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PubMed2026

Predictive value of Rectal and Throat-nose Screening for the presence of Multidrug-Resistant Organisms in Duodenal Fluid as a Risk of Duodenoscope Contamination: A Multicenter Study.

BACKGROUND: Duodenoscopes have been implicated in patient-to-patient transmission of multidrug-resistant organisms (MDROs). Current gastrointestinal MDRO surveillance relies on rectal screening, yet the duodenum is the primary site of duodenoscope exposure. This study evaluated the predictive value of rectal and throat-nose screening for detecting duodenal MDROs as a marker of duodenoscope contamination risk. METHODS: Adult patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) at tertiary care centers in the Netherlands and India were included. Rectal swabs, throat-nose swabs, and duodenal aspirates were analyzed for MDROs. The detected MDROs were compared using species identification, antibiotic susceptibility patterns, and whole-genome sequencing. RESULTS: Among 512 participants (Netherlands: 339; India: 173), rates of duodenal and rectal MDRO carriage were higher in India (56.6% (98/173); 79.8% (138/173), respectively) than in the Netherlands (5.6% (19/339); 10.3% (35/339)). Given the low prevalence of throat-nose carriage, only the predictive value of rectal screening was assessed. Rectal screening sensitivity for genetically related strains in duodenal fluid was 32.7% in India and 68.4% in the Netherlands . For detecting any duodenal MDRO, sensitivity reached 91.8% in India and 84.2% in the Netherlands, with specificities of 36.0% and 94.1%. Positive predictive value (PPV) was low (India: 65.2%; Netherlands: 45.7%), while negative predictive value was 77.1% and 99%, respectively. CONCLUSIONS: Rectal screening is unreliable for detecting strain-specific duodenal MDROs and overestimates true carriage due to low PPV values. However, it provides excellent rule-out value in low-prevalence settings. Consequently, its utility for guiding infection prevention strategies for duodenoscope contamination is greatest in low-MDRO-prevalence regions.

Bacterial↗

PubMed2026

iMTSS: an integrated framework for biology- and patient-driven prognosis in myelofibrosis undergoing transplantation.

BACKGROUND: Allogeneic hematopoietic cell transplantation is the only curative treatment for myelofibrosis, but failure occurs by two mechanistically distinct routes: relapse of the neoplasm, which reflects its underlying genetics, and non-relapse mortality, which reflects whether the patient and graft tolerate the procedure. Established prognostic systems either lack molecular granularity or were derived in the non-transplant setting, and all collapse these two routes into a single survival estimate. None can indicate why an individual patient is at risk, or which class of intervention might reduce that risk. OBJECTIVE: To determine why an individual patient is at risk and to develop and validate an integrated framework that quantifies biology- and patient-driven prognosis. STUDY DESIGN: We analyzed 1,550 adults undergoing first allogeneic transplantation for primary or secondary myelofibrosis across international centers, the largest genomically annotated transplant cohort in this disease. The cohort was split into development (n=930) and validation (n=620) sets. Overall survival was modeled by Cox regression; relapse and non-relapse mortality were modeled as competing events by Fine-Gray subdistribution-hazard regression at 2 years. Discrimination was assessed by the concordance index with bootstrap confidence intervals. The molecular contribution was quantified by variance decomposition of, and robustness to the analytic choices was examined by resampling. RESULTS: A genetically defined disease-intrinsic axis, including TP53 allelic state, RAS pathway mutations, ASXL1 and driver genotype, blasts and blood counts, predicted 2 year relapse incidence (validation concordance 0.69, 95% CI 0.63 to 0.74), whereas a non-overlapping host and structural axis, including portal vein thrombosis, donor type, patients' performance status, and age predicted 2-year non-relapse mortality (0.63, 95% CI 0.59 to 0.68). The two scores shared only 3.4% of their variance, indicating that a patient's disease genetics carried almost no information about non-relapse mortality. Variance decomposition showed that TP53 allelic state alone accounted for 30% of the relapse score. Recombined, the framework discriminated overall survival (concordance 0.640, 95% CI 0.616 to 0.662) better than every established prognostic system. For proof of concept, 3 risk groups separated in the validation cohort, with 5 year survival of 72%, 58%, and 39% (P<0.001), and the models were well calibrated. CONCLUSIONS: Relapse and non-relapse mortality after transplantation for myelofibrosis are governed by distinct dimensions. Estimating both outcomes independently with genetic and clinical information, in addition to overall survival, establishes an individualized basis for transplant decision-making. The calculator is openly available (https://imtss-calculator.com).

