Citations

Abstract We present chromosome-level, phased diploid genome assemblies of two widely used human fibroblast cell lines: BJ (46,XY) and IMR-90 (46,XX). Using Oxford Nanopore, PacBio HiFi, and Hi-C sequencing data, we generated assemblies spanning 5.9 and 6.0 Gbp with diploid quality values exceeding QV 60. To validate structural integrity, we developed KaryoScope, an alignment-free tool for generating computational karyograms from k-mer feature databases. We identify >50 000 structural variants relative to T2T-CHM13v2.0, the majority of which are heterozygous and cell-line-specific. Combining reference-based and de novo gene annotation, we uncover a previously unreported 1 Mbp homozygous duplication at the 16p11.2 locus in BJ, demonstrating that even karyotypically normal cell lines can harbor clinically relevant submicroscopic rearrangements. We show that mapping publicly available short-read, RNA-seq, and ChIP-seq data to sample-matched diploid assemblies substantially improves read alignment and enables haplotype phasing of 23%–28% of short reads. The BJ and IMR-90 assemblies and associated variant calls are publicly available as a resource for the research community.

Abstract Background/Aims The aim of this prospective cohort study was to evaluate the extent that kinesiophobia at baseline contributed to pain intensity at follow-up after starting first line treatments in patients with a range of musculoskeletal conditions, including rheumatoid arthritis (RA), fibromyalgia (FM) and knee osteoarthritis (OA). Methods 469 patients (RA n = 156, FM n = 149, OA n = 164) recruited from the Nuffield Orthopaedic Centre, Oxford University Hospitals, participated in this study. Pain was assessed with the pain detect questionnaire, with the item average pain severity over the last 4 weeks used for the primary analysis. The Tampa Scale for Kinesiophobia (TSK) was administered to assess fear of movement. The association between TSK and pain at baseline was investigated by analysing their correlation using Pearson’s Product-Moment Correlation. RA, FM and OA groups were treated with standard care, which consisted of DMARDs, pain rehabilitation therapy, and total knee arthroplasty, respectively. The correlation between baseline TSK and change from baseline in 4-week average pain severity was calculated at 3-, 6- and 12-month follow-up using Pearson’s Product-Moment Correlation. A simple linear regression model was used for each cohort to evaluate the extent TSK contributed to change in pain from baseline. Results At baseline, mean TSK was 38.8±7.0 and mean 4-week average pain severity was 6.6±2.0 (all conditions pooled), with a Pearson’s Product-Moment Correlation of 0.28 [95% CI: 0.18-0.37], representing a small positive correlation (p < 0.01) between baseline TSK and baseline pain. The results were similar for all 3 conditions independently (RA correlation 0.30 [95% CI: 0.14-0.44], FM correlation 0.31 [95% CI: 0.15-0.46], OA correlation 0.25 [95% CI: 0.06-0.41], all ps < 0.01). No correlation was found between TSK and change from baseline in pain severity for the RA or FM cohorts at any follow-up. A weak negative correlation between TSK and change in pain severity was found in the knee OA group at 3 months (correlation: -0.18 [95% CI: -0.39-0.04]) and 12 months (correlation: -0.16 [95% CI: -0.39-0.08]); however, these results were not statistically significant (p = 0.12 and 0.19 respectively). The linear regression analysis showed that TSK was not associated with change in pain from baseline for any condition at any timepoint. Mean pain decreased in the RA and OA groups irrespective of TSK, with no improvement in pain seen in the FM group (RA mean pain at baseline: 6.5±2.1, at 12 months: 4.3±2.6; FM mean pain at baseline: 6.6±1.6, at 12 months: 6.6±1.8; OA mean pain at baseline: 6.5±2.2, at 12 months: 1.9±2.6). Conclusion Whilst kinesiophobia and pain severity were correlated at baseline, kinesiophobia did not negatively influence change in pain with treatment in any of the cohorts studied. Disclosure R.C. Murphy: None. A. Irani: None. E. Kelleher: None. A.J. Wall: None.

