined both, with greater variability. Phonological context, including preceding nasals and following vowels, further modulated cue realization in region-specific ways. These findings demonstrate how native phonological background and phonological environment shape the phonetic implementation of a shared Mandarin contrast and illustrate the value of combining acoustic and classification-based approaches for modeling gradient phonetic variation.

Introduction Large-scale production of mammalian cells is pivotal for applications in biotechnology, regenerative medicine, and therapeutic manufacturing. However, current bioreactor technologies face significant technical and economic challenges, including excessive cell aggregation, shear stress-induced cell death, batch-to-batch inconsistencies, and limited scalability. We propose that engineering a cell-friendly microenvironment can enhance culture efficiency. Previously, we developed alginate hydrogel microtubes (AlgTubes) that significantly improved cell density and growth rates; however, AlgTubes lack adhesion sites essential for anchorage-dependent cells and frequently break, causing cell leakage and production inconsistencies. Methods To address these limitations, we reinforced AlgTubes with collagen nanofibers, creating collagen-alginate hybrid hydrogel microtubes (ColAlgTubes). Collagen was integrated to form a dense nanofiber network interwoven with the alginate mesh, with the dual aim of enhancing mechanical properties and providing cell adhesion sites. ColAlgTubes were fabricated to maintain cell mass within a 400 μm diameter to ensure efficient nutrient exchange and waste removal. Results ColAlgTubes successfully formed a reinforced hybrid hydrogel structure in which the collagen nanofiber network improved the mechanical integrity of the alginate matrix while supplying adhesion sites for anchorage-dependent cells. The optimized 400 μm diameter microenvironment supported high cell viability, rapid proliferation, and exceptional yields of 5 × 10 8 cells/mL. Discussion These results demonstrate that ColAlgTubes overcome the key limitations of AlgTubes by combining structural reinforcement with biological functionality. The improved mechanical properties reduce tube breakage and cell leakage, while collagen-derived adhesion sites broaden compatibility to anchorage-dependent cell types. With their scalability, cost-effectiveness, and high efficiency, ColAlgTubes represent a transformative solution for large-scale mammalian cell production across biotechnology, regenerative medicine, and therapeutic manufacturing.

Abstract Surgery continues to be a mainstay of treatment for patients with symptomatic fibroids. Hysterectomy is an option for those desiring definitive treatment and myomectomy is preferred for those that have not yet completed childbearing or wish to retain their uterus. While open laparotomy remains a viable approach to both hysterectomy and myomectomy, minimally invasive techniques for the surgical management of symptomatic fibroids are preferred options for many due to improved patient outcomes. These include hysteroscopic myomectomy, laparoscopic and robotically assisted myomectomy, and vaginal, laparoscopic, and robotically assisted hysterectomy. Patients have a faster recovery and less postoperative pain compared to a laparotomic approach. More recently, uterine‐sparing outpatient modalities such as ultrasound‐guided radiofrequency ablation and high‐intensity focused ultrasound have emerged as promising alternatives for selected patients. Benefits include clinically significant reduction in fibroid size and menstrual bleeding with small or no abdominal incisions and an expedited convalescence. This article reviews preoperative evaluation and imaging for fibroids, as well as the techniques, approach, indications, patient selection, procedural management, and surgical and fertility outcomes for each surgical and procedural management of uterine fibroids.

Diffuse large B-cell lymphoma (DLBCL), the most common type of lymphoma, arises from various pathogenic mechanisms including gene translocations and fusions. Detection of gene rearrangements using fluorescence in situ hybridization (FISH) is a standard practice for DLBCL diagnosis and guides treatment decisions. High-throughput chromosome conformation capture (Hi-C) DNA sequencing is a next-generation sequencing-based technology to identify genome-wide rearrangements using a single assay. In this study, Hi-C sequencing was performed using FFPE tissues from 159 patients with DLBCL, and identified 746 cancer genes at or proximal to the rearrangement breakpoints with a total of 1903 occurrences. Focusing on clinically important rearrangements, Hi-C detected 102 rearrangements of MYC, BCL2, and/or BCL6 in 92 patients and revealed the fusion partners, including 25 rearrangements missed by FISH. Causes of FISH negative results included FISH-cryptic breakpoints, complex or faint FISH signals, low percentage of FISH positivity, and issues related to tissue fixation. Moreover, in 20 patients (12.6%), Hi-C sequencing detected 22 rearrangements characteristic of other lymphoma types, including CCND1 rearrangements that could lead to reclassification as mantle cell lymphoma. Survival analysis for genome-wide rearrangements using machine learning models identified MYC, PD-L1, CCND1, BCL2, NTRK1/PRCC, RRAS, and FANCE rearrangements with significant prognostic effects in the DLBCL cohort. In conclusion, Hi-C sequencing detects gene rearrangements crucial for diagnosis in an unbiased and molecular manner and showed high sensitivity and specificity in our study. These advantages of Hi-C sequencing offer help to improve the workflow of clinical pathology laboratories, diagnostic precision, and treatment of large B-cell lymphoma.

ABSTRACT First‐line therapy for mantle cell lymphoma (MCL) represents a critical opportunity for clinical benefit via sustained complete response. We conducted a phase 2 multicenter trial in the academic and community cancer research united (ACCRU) network, testing a multitargeted 1st line regimen. CARiBOU (ACCRU‐LY‐1804) employs alternating VR‐CAP and R‐cytarabine with continuous acalabrutinib, in six 21‐day cycles, for previously untreated MCL. The primary endpoint was complete metabolic response (CMR) rate. Secondary endpoints included safety, feasibility of stem cell collection, proportion proceeding to ASCT, and progression‐free (PFS) and overall survival (OS). Peripheral blood measurable residual disease (MRD) was tested using the ClonoSEQ assay (Adaptive Biotechnologies). Of 41 patients enrolled, 39 (95%) responded to therapy, including 37 patients achieving CMR (90%). Two nonresponders discontinued therapy for toxicity early, prior to study‐defined restaging, and received alternate therapy. Undetectable MRD at a 10 6 threshold was achieved in 26/33 tested patients (79%), and 94% at 10 5 . 18‐month estimated PFS is 79% (95% CI 64%–97%), and OS is 96% (95% CI 88%–100%). Toxicities were primarily hematologic (grade 3 hematologic AE in 32 patients, [78%]). Twelve required platelet transfusions, and one grade 3 bleeding event occurred. Febrile neutropenia occurred in 4 patients, and 6 (14%) experienced SAEs. There were no treatment‐related deaths. CARiBOU is an efficient, highly effective outpatient 1st line MCL regimen, employing intermediate‐dose cytarabine and continuous acalabrutinib for 6 cycles. This multitargeted regimen addresses the biologic heterogeneity of MCL and permits flexible MRD‐guided decisions on consolidation and maintenance. Trial Registration: ClinicalTrials.gov identifier: NCT04626791