mortality↗

PubMed2026

Identification of Two Novel Compound Heterozygous ADAMTS17 Variants Associated With Weill-Marchesani Syndrome 4.

PURPOSE: Weill-Marchesani syndrome 4 (WMS4) is frequently underdiagnosed when standard exome sequencing fails to detect noncoding pathogenic variants. We aimed to identify the genetic cause in a patient with suspected WMS4 and to characterize the splicing-altering mechanism of a deep intronic variant in ADAMTS17. MATERIALS AND METHODS: Whole-exome sequencing combined with whole-genome sequencing was conducted in the proband, who presented with ocular and skeletal manifestations of WMS4. A minigene splicing assay was applied to verify the splicing abnormality caused by the deep intronic variant. RESULTS: The patient showed high myopia, brachydactyly, accelerated growth velocity, and advanced bone age. Two novel compound heterozygous variants in ADAMTS17, c.1655G>A and c.450+38C>A, were identified. The deep intronic variant c.450+38C>A was confirmed by minigene assay to disrupt normal pre-messenger RNA splicing by inducing retention of a 35-base pair intronic segment, leading to a frameshift and premature termination (p.G152Lfs*23). CONCLUSIONS: This study broadens the mutational spectrum of ADAMTS17. Whole-genome sequencing combined with functional splicing validation is essential for resolving molecularly undiagnosed cases of WMS4, particularly when deep intronic variants are suspected, and supports clinical genetic testing and genetic counseling of hereditary connective tissue disorders.

ADAMTS17↗

PubMed2026

Global inequalities in cardiometabolic care and achievable cardiovascular risk reduction by wealth, region, and sex: a pooled analysis of individual participant data from 76 countries.

BACKGROUND: Wealth-related inequalities affect cardiometabolic health worldwide, but their implications for cardiometabolic care and potentially preventable cardiovascular disease remain poorly understood. We aimed to quantify wealth-related inequalities in the care cascade for hypertension, diabetes, and hypercholesterolaemia by wealth quintile, region, and sex. METHODS: In this cross-sectional, individual-level analysis, we analysed harmonised, nationally representative health examination surveys conducted in five WHO regions. Adults aged 18 years or older with data on age, sex, wealth, and at least one cardiometabolic outcome were eligible. All variables in the surveys were obtained from standardised in-person examinations. We evaluated hypertension, diabetes, and hypercholesterolaemia and applied a care cascade of disease awareness, treatment, and control for each condition uniformly across all surveys. Disease status was defined from measured biomarkers, self-reported diagnosis, or current medication; awareness and treatment were based on self-reported information, and control on measured biomarkers. Each indicator was expressed as the proportion of all individuals with the corresponding condition. Socioeconomic position was assessed using household wealth indices derived within each survey, and participants were ranked within each country and categorised into country-specific quintiles (quintile 1 to quintile 5), with quintile 1 including those with the least household wealth. Inequality was quantified by the quintile 5 minus quintile 1 difference, the slope index of inequality (SII), and relative index of inequality (RII). Predicted 10-year cardiovascular risk was estimated with the Globorisk equations, and trial-derived relative risk reductions were applied to estimate achievable absolute risk reduction. The ASANDE consortium is registered with ClinicalTrials.gov (NCT07427355). FINDINGS: We analysed data from 109 surveys conducted in 76 countries between 2002 and 2024. 315 403 (65·9%) of 478 947 survey participants with available data were included in this analysis (median age 40 years [IQR 30-52], 185 209 [58·7%] women, and 130 194 [41·3%] men). Inequalities widened progressively across the care cascade in all regions and were most pronounced for disease control. Pooled across regions, the SII for control was 4·4% (95% CI 2·4-6·4) for hypertension (RII 1·1, 1·1-1·2), 4·8% (0·6-9·0) for diabetes (RII 1·1, 1·0-1·2), and 6·5% (3·8-9·2) for hypercholesterolaemia (RII 1·1, 1·0-1·1). However, regional patterns varied substantially. In the region of the Americas, disease control consistently favoured wealthier individuals (SII 9·2% for hypertension, 4·8-13·5; RII 1·2, 1·1-1·3). In the African region, coverage was uniformly low, and the largest absolute inequality favoured individuals with the least wealth, particularly for hypercholesterolaemia treatment (SII -37·6%, -49·7 to -25·5; RII 0·6, 0·5 to 0·7). Baseline cardiovascular risk was higher in individuals with the least wealth than among the wealthiest (13·6% vs 12·2%), but achievable absolute risk reduction was correlated with baseline risk rather than with treatment coverage: achievable reduction was greatest in the European Region (3·9%) and lowest in the Africa region (2·5%). Across all regions, achievable absolute risk reduction was greater in men than in women (4·6% vs 3·5% in the European region). INTERPRETATION: The populations with the largest treatment gaps are not necessarily those that could achieve the greatest absolute reduction in cardiovascular risk through treating individuals who are currently untreated. In settings where coverage is uniformly low, expanding the supply of care matters more than redistributing access to it. Moreover, because socioeconomic inequalities widen after diagnosis, screening alone is unlikely to reduce disparities unless accompanied by sustained access to treatment. Policy should prioritise overall population health over maximise equity within the population. FUNDING: None.

