Citations

ABSTRACTTherapeutic treatment of lung nodules by ablation is a new field. Even though not considered standard of care, lung nodule ablation can be appropriate for select cases. Even though ablation is a safe and well‐tolerated procedure, bleeding is a potential complication. We introduce our stepwise approach through two cases on how we AIM (Anticipate/Adjust, Image, Manage) to prevent uncontrolled bleeding during Robotically Assisted Bronchoscopic Ablation: 1. Anticipate structures with high risk for bleeding and adjust accordingly, accounting for the needle ablation field; 2. Image: utilise cone beam CT before the first and after each ablation session to screen for bleeding; 3. Manage bleeding by pre‐emptively utilising Fogarty balloon occlusion.

Abstract We investigated the influence of 55 583 autophagy-related single-nucleotide polymorphisms (SNPs) on chronic lymphocytic leukemia (CLL) risk across 4 independent populations comprising 5472 CLL cases and 726 465 controls. We also examined their impact on overall survival (OS), time to first treatment (TTFT), autophagy flux, and immune responses. A meta-analysis of the 4 populations identified, to our knowledge, for the first time, significant associations between CDKN2A (rs3731204) and BCL2 (rs4940571, rs12457371, and rs1026825) SNPs and CLL risk, with CDKN2A showing the strongest association (P = 1.57 × 10−12). We also validated previously reported associations for FAS, BCL2, and BAK1 SNPs with CLL risk (P = 4.73 × 10−21 to 3.39 × 10−9). The CDKN2Ars3731204 and FASrs1926194 SNPs associated with increased CDKN2A and ACTA2 messenger RNA expression levels in the whole blood and/or lymphocytes (P = 5.1 × 10−7, P = 1.58 × 10−21, and P = 7.8 × 10−41), although no significant effect on autophagy flux was observed. However, associations were found between CDKN2A, BCL2, and FAS SNPs and various T-cell subsets, cytokine production, and circulating concentrations of interferon gamma, tumor necrosis factor–related apoptosis-inducing ligand, CD40, chemokine ligand 20, and interleukin-2 receptor subunit β proteins (P ≤ .005). No significant association was detected between autophagy variants and OS or TTFT, suggesting that these variants drive disease initiation rather than progression. In conclusion, this study identified 4 novel associations for CLL and provided insights into the biological pathways that influence CLL development.

ABSTRACT Aims X‐linked McLeod neuroacanthocytosis syndrome (MLS) is a rare neurodegenerative disorder characterised by the presence of red blood cell acanthocytosis and a chorea syndrome. Analogous to Huntington's disease (HD), MLS displays cognitive and behavioural symptoms besides the progressive movement disorder. This study aimed to describe the neuropathology of MLS in the largest case series to date. Methods Clinical data were collected, and neuropathological assessments were performed on eight male MLS patients originating from Finland, New Zealand, Switzerland, Scotland and the United States. Results Macroscopic data were available from six patients, with five showing atrophy of the basal ganglia, which was more pronounced in the caudate nucleus and to a lesser extent in the putamen and pallidum. Histology revealed neuronal loss and accompanying gliosis in the basal ganglia of all patients. The extent of these alterations varied widely, with a decreasing gradient of severity from the caudate nucleus to the putamen and the pallidum, mirroring the macroscopic findings. In addition, we detected intraneuronal vacuoles in the striatum in half of the patients. Conclusions MLS neuropathology is characterised macroscopically by atrophy and microscopically by neuronal loss and gliosis of the basal ganglia, with a decreasing gradient of severity from the caudate nucleus, the putamen to the pallidum. Analogous to the grading system for HD, we propose a neuropathological grading system for MLS based on the current observations in the largest MLS cohort examined to date. Standardised criteria are crucial for neuropathological assessment of this extremely rare disease.

