Citations

Abstract Rationale: Diffuse idiopathic pulmonary neuroendocrine cell hyperplasia (DIPNECH) is a pulmonary condition characterised by neuroendocrine cell proliferation along respiratory bronchioles resulting in tumourlet formation which may progress to pulmonary carcinoid. DIPNECH is a rare and under-recognised condition that predominantly affects females, with an estimated worldwide incidence of 5-6 people per million population. Given it's rarity and the poor understanding around the pathogenesis and treatment of this condition, we undertook the largest international case series to date of DIPNECH patients. We aim to further characterise this patient cohort to better understand the clinical features, identify common pulmonary function test (PFT) patterns and radiographic findings and describe current treatment practices. Methods: We collated data from 17 centres across 8 different countries comprising a total of 258 patients. Data collected included patient demographics, smoking history, symptoms, co-morbidities, pathological diagnosis, imaging findings, PFT pattern and therapies. Results: In total 258 patients were identified. The median age was 65 (SD+/- 10.6). 241 (93%) were female. 39% (n= 94/243) were ex-smokers. 79% (n=186/234) of patients reported pulmonary symptoms with cough being the most common symptom reported in 81% (n=151/186) of patients. Many patients were polysymptomatic, with cough and dyspnoea being the most common combination of symptoms described. (50.54%; n=94/186). Complete spirometry pattern was documented for 180 patients (69.78%) with an obstructive pattern being the most commonly observed (n=76/180; 42%). 27.5% (n=41/139) had clinically significant FEV1 reversibility post bronchodilator administration. Pathology specimens were available in 219 cases. Most common pathological features were neuroendocrine hyperplasia which was observed in 75% (n=165/219) and tumourlets in 74% (n=162/219) of cases. Carcinoid, either typical or atypical, was observed in 64% (n=141/219) of samples. 252 patients had computed tomography (CT) imaging performed. Pulmonary nodules were the most common feature identified in 99.60% of cases (248/250). Mosaic attenuation (69.30%; n=50/173) and airway dilatation (28.90%; n=50/173) were also frequently reported. There was no significant correlation between symptoms (cough, dyspnoea, wheeze) and airway dilatation (p=0.496), mosaic attenuation (p=0.496) and PFT pattern (p=0.837). There was a significant association between presence of symptoms and mosaic attenuation on CT (p=0.003). Conclusions: DIPNECH, while a rare disorder, is understudied. This international case series is the largest performed to date and highlights the complexity in management of these patients.

Abstract The advent of high-throughput sequencing has led to an exponential increase in genomic data, highlighting the need for efficient and accurate models to analyze and interpret this information. Here, we introduce a novel, exomic foundational model that leverages a combination of human reference genome and multispecies data to improve variant detection and interpretation. Our model utilizes a short- range transformer architecture and is trained on a large dataset of human exomic sequences derived from the Tapestry study. Through a series of ablation studies and scaling experiments, we demonstrate the effectiveness of our model in pre- dicting next token accuracy and identifying clinically pathogenic variants. We also show that our model outperforms existing models in a range of downstream tasks, including variant effect prediction and disease state identification. In fact, our largest STRAND variant (1B parameters) surpassed previous benchmarks, demonstrating a mean accuarcy of 0.880 (8.2% improvement over the original NT and 7% improvement over NT-v2). Furthermore, we construct a unique exomic ClinVar dataset to evaluate the model’s performance on pathogenicity and disease states. Our results highlight the potential of this model to improve our understanding of the human exome and its role in disease. The model and its applications have significant implications for genomic based diagnosis and personalized medicine including tailored therapeutic development.

Abstract Background/Objective: Decentralized research has many advantages; however, little is known about the representativeness of a source population in decentralized studies. We recruited participants aged 18-64 years from four states from June to December 2022 for a prospective cohort study to assess viral epidemiology. Our aim was to determine the association between age, gender, race/ethnicity, rurality, and socioeconomic status (SES) on study participation in a decentralized prospective cohort study. Methods: We consented 9,286 participants from 231,099 (4.0%) adults with the mean age of 45.6 years (±12.0). We used an electronic decentralized approach for recruitment. Consented participants were more likely to be non-Hispanic White, female, older, urban residents, have more health conditions, and possessed higher socioeconomic status (SES) compared to those non-consented. Results: We observed an interaction between SES and race-ethnicity on the odds of consent (P = 0.006). Specifically, SES did not affect non-Hispanic white participation rates(OR 1.24 95% CI 1.16 – 1.32] for the highest SES quartile compared to those with the lowest SES quartile) as much as it did participants combined across the other races (OR 1.73; 95% CI 1.45 – 2.98]) Conclusion: The relationship between SES and consent rates might be disproportionately greater in historically disadvantaged groups, compared to non-Hispanic White. It suggests that instead of focusing on enrollment of specific minority groups in research, there is value in future research exploring and addressing the diversity of barriers to trials within minority groups. Our study highlights that decentralized studies need to address social determinants of health, especially in under-resourced populations.