Journal Article↗

PubMed2026

Auditing bacterial dark-gene screens for superimposed open reading frame artefacts: A multi-layer analysis of Rv2438A in Mycobacterium tuberculosis.

Essentiality and knockdown-vulnerability screens can promote spurious bacterial open reading frames when those frames overlap essential genes, because such a frame inherits its neighbour's signals undiluted and therefore satisfies the screen's criteria better than a genuine small gene. We present a multi-layer audit that tests this failure mode across genome annotation, transposon mutagenesis, CRISPR interference, homology, transcript mapping, proteomics, and population variation. We apply it to Rv2438A, a 92-codon conserved hypothetical open reading frame of Mycobacterium tuberculosis ranked first by our own dark-gene target screen. Rv2438A is superimposed on the essential NAD synthetase locus nadE: 44% lies within its coding sequence on the opposite strand, and the remainder covers its promoter and transcription start site. Consequently, three of five Himar1 sites lie within nadE, no CRISPRi guide can target Rv2438A without binding nadE, and the cross-species hit maps to the same nadE start junction. Rv2438A lacks its own transcription start site and is absent from every proteomic dataset that detects nadE. A genome-wide scan identifies six short, overlapping, uncharacterised loci among 3907 annotated genes, but only Rv2438A combines overlap and essentiality with non-detection across all proteomic datasets; rare genome-wide, it ranked first among screen hits. We provide an implementable audit workflow and a codon-position control, but measure the control's sensitivity as only two of five genes with attested protein, limiting it to confirmatory use. Overlap coordinates and neighbour-specific experimental resolution should therefore be reported before bacterial dark genes are prioritised.

CRISPR interference↗

PubMed2026

Disentangling the cellular composition of FLCN-mutated tumors in Birt-Hogg-Dubé Syndrome by spatial transcriptomics.