A new systems approach to diseased states and wellness result in a new branch in the healthcare services, namely, Personalized and Precision Medicine (PPM). To achieve the implementation of PPM concept, it is necessary to create a fundamentally new strategy based upon the recogni-tion of biomarkers and thus the targets to secure the grand future of drug design and drug dis-covery.Each decision-maker values the impact of their decision to use PPM on their own budget and well-being, which may not necessarily be optimal for society as a whole. It would be extremely useful to integrate data harvesting from different databanks for applications to provide more tai-lored measures for the patients resulting in improved patient outcomes, reduced adverse events, and more cost-effective use of the latest health care resources including diagnostic (companion ones or theranostics), preventive and therapeutic (targeted molecular and cellular) etc.Meanwhile, along with the impact of genomics and bioinformatics, pathology is the central specialty of PPM-related resources. Coupled with IT, the upgraded tools are ever more efficient and robust within clinical cancer settings. The latest algorithms may be able to identify and vali-date patterns which humans are not capable of quantifying easily, such as slight differences in textures or morphologies. In this sense, the impact of pathology allows a modular approach, as its various aspects are under development in several areas of PPM.Among the above-mentioned medical specialists involved in PPM, the pathologists play an im-portant and key role in the implementation and development of PPM-driven resources that are in the center of decision of many therapeutic choices. Recent advances in systems biology have tremendously affected the practice of precision pathology, gradually transforming it from a morphology-based into a precise molecular-based discipline. The enormous development of precision pathology research (integrating molecular OMICS and digital approaches) has raised great expectations concerning its impact on PPM aiming to custom-ize medical practice with a focus on the individual, based on the use of molecular tests, identifi-cation of genomic biomarkers, and development of targeted drugs.The precision pathology process introduces a new paradigm in pathology by leveraging digital imaging and IT technologies, and provides significant advancements in accuracy, efficiency, and collaboration. Among the latest innovations the precision pathology supported by digital tools, would dictate the implementation of high-resolution imaging, image analysis tools and integra-tion with molecular OMICS data. Integration of the approaches and resources will provide a true challenge for the future, requiring collaboration between oncologists, pathologists, biodesigners and bioengineers and remaining a challenge to precision cancer practice and profiled bioindustry.The latter requires precision pathologists highly trained in pre-analytic processes, tumor area mi-crodissection for tumor cell enrichment, methodology analysis and results. The in-depth study of molecular alterations in patients allows optimizing molecular diagnosis and selecting candidates for receive novel treatments against specific molecular targets. These patients would benefit from multidisciplinary approach and learning. In this sense, molecular diagnostics has a long tradition in pathology, especially in clinical one, where various OMICS-analyses of cancers are incorpo-rated into diagnostic and decision-making algorithms to secure a way where the pathologists con-tinue to play an essential role in developing and implementing molecular profiling tests in practice and communicate the results and their relevance with cancer practitioners.Cancer pathology is the central specialty of personalized and precision oncology (PPO). Meanwhile, the combination of comprehensive biobanking and the next wave of theranostic pathology technologies provides a natural, externally visible infrastructure that now allows pa-thology as a discipline – to engage directly with the biotechnology and pharma sector. We’re at an exciting junction in precision cancer pathology’s growth as a medical specialty, and pathology-driven biobanking is becoming both central to our core expertise and, even more importantly, a powerful enabler for many of the most promising growth areas of our discipline: PPM healthcare, clinical trials and drug development, theranostics, and functional assessment and monitoring of disease. In the context of these changes and challenges, the precision cancer pathology can play a fundamental role in both PPO-guided clinical practice and biodesign-driven cancer research.