Diagnosing pulmonary rheumatoid nodules (RN) is challenging because they are rare and share clinical, radiologic, and histopathologic features with other necrotizing granulomatous diseases such as infectious granulomas (IG) and granulomatosis with polyangiitis (GPA). Herein, we revisit the histopathologic features of RN and the findings in the adjacent lung tissue, in comparison with IG and GPA, to identify distinguishing features. Twenty-eight cases with surgically resected RN evaluated at our institution (1991 to 2024), 33 IG (10 mycobacterial infection, 10 histoplasmosis, 13 coccidiomycosis), and 10 GPA cases were included in the study. All available slides with H&E and special stains were reviewed for various histologic parameters within the nodules and in surrounding lung tissue. Many histopathologic features of RN overlap with the necrotizing granulomas seen in infections and GPA. However, some findings in the adjacent lung tissue showed significant differences. The lack of airspace granulomas/non-necrotizing granuloma and the absence of necrotizing vasculitis in the setting of RN can help to differentiate between infection cases and GPA, respectively. Given their considerable overlap, correlation with clinical context, serologic and microbiologic studies, as well as careful evaluation of special stains is crucial in the diagnosis of RN.

Purpose The Sangre Por Salud (SPS) Biobank was established to facilitate biomedical research opportunities for the Latino community by creating an easily accessible prospective cohort for scientists interested in studying health conditions and health disparities in this population. Participants Individuals self-identifying as Latino, aged 18–85 years, were prospectively recruited from the primary care Internal Medicine clinic at Mountain Park Health Center in Phoenix, Arizona. After obtaining informed consent, detailed medical history questionnaires were captured, and blood samples were obtained for common laboratory tests. Participants authorised the research team to access their electronic health records for research purposes. In addition, participants had serum, plasma and DNA samples isolated and stored at the Mayo Clinic Arizona Biorepository Laboratory for long-term storage and future access. As part of the study, participants consented and agreed to be contacted for potential participation in future research studies. Findings to date 3756 participants provided informed consent, of whom 3733 completed all study questionnaires, an oral glucose tolerance test and had blood collected and stored. The SPS cohort is predominantly composed of females (72%), with a median age at time of consent of 42 years. All participants self-identified as Hispanic/Latino, 45% were married, 53% were employed for wages and 60% had less than a high school degree. Around 25% of participants met diagnostic criteria for overweight (BMI 25–29 kg/m 2 ), and 49% met for obesity (BMI≥30 kg/m 2 ). At time of recruitment, hypertension, hyperlipidaemia and depression affected 22%, 20% and 13% of the cohort, respectively. Future plans We plan to regularly update the participants’ electronic health records and self-reported health data to longitudinal research. Additionally, we plan to obtain a more comprehensive genomic analysis on the entire cohort, ensuring greater research interest and investigation into the underlying genetic factors that contribute to disease susceptibility in this cohort.

Background Multimorbidity is common in patients with atrial fibrillation (AF), yet comorbidity patterns are not well documented. Methods The prevalence of 18 chronic conditions (6 cardiometabolic, 7 other somatic, 5 mental health) was obtained in patients with new-onset AF from 2013-2017 from a 27-county region and controls matched 1:1 on age, sex, and county of residence. For AF patients and controls separately, clustering of conditions and co-occurrence beyond chance was estimated (using the asymmetric Somers’ D statistic), overall and for ages <65, 65-74, 75-84, and ≥85 years. Results Among 16,509 patients with AF (median age 76 years, 57% men), few (4%) did not have any of the 18 chronic conditions, whereas nearly one-quarter of controls (23%) did not have any chronic conditions. Clustering of cardiometabolic conditions was common in both AF patients and controls, but clustering of other somatic conditions was more common in AF. Although the prevalence of most condition pairs was higher in AF patients, controls had a larger number of condition pairs occurring together beyond chance. In persons aged <65 years, AF patients more frequently exhibited concordance of condition pairs that included either pairs of somatic conditions or a combination of conditions from different condition groups. In persons aged 65-74 years, AF patients more frequently had pairs of other somatic conditions. Conclusion Patterns of co-existing conditions differed between patients with AF and controls, particularly in younger ages. A better understanding of the clinical consequences of multimorbidity in AF patients, including those diagnosed at younger ages, is needed.

Background. The limitations of conventional measures of socioeconomic status (SES) limit our ability to elucidate the role of SES as a key element of social determinants of health in kidney transplantation. This study’s objective was to use an innovative SES measure, the HOUsing-based SES measure (HOUSES) index, to examine the effects of social determinants of health on access to and outcomes of kidney transplantation. Methods. Our study included residents of Minnesota (age older than 18 y) who underwent kidney transplantation at a single center between 2010 and 2020. SES was determined using the HOUSES index, categorized into quartiles (Q1 for lower, Q2–Q4 for higher SES). We used mixed-effects multivariable logistic and Cox models to examine the effects of HOUSES on preemptive transplants, pretransplant dialysis duration, and death-censored graft loss, adjusting for covariates. Results. Among 1975 eligible patients, 29.4% received preemptive transplants, 34.9% underwent pretransplant dialysis for >3 y, and 15.1% experienced death-censored graft loss for a median follow-up of 7.15 (interquartile range, 4.25–11.38) y. Lower SES recipients (Q1) demonstrated decreased preemptive transplant likelihood (adjusted odds ratio [aOR]: 0.74; 95% confidence interval [CI], 0.57-0.97; P = 0.03), longer dialysis duration (>3 y; aOR: 1.43; 95% CI, 1.01-2.03; P = 0.046), and higher death-censored graft loss (adjusted hazard ratio 1.36; 95% CI, 