Birt-Hogg-Dubé (BHD) syndrome is a hereditary cancer predisposition syndrome caused by pathogenic variants in the folliculin (FLCN) gene and is associated with an increased risk of multifocal renal tumors. FLCN-mutated tumors (FMTs) often exhibit morphological heterogeneity with mixed morphological features resembling renal oncocytoma (RO) and chromophobe renal cell carcinoma (chRCC), yet the molecular basis underlying the heterogeneous morphologic features and the morphologic-genomic correlations remain poorly defined. In our prior work, we identified mutually exclusive expressions of L1 cell adhesion molecule (L1CAM) and forkhead box I1 tboxI1 (FOXI1) labeling the two morphologically distinct cellular populations in BHD-associated FMTs, leading to the hypothesis that these two tumor compartments may have distinct molecular features and may reflect different nephron epithelial differentiation states. In this follow-up study, we tested this hypothesis using L1CAM and FOXI1 as morphology-guided markers for spatial transcriptomic profiling of the distinct tumor compartments in FMTs with the NanoString GeoMX Digital Spatial Profiler (DSP). Six FMTs from three patients with BHD and three normal kidney tissues were analyzed. L1CAM+ and FOXI1+ area of interest (AOI) were collected from tumor areas with various tumor compositions, including L1CAM+ dominant, FOXI1+ dominant, and mixed tumor areas. Spatial transcriptomic analysis identified distinct gene expression signatures in L1CAM+ and FOXI1+ FMT compartments independent of the local tumor compositions. FOXI1+ tumor cells showed robust enrichment for intercalated cells (IC)-associated gene signatures. In contrast, L1CAM+ tumor cells exhibited a heterogeneous transcriptional profile, with partial overlap across a spectrum of renal tubular epithelial cell types rather than a definitive principal cell-like identity. Despite this compartment-specific differences, both compartments share expression of a panel of tumor signature genes, including glycoprotein nmb (GPNMB) gene, and a core of cancer related biological functions and signaling pathways. Together, these findings refined the prior dichotomous model of BHD-associated renal tumors and support a model in which L1CAM+ and FOXI1+ tumor compartments represent divergent evolutionary or differentiation states with a common FLCN-mutant neoplastic transcriptional program. This spatial transcriptomic profiling provides molecular evidence for the morphological heterogeneity of FMTs and insights on the tumor biology of BHD-associated FMTs.

Birt-Hogg-Dubé↗

PubMed2026

sWGS Identifies a Copy-Number-High Subset of TP53-mutated Multiple-Classifier Endometrial Carcinomas With Adverse Clinicopathological Features.

TP53-mutated "multiple-classifier" endometrial carcinomas represent a diagnostically challenging subgroup within current molecular classification algorithms. Although these tumors are assigned to POLE-mutated or mismatch repair-deficient categories according to current ESGO/FIGO-based algorithms, their biological heterogeneity remains incompletely characterized. Herein, we retrospectively analyzed TP53-mutated multiple-classifier endometrial carcinomas identified through routine molecular profiling at our institution between 2022 and 2025 using an integrated histopathological, immunohistochemical, targeted sequencing, and shallow whole-genome sequencing approach. Copy-number alteration-high (CNA-high) status was defined as ≥5 large-scale genomic alterations, corresponding to copy-number gains or losses ≥3 Mb within a single chromosomal arm excluding whole-arm alterations. Among 33 analyzable TP53-mutated multiple-classifier endometrial carcinomas, sWGS identified 12 CNA-high tumors (36.4%) and 21 CNA-low tumors (63.6%). CNA-high tumors were more frequently non-endometrioid, high-grade, and advanced-stage according to FIGO 2023. They showed higher TP53 variant allele frequencies (VAF) and higher TP53 VAF-to-tumor-cellularity ratios. After a median follow-up of 12.8 months, recurrences (6/33; 18.2%) and disease-related deaths (3/33; 9.1%) were observed in the CNA-high subgroup, whereas no recurrence or disease-related death was observed among CNA-low patients. These findings indicate that TP53-mutated multiple-classifier endometrial carcinomas comprise biologically distinct subsets that are not fully captured by current 4-tier TCGA-based molecular classification and ESGO-based risk stratification. In this cohort, sWGS identified a CNA-high group with adverse clinicopathological features and clinical events suggesting a potentially more aggressive clinical course. Integration of genome-wide copy-number profiling may therefore refine the biological interpretation of TP53 alterations in multiple-classifier endometrial carcinomas and warrants validation in larger multicenter cohorts.

TP53↗

PubMed2026

Acute Myeloid Leukemia With KMT2A Amplification: A TP53-Alteration-Enriched Subgroup Associated With Chromoanagenesis and Poor Prognosis.