ABSTRACT IDH-mutant astrocytomas maintain telomeres through the alternative lengthening of telomeres (ALT) pathway, producing extreme inter-arm telomere length heterogeneity, yet how this heterogeneity shapes structural genome evolution remains unknown. Using Oxford Nanopore long-read sequencing of 20 IDH-mutant astrocytomas, we profiled structural variants (SVs), copy number variants, extrachromosomal DNA (ecDNA) and measured allele-specific telomere lengths from individual long reads. We identified pervasive complex rearrangements, including chromothripsis and foldback events consistent with breakage-fusion-bridge cycles, and widespread ecDNAs. SV breakpoints were enriched at telomeric and centromeric regions regardless of local telomere length, revealing constitutive structural fragility. Arm-level telomere length analysis uncovered a dual-mode model: arms with short telomeres preferentially harbored breakage-associated events, while arms with long ALT-maintained telomeres were enriched for ecDNA and amplification-associated events. These findings identify chromosome-arm-specific telomere length as a determinant of structural genome evolution in ALT-driven tumors.

ABSTRACT Sodium glucose co‐transporter 2 inhibitors (SGLT2i) and glucagon‐like peptide‐1 receptor agonists (GLP‐1 RAs) are nephroprotective and their use is recommended for adults with chronic kidney disease (CKD). The role of SGLT2i and GLP‐1 RAs in patients with acute kidney injury (AKI) is unknown. This systematic review aimed to estimate the effect of SGLT2i or GLP‐1 RAs on clinical outcomes in AKI. We systematically searched Embase, MEDLINE, Scopus, Web of Science Core Collection, and clinical trials registries for observational studies and clinical trials from database inception to July 3, 2025. Included studies evaluated adults (≥ 18 years) with AKI during a hospitalization and compared patients subsequently exposed to either SGLT2i or GLP‐1 RAs to a non‐exposed control group. Random effects meta‐analyses were performed. Six studies related to SGLT2i (five observational, one randomized trial) and one related to GLP‐1 RAs (one observational) met eligibility criteria ( N = 432,048 patients). SGLT2i/GLP‐1 RA exposure was associated with lower odds of major adverse kidney events (MAKE) (OR 0.63, 95% CI 0.46–0.86) and all‐cause mortality [odds ratio (OR) 0.36, 95% confidence interval (CI) 0.21–0.62] compared to controls. The odds for kidney replacement therapy were lower with SGLT2i therapy in the three studies where it was evaluated (OR 0.61, 95% CI 0.40–0.93). Sensitivity analyses restricted to SGLT2i data were consistent with the overall findings [MAKE OR 0.63 (95% CI 0.42–0.95); Mortality OR 0.34 (95% CI 0.18, 0.65)]. Exposure to SGLT2i or GLP‐1 RAs after AKI, examined primarily in observational studies, was associated with improved clinical outcomes. These findings are promising and warrant evaluation in randomized clinical trials.

PURPOSE Hepatocellular carcinoma (HCC) is the third leading cause of cancer-related deaths worldwide. The higher incidence and earlier onset of HCC in sub-Saharan Africa suggest a potential role for a genetic predisposition. This study evaluated the association of TERT -rs2242652-(A), a variant linked to lower HCC risk, with HCC in populations from Ghana, Nigeria, and Cameroon, compared with a population from the United States. METHODS The study included 537 patients with HCC: United States (n = 348), Ghana (n = 79), Nigeria (n = 43), and Cameroon (n = 67). The control group had 2,872 cancer-free individuals: United States (n = 2,399), Ghana (n = 323), Nigeria (n = 85), and Cameroon (n = 65). Whole-exome sequencing was conducted using germline DNA, and data for TERT -rs2242652 were analyzed. Odds ratios (ORs) and 95% CIs were calculated using unconditional logistic regression. Chi-square tests assessed protective allele frequencies. RESULTS In the US cohort, TERT -rs2242652 was significantly associated with lower HCC risk (OR, 0.75 [95% CI, 0.58 to 0.96]; P = .02), with an allele frequency of 18.8% (15.4% in HCC cases v 19.3% in controls). In the combined sub-Saharan African population, no significant association was observed, but there was a trend toward decreased HCC risk (OR, 0.80 [95% CI, 0.53 to 1.22]; P = .29), with an allele frequency of 12.2% (10.6% in HCC cases v 12.9% in controls). Separate analyses of Ghanaian, Nigerian, and Cameroonian populations showed similar nonsignificant trends. The protective allele frequency in the combined African populations was significantly lower than in the US cohort ( P < .0001). CONCLUSION In sub-Saharan African populations, there was a lower frequency of the HCC protective allele TERT -rs2242652 compared with European Americans. These findings underscore the importance of multiethnic genetic studies in understanding population differences in HCC risk and developing prevention strategies.