Abstract Background Physical activity (PA) is an established protective factor for colorectal cancer (CRC), but it is unclear if genetic variants modify this effect. To investigate this possibility, we conducted a genome-wide gene–PA interaction analysis. Methods Using logistic regression and two-step and joint tests, we analyzed interactions between common genetic variants across the genome and PA in relation to CRC risk. Self-reported PA levels were categorized as active (≥ 8.75 MET-h/wk) vs. inactive (< 8.75 MET-h/wk) and as study- and sex-specific quartiles of activity. Results PA had an overall protective effect on CRC (OR [active vs. inactive] = 0.85; 95%CI = 0.81–0.90). The two-step GxE method identified an interaction between rs4779584, an intergenic variant near the GREM1 and SCG5 genes, and PA for CRC risk (p-interaction = 2.6×10 − 8 ). Stratification by genotype at this locus showed a significant reduction in CRC risk by 20% in active vs. inactive participants with the CC genotype (OR = 0.80; 95%CI = 0.75–0.85), but no significant PA–CRC association among CT or TT carriers. When PA was modeled as quartiles, the 1-d.f. GxE test identified that rs56906466, an intergenic variant near the KCNG1 gene, modified the association between PA and CRC (p-interaction = 3.5×10 − 8 ). Stratification at this locus showed that increase in PA (highest vs. lowest quartile) was associated with a lower CRC risk solely among TT carriers (OR = 0.77; 95%CI = 0.72–0.82). Conclusions In summary, we identified two genetic variants that modified the association between PA and CRC risk. One of them, related to GREM1 and SCG5 , suggests that the bone morphogenetic protein (BMP)-related, inflammatory, and/or insulin signaling pathways may be associated with the protective influence of PA on colorectal carcinogenesis.

Abstract Hereditary adult-onset ataxias are a heterogeneous group of phenotypically overlapping conditions, often caused by pathogenic expansions of short tandem repeats. Currently, 18 repeat disorders with a core phenotype of adult-onset ataxia are known. Diagnosis typically relies on sequential PCR-based methods, which are labour-intensive and lack precision. Long-read sequencing (LRS) has the potential to overcome these limitations and is currently implemented and validated in clinical genetics. Using clinical nanopore Cas9-targeted sequencing (Clin-CATS) for parallel in-depth repeat analysis, we evaluated a diagnostic cohort of 513 adult-onset ataxia patients, determining frequencies of all known repeat-associated ataxias except Spinocerebellar ataxia 4 (SCA4), as well as the carrier frequencies for autosomal-recessive disorders, RFC1 spectrum disorder and Friedreich’s ataxia (FRDA). Additionally, phenotypes of patients with established genetic diagnoses were characterized, especially those of patients living with RFC1 spectrum disorder and SCA27B. Repeat-associated ataxias were confirmed in 33.3% of cases, including rare ataxias, such as SCA10, SCA36 and SCA37, alongside as the most prevalent conditions SCA27B and RFC1 spectrum disorder. Potentially pathogenic expansions in FGF14 were identified in an additional 4.7% of patients. Testing of another 347 patients for ZFHX3 expansions linked to SCA4 did not identify any cases. Dual diagnoses were frequent, occurring in 6.4% of patients with repeat-associated ataxia. We confirmed a high RFC1 spectrum disorder carrier frequency (7.2%) and reclassified certain FXN expansions as likely non-pathogenic, resulting in a lower than estimated carrier frequency for FRDA of 0.8%. We also identified novel repeat configurations in several loci and illustrated the high heterogeneity of repeat expansions in RFC1, highlighting it as a potential source of false results when using PCR-based methods. This study underscores the diagnostic advantages of LRS for comprehensive repeat analysis and recommends its adoption as a standard in clinical genetics, replacing Southern blot and PCR-based approaches. Furthermore, based on our findings in a large patient cohort a re-evaluation of existing phenotype-genotype correlations is recommended as well as evaluating additional parameters alongside the repeat length to improve diagnostic precision of repeat analysis.

Abstract With the increasing volume of biomedical experimental data, standardizing, sharing, and integrating heterogeneous experimental data across domains has become a major challenge. To address this challenge, we have developed an ontology-supported Study-Experiment-Assay (SEA) common data model (CDM), which includes 10 core and 3 auxiliary classes based on object-oriented modeling. SEA CDM uses interoperable ontologies for data standardization and knowledge inference. Building on the SEA CDM, we developed the Ontology-based SEA Network (OSEAN) relational database and knowledge graph, along with a set of ETL (Extract, Transform, Load) and query tools, and further applied them to represent 1,278 immune studies with over two million samples from three resources: VIGET, ImmPort, and CELLxGENE. Using simple, robust queries and analyses, our research identified multiple scientific insights into sex-specific immune responses, such as neutrophil degranulation and TNF binding to physiological receptors, following live attenuated and trivalent inactivated influenza vaccination. The novel SEA CDM system lays a foundation for establishing an integrative biodata ecosystem across biological and biomedical domains.