KMT2A amplification (KMT2A-amp) is a rare but aggressive genomic abnormality in acute myeloid leukemia (AML), with limited characterization in prior studies. We retrospectively analyzed 96 patients with AML harboring KMT2A-amp, including 56 newly diagnosed (ND) and 40 relapsed/refractory (RR) cases, with a median age of 68 years. Approximately half of the cases had therapy-related or secondary AML. All cases demonstrated highly complex karyotypes, with frequent -5/del(5q), -7/del(7q), and -17/del(17p). TP53 alteration was present in 93% of patients, whereas other recurrent AML-associated mutations were uncommon, and no AML-defining gene fusions or mutations were identified. In cases evaluated by optical genome mapping, all showed chromoanagenesis involving chromosome 11q23 region. Clinical outcomes were poor, with a median overall survival of 5.5 months in ND and 2.3 months in RR patients. Intensive chemotherapy did not improve survival compared with lower-intensity therapy, whereas venetoclax-based regimens were associated with improved overall survival (7.1 vs 4.6 months; p = 0.04) and event-free survival (6.7 vs 0.17 months; p < 0.01). We conclude that KMT2A-amp AML represents an extremely high-risk subgroup occurring in the context of TP53-associated genomic instability and chromoanagenesis. Its refractoriness to conventional chemotherapy highlights the urgent need for more effective, targeted therapeutic strategies.

KMT2A amplification↗

PubMed2026

Molecular mechanism of HUWE1-HAPSTR1-USP7-mediated ubiquitin chain amplification on nuclear proteins.

Rapid protein turnover is essential for cellular stress adaptation. HUWE1 (HECT, UBA, and WWE domain containing 1), a large HECT-type E3 ligase, regulates many short-lived stress-responsive proteins, yet the mechanisms underlying its substrate selectivity remain unclear. Here, we reveal that HUWE1 functions as a ubiquitin chain amplifier that captures pre-ubiquitinated substrates and amplifies the degradation signal by assembling long ubiquitin chains containing K11-K48 branch points, a process regulated by its partners HUWE1-associated protein stress response 1 (HAPSTR1) and USP7 (ubiquitin-specific-processing protease 7). Structural and biochemical analyses show that HAPSTR1 engages HUWE1's ubiquitin-binding motifs to drive nuclear import and modulate substrate recruitment. A cryo-EM structure of the HUWE1-USP7 complex reveals a bidirectional regulatory mechanism: HUWE1 activates USP7's catalytic activity, while USP7 modulates HUWE1 conformational states. Global proteomic analyses demonstrate that this axis drives extensive remodeling of the short-lived nuclear proteome. These findings establish the HUWE1-HAPSTR1-USP7 complex as a key ubiquitin code modifier, providing a molecular rationale for HUWE1 dysregulation in neurodevelopmental disorders and cancer.

Ubiquitin-Specific Peptidase 7↗

PubMed2026

"Updates on diagnostic and prognostic molecular biomarkers of CNS tumors".

The diagnosis and classification of central nervous system (CNS) tumors has undergone a paradigm shift over the past decade, evolving from a purely histology-based approach to an integrated framework that incorporates molecular and epigenetic features. This review summarizes recent updates in key genomic and epigenomic biomarkers across major CNS tumor categories, with a focus on their diagnostic, prognostic, and therapeutic implications. DNA methylation profiling has emerged as a valuable tool for tumor classification, subgrouping, and grading, complementing traditional histopathologic assessment. Across diffuse gliomas, newly characterized molecular alterations have refined grading criteria and clarified the boundaries between tumor types, including important caveats about the use of individual molecular features as sole diagnostic criteria. In ependymomas, medulloblastomas, atypical teratoid/rhabdoid tumors, meningiomas, pineal tumors, and embryonal tumors, methylation profiling now defines biologically and clinically meaningful subgroups that inform risk stratification and treatment selection. The emerging recognition of mismatch repair-deficient gliomas and fusion-driven tumor entities further underscores the expanding complexity of CNS tumor taxonomy. As molecular technologies continue to advance, the integration of genomic, epigenomic, histopathologic, and clinical data will be essential to improving diagnostic precision, guiding therapy, and ultimately enhancing patient outcomes.