ABSTRACT Purpose Malignant rhabdoid tumor of the kidney (MRTK) is a rare, aggressive tumor seen in young children. The optimal timing of resection for locally advanced tumors is not well‐defined. The purpose of this study is to evaluate modern oncologic outcomes and the impact of surgical timing. Methods A multicenter retrospective review was performed by institutions participating in the Pediatric Surgical Oncology Research Collaborative. Children younger than 21 years old with MRTK diagnosed between 2000 and 2022 were included. Results Sixty‐nine patients were identified with MRTK and met the inclusion criteria. Median age of diagnosis was 10.1 months. Overall survival (OS) at 1, 5, and 10 years was 49%, 32%, and 19%, respectively. Patients with local Stage III disease who underwent upfront resection ( n = 18) compared to those who had delayed resection after NAT ( n = 15) had a similar OS, median OS greater than 60 months versus 14.6 months, respectively; p = 0.396. The surgical timing groups were balanced in terms of the presence of metastasis, length of follow‐up, and tumor characteristics. There was one occurrence of primary intraoperative tumor spill and two occurrences of organ injury in the upfront resection group compared to none in the delayed resection group. Conclusion MRTK carries a poor prognosis despite multimodal treatment. Histologic diagnosis may not be confirmed at presentation, and MRTK cannot be reliably distinguished from Wilms tumor on imaging alone. As overall survival is similar, the decision regarding surgical timing in locally advanced tumors should be individualized based on perceived resectability, balancing the risk of intraoperative complications against the possibility of tumor progression during neoadjuvant therapy.

ABSTRACT Candida auris is an emerging pathogen known for causing invasive, multidrug-resistant infections and healthcare-associated outbreaks. Measuring the relatedness of C. auris strains is critical for detecting and preventing healthcare-associated transmission. Whole genome sequencing (WGS) and analysis of single-nucleotide polymorphisms (SNPs) offer high-resolution assessments of genetic relatedness and antifungal susceptibility; however, interpretation requires an understanding of inter- and intra-patient C. auris diversity and genotypic markers of resistance, respectively. This study aimed to define SNP thresholds for assessing C. auris relatedness in healthcare-associated outbreak investigations, predict antifungal resistance via genotypic markers, and evaluate patient risk factors to inform future surveillance strategies. WGS was performed on 68 C. auris isolates (clades I and III) obtained from 31 hospitalized patients across a healthcare system between 2021 and 2024. Using MycoSNP analysis, we observed a maximum intra-patient variation of 14 SNPs. Five probable transmission clusters were identified based on epidemiologic links, with patient isolates differing by a median of 5 SNPs (range: 0−12). Analysis with a commercial pipeline (refMLST, BugSeq) showed similar clustering patterns. All new detections occurring more than 1 month after admission were linked to a cluster, representing a highly specific indicator of healthcare-associated infection. WGS detected known genotypic markers for fluconazole (ERG11 Y132F, F126L, and MRR1 N647T) and micafungin (FKS1 F635C) resistance, with the latter emerging during antimicrobial therapy. In addition, putative FUR1 mutations (G207R and Q16::STOP) associated with flucytosine resistance were identified. These findings emphasize the utility of WGS for identifying healthcare-associated clusters of C. auris and predicting antifungal resistance. IMPORTANCE Candida auris is a difficult-to-treat yeast that causes invasive infections in vulnerable patient populations. Healthcare exposure is a key risk factor for becoming colonized or infected with C. auris , and infection prevention groups focus on curbing the spread of this organism within the healthcare environment. Whole genome sequencing approaches are key for supporting these efforts, as they can help define clusters of C. auris transmission and can also provide insight into antifungal resistance. Our work provides practical guidance for interpreting genomic data in this setting, helping infection prevention teams respond more effectively to outbreaks and expanding the use of genotypic predictions for antifungal resistance.