Abstract Rationale High-attenuation area (HAA) is a computed tomography (CT) tool that correlates with lung inflammation and fibrosis. Systemic molecular correlates of HAA (e.g., plasma proteins) may inform biological processes involved in interstitial lung disease. Objectives To identify plasma proteins that associate with HAA and correlate with a higher probability of developing new-onset fibrotic or subpleural interstitial lung abnormalities (ILAs). Methods Plasma protein levels were measured using a semiquantitative aptamer-based platform in MESA (the Multi-Ethnic Study of Atherosclerosis; N = 5,486) and SPIROMICS (Subpopulations and Intermediate Outcome Measures in COPD Study; N = 1,781). Linear regression models identified HAA-associated proteins after adjustment for demographic and socioeconomic factors, CT scanner parameters, study center, and batch. Associations of HAA-related proteins with new-onset fibrotic or subpleural ILAs were examined in MESA participants with ILA assessments on full-lung CT 10 years later. Immunohistochemical staining of select proteins was performed in lung tissue from pulmonary fibrosis cases. Measurements and Main Results There were 75 proteins detected that were significantly associated with HAA in MESA and SPIROMICS. Gene Ontology analysis of these proteins identified processes involved in immune cell chemotaxis and cellular growth and apoptosis. Seven proteins were associated with a higher probability of new-onset fibrotic or subpleural ILAs in MESA, and two of these, junctional adhesion molecule-like protein and GTP cyclohydrolase 1 feedback regulatory protein, stained in areas of fibrosis in lung tissue from patients with interstitial lung disease. Conclusions Plasma proteins associated with more HAA are involved in immune and cellular processes and associate with new-onset fibrotic-subpleural ILA.

Background: Intracardiac thrombosis (ICT) during liver transplantation (LT) is a rare but life-threatening complication with limited data regarding its risk factors, management, and outcomes. This study aimed to identify factors associated with ICT development, define predictors of intraoperative outcomes, and propose a novel classification and management algorithm for ICT. Methods: A multicenter, international retrospective case-control study was conducted on liver transplant recipients from seven centers between January 2005 and December 2023. ICT cases were identified through transesophageal echocardiography (TEE) or autopsy and matched 1:1 with controls. Results: Among 11 077 liver transplant recipients screened, 133 patients (1.2%) developed ICT. ICT occurred predominantly after reperfusion (58%). Compared to controls, ICT cases exhibited higher preoperative international normalized ratio ( P = 0.001) and fibrinogen levels ( P = 0.014). Post-reperfusion syndrome ( P < 0.001), disseminated intravascular coagulation ( P < 0.001), and primary graft failure ( P = 0.002) were also more common in the ICT group. Continuous veno-venous hemofiltration during surgery (odds ratio [OR] 8.20, 95% confidence interval [CI]: 2.09–38.1; P = 0.004) was associated with ICT development. ICT was associated with markedly higher rates of cardiac arrest ( P < 0.001) and intraoperative mortality ( P < 0.001), with thrombus location in the left heart chambers representing a significant predictor of mortality (OR 20.7, 95% CI: 6.25–81.3; P < 0.001). ICT grades 2 and 3 were associated with a markedly increased risk of intraoperative cardiac arrest ( P < 0.05). Importantly, delayed use of TEE was strongly associated with intraoperative death (OR 6.27, 95% CI: 1.45–27.1; P = 0.014). The 90-day mortality was 43% in ICT cases compared to 4.5% in controls, while 1-year mortality was 46% versus 10.5%, respectively. Conclusions: ICT during LT is a rare but severe complication associated with intraoperative mortality and poor short-term survival. Coagulation profile and intraoperative management play critical roles in ICT development. The early use of TEE enables timely diagnosis and intervention, improving patient outcomes. We propose a novel ICT classification offering a systematic framework for risk stratification and management to mitigate progression and mortality.