Embryonal↗

PubMed2026

Genomic and transcriptomic quality control for an autologous iPSC-derived cell therapy for Parkinson's disease.

Toward development of an autologous, induced pluripotent stem cell (iPSC)-based cell therapy for Parkinson's disease (PD), we demonstrate successful, reproducible genomic and transcriptomic qualification of patient-derived dopaminergic neuron precursor cells (DANPCs) across multiple donors. Our analysis includes whole-genome sequencing data from fibroblasts, iPSCs, and DANPCs and the development of NeuriTest, an RNAseq-based bioinformatic analysis of DANPCs designed to predict cell quality based on empirical animal data. Autologous cell therapies are immune matched to the patient, potentially augmenting durability of benefit compared to allogeneic cells while negating the need for immunosuppression and accompanying side effects. Patient-specific iPSCs are an autologous cell source that can be differentiated to dopaminergic neurons, the cell type lost in PD. We report here our preclinical manufacturing strategy and results demonstrating efficacy in a PD rodent model and safety in a 9-month GLP toxicology study.

Parkinson’s disease↗

PubMed2026

Gene polymorphisms associated with progression of primary open-angle glaucoma: A systematic review.

Glaucoma is the leading global cause of irreversible blindness, with primary open-angle glaucoma (POAG) its most prevalent subtype. While elevated intraocular pressure is a major risk factor, glaucoma progression is multifactorial, influenced by genetic, environmental, vascular and mechanical factors. Genetic polymorphisms have been linked to both POAG susceptibility and progression, yet most studies focus on risk factors for disease onset rather than progression. We provide an overview of the current literature on gene polymorphisms associated with POAG progression. We conducted a systematic search following PRISMA guidelines in MEDLINE, EMBASE, Web of Science, Cochrane Library, Scopus and Public Health Genomics and Precision Health Knowledge Base. Eligible studies investigated associations between genetic variants and structural or functional markers of glaucoma progression in adult-onset POAG patients. Eighteen articles were included. HLA class I haplotypes (A1-B8 and A2-B40) and MYOC.mt1+ carriers showed faster progression of optic nerve head damage. The APOE ε4 allele was linked to faster macular thinning in normal tension glaucoma patients. BDNF rs6265 Val/Val homozygotes exhibited accelerated retinal nerve fiber layer loss, particularly in females. TGFBR3-CDC7 (rs1192415: G) and MYOC.mt1+ carriers experienced accelerated visual field deterioration. Carriers of GAS7 (rs9913911: AA), IL1B (rs1143627: CT and rs16944: CT) and OPTN (rs2234968) had a higher likelihood of requiring surgery. Variants in ABCA1, CDKN2B-AS, eNOS and Piezo1 showed inconclusive results. These findings support a role for genetic polymorphisms in POAG progression and highlight the potential of genetic screening to identify patients at increased risk for rapid disease progression.

Disease progression↗

PubMed2026

Have we entered a 'post-model' era in plant biology?

Models such as arabidopsis (Arabidopsis thaliana) have underpinned genomic and physiological research in plant science. Advances in genome sequencing, pangenomics, and genome editing have prompted claims of a 'post-model' era, with model-crops and crops such as rice and bread wheat combining agricultural relevance with experimental tractability. We argue that the 'simplicity-to-complexity' approach remains valid, although model systems have evolved. Arabidopsis remains indispensable for interpreting multi-omics data, testing developmental hypotheses, and generating mechanistic insights difficult to obtain in crops. Linking these strengths to model-crops adds translational value by bridging discovery and breeding, while niche models such as Brachypodium distachyon and legumes address grass cell wall biology and nitrogen fixation. Future progress depends on diverse species with complementary strengths across fundamental and applied plant biology.

arabidopsis↗

PubMed2026

Proteogenomic analysis of pediatric and AYA high-grade glioma reveals age-dependent biology, female-male differences, and kinase targets.