Abstract Despite effective control of inflammation in rheumatoid arthritis (RA), persistent and severe pain remains a challenge. Dysregulated pain processing in the central nervous system may underlie this disconnect. The PainDETECT questionnaire, originally developed to identify neuropathic pain, may capture features of central sensitization. We hypothesized that neuropathic-like pain at diagnosis predicts worse pain prognosis in early RA, independent of baseline pain severity and inflammation. We also explored brain activation patterns using neuroimaging. In this prospective cohort study, adults with newly diagnosed RA completed the PainDETECT questionnaire at baseline. Bodily pain was measured using the SF-36 Bodily Pain Subscale at baseline, 3, 6, and 12 months. C-reactive protein (CRP) was monitored. Linear mixed-effects models examined associations between PainDETECT, as a continuous measure, and bodily pain and CRP over time, adjusting for baseline outcome values. A neuroimaging substudy (n = 27) used task-based functional MRI to assess brain responses to evoked pressure pain. Among 158 participants (mean age 58.4 years; 35% male), 24.7% had likely neuropathic-like pain (PainDETECT ≥19) at baseline. Higher baseline PainDETECT scores were associated with worse bodily pain throughout follow-up in fully adjusted models (β = −0.43; 95% CI: −0.84 to −0.02; P = 0.043), independent of socio-demographics and comorbidities. No association was found between PainDETECT and CRP. On neuroimaging, higher PainDETECT scores correlated with increased activation in the left insula, dorsal anterior cingulate cortex, and left amygdala during evoked wrist pain. Neuropathic-like pain at diagnosis predicts a worse pain prognosis in early RA, independently of inflammation. Early identification may support more targeted and effective pain management.

Abstract Hereditary hemorrhagic telangiectasia (HHT), an autosomal dominant vasculopathy affecting 1 in 5000 individuals, is the second most common inherited bleeding disorder worldwide. Despite this prevalence, comprehensive data on disease manifestations and complications remain limited. To address this gap, the US Congress allocated funding leading to the Comprehensive HHT Outcomes Registry of the United States (CHORUS), a prospective, 15-center longitudinal registry enrolling unselected patients with confirmed HHT. In this initial report, we describe findings from the first 600 participants, with a median age of 53 (range, 0-88) years and 60% female. Despite most participants developing typical HHT manifestations by age 13 years, the majority (63%) were not diagnosed until mid-to-late adulthood. Recurrent spontaneous epistaxis occurred in 95% of participants, chronic gastrointestinal bleeding in 30%, and heavy menstrual bleeding in 35% of postmenarche females, together resulting in moderate-to-severe mucosal bleeding in 76%. Iron deficiency and/or anemia were diagnosed in 68%, with 41% requiring IV iron and 25% requiring red cell transfusions. Serious complications of solid-organ arteriovenous malformations were frequent, including intracranial hemorrhage (3%), pulmonary hemorrhage (2%), venous thromboembolism (7%), arterial thromboembolism (11%), heart failure (7%), and pulmonary hypertension (7%). These data from CHORUS, the first national US registry of its kind, provide reliable, real-world estimates of the incidence, prevalence, and severity of numerous HHT manifestations and complications. HHT has a high burden of moderate-to-severe bleeding, anemia, thrombosis, and major neurologic and cardiopulmonary complications. There is a mean interval between first symptoms and diagnosis of &gt;2 decades, during which substantial, serious, and preventable HHT morbidity, including early intracranial hemorrhage, may occur. This trial was registered at clinicaltrials.gov as NCT06259292.