High-grade gliomas (HGGs) in children and adolescents and young adults (AYA) exhibit distinct biology across the neurodevelopmental spectrum. To dissect tumor-intrinsic molecular characteristics independent of developmental variation, we perform comprehensive proteogenomic analyses of tumors from 112 HGG patients aged 0-40 years. Our multi-omics analysis identifies two AYA subgroups-adolescents (aged 15-26 years) and young adults (aged 26-40 years)-with distinct molecular profiles and survival outcomes. Tumor-normal comparisons and survival modeling highlight roles of oxidative phosphorylation and neuronal system biology in glioma progression. Causal network analysis and cell line studies provide a rationale for personalized therapies targeting candidate kinases, such as CDK8. Survival modeling, clustering, and immune-landscape analyses identify proteins, post-translational modifications, and immune signatures linked to outcomes and reveal clinically relevant differences between male and female patients.

adolescent and young adult glioma↗

PubMed2026

Characterisation of whole-blood extrachromosomal circular DNAs in Kawasaki disease complicated by coronary artery aneurysm.

BACKGROUND: Extrachromosomal circular DNAs are critical regulators of stress responses, immunity, and inflammation pathways. However, their role and underlying mechanisms in Kawasaki disease complicated by coronary artery aneurysm remain poorly understood. METHODS: Whole blood samples from six children with Kawasaki disease, including three with coronary artery aneurysm group and three without coronary artery aneurysm (control group), were subjected to extrachromosomal circular DNA sequencing. Putative extrachromosomal circular DNAs were identified using Circle-Map. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were performed on genes associated with upregulated extrachromosomal circular DNAs, and an exploratory immune-signature profiling was performed using the single-sample gene set enrichment analysis algorithm. RESULTS: We identified 4,790 differential extrachromosomal circular DNAs between the coronary artery aneurysm and control groups, of which 4,789 were upregulated in the CAA group. The extrachromosomal circular DNAs in the coronary artery aneurysm group were more concentrated and shorter in length than those in the control group. Upregulated extrachromosomal circular DNAs were mainly derived from autosomes, particularly chromosomes 3, 4, and 7. Functional enrichment analysis indicated that genes associated with upregulated extrachromosomal circular DNAs were mainly involved in response to stimulus-related terms and pathways, including chemokine signalling, cGMP-PKG signalling, and calcium signalling. Immune-signature analysis suggested that the coronary artery aneurysm group exhibited more specific immune responses, whereas the control group tended towards broader immune regulatory processes. CONCLUSIONS: Coronary artery aneurysm and control groups exhibited distinct extrachromosomal circular DNA profiles. These findings suggest that extrachromosomal circular DNA alterations are associated with coronary artery aneurysm in Kawasaki disease and may provide new insights into the molecular features underlying this condition.

Coronary artery aneurysm↗

PubMed2026

CRISPR/Cas9 screening revealed BIRC6-AS1/BIRC6 mediates abiraterone resistance via NHEJ pathway-dependent A20 degradation in prostate cancer.

Abiraterone acetate is a standard-of-care therapy for prostate cancer (PCa). However, resistance frequently emerges, often characterized by the progression to AR-independent phenotypes. Employing a genome-wide CRISPR/Cas9 library screening strategy, we identified 523 long non-coding RNAs (lncRNAs) and 2,183 protein-coding genes as potential candidates associated with abiraterone resistance. Notably, a pair of sense-antisense genes, BIRC6-AS1/BIRC6, was identified as a significant contributor to abiraterone resistance, serving as a critical survival factor in AR-independent contexts. BIRC6-AS1 depletion led to a reduction in both the mRNA and protein levels of BIRC6. Moreover, depletion of either BIRC6-AS1 or BIRC6 enhanced the sensitivity of PCa cells to abiraterone in both in vitro and in vivo settings. Further investigation revealed that BIRC6-AS1 stabilized the mRNA of BIRC6 through interaction with ILF2. Suppression of either BIRC6-AS1 or BIRC6 attenuated non-homologous end joining (NHEJ) repair activity, resulting in the disassembly of 53BP1 foci at DNA damage sites and an increased accumulation of DNA damage, thereby exposing a vulnerability in AR-independent resistant cells. Mechanistically, BIRC6 interacted with A20 and facilitated the K48-linked ubiquitination and subsequent degradation of A20 at the K337 residue. Additionally, A20 knockdown effectively reversed the abiraterone sensitivity induced by BIRC6-AS1 depletion. Collectively, our study provides a landscape of lncRNAs and protein-coding genes associated with abiraterone resistance and suggests that targeting the BIRC6-AS1/BIRC6 axis represents a potential therapeutic strategy to eradicate AR-independent resistant tumors in prostate cancer.

Journal Article↗

PubMed2026

Targeting super elongation complex-driven RNA polymerase II elongation reduces plaque vulnerability.

Atherosclerotic plaque rupture is a major cause of myocardial infarction and stroke, yet the mechanisms governing plaque stability remain incompletely understood. Endothelial activation can trigger endothelial-to-mesenchymal transition, a program linked to endothelial dysfunction and lesion vulnerability. Here we investigated whether transcriptional pause release and RNA polymerase II elongation constitute an early regulatory layer that promotes endothelial-to-mesenchymal transition and atherosclerosis. Analysis of human plaque single-cell transcriptomics indicated increased expression of super elongation complex components in endothelial cells with a transition signature. In primary human endothelial cell models, pharmacological inhibition of the super elongation complex attenuated the induction of mesenchymal markers. AFF4, pCDK9, and pSMAD2/3 showed physical interaction during endothelial transition. Genome-wide profiling of RNA polymerase II occupancy revealed reduced promoter-proximal pausing during early transition, accompanied by a rapid increase in nascent transcriptional elongation rates. Super elongation complex inhibition restored pausing and suppressed fast-responding transition-associated target genes. In a human cardiac organoid model, inhibition of the super elongation complex prevented EndMT-induced fibrillar collagen deposition and prevented the loss of beating rate. In a hyperlipidemic Pcsk9 gain-of-function mouse model, super elongation complex inhibition administered both prophylactically and therapeutically after established atherosclerosis reduced plaque burden and reduced features of plaque vulnerability. Finally, analysis of 1048 human plaque segments from the Athero-Express biobank showed significant associations between the elongation axis and multiple vulnerability-related plaque traits. Together, these findings identify rapid transcriptional elongation as a mechanistic driver of endothelial plasticity and features of plaque vulnerability and support targeting the elongation machinery as a potential strategy to reduce features of plaque vulnerability in atherosclerotic disease.

Humans↗

PubMed2026

Early-adulthood body mass index, mammographic density and post-menopausal breast cancer risk: a mediation analysis.

BACKGROUND: To explore potential mechanistic pathways and inform prevention strategies, this study examined whether mammographic density (MD) mediates the inverse association between higher early-adulthood body mass index (BMI) and lower post-menopausal breast cancer risk. METHODS: We analysed data from 33,816 post-menopausal women in the UK PROCAS cohort, with self-reported BMI at age 20. MD was measured using full-field digital mammography and assessed using the visual analogue scale (VAS) percentage density and Volpara®-derived fibroglandular volume (FGV). Counterfactual mediation modelling estimated natural direct and indirect effects. RESULTS: Over a median follow-up of 10.44 years, there were 1261 new post-menopausal breast cancers. Higher VAS and FGV were associated with increased breast cancer risk. BMI at age 20 was associated with lower VAS density and reduced breast cancer risk [Hazard Ratio per 5 kg/m²: 0.849 (0.771-0.938)]. The calculated proportion mediated by VAS density was 59.9% (32.6-150), after accounting for intermediate confounding by BMI in later adulthood. FGV was positively associated with higher BMI at cohort entry but not at age 20. CONCLUSIONS: Lower VAS density may partially explain the inverse association between early-adulthood BMI and post-menopausal breast cancer risk. The link between FGV and breast cancer risk may represent a different biological pathway.

Journal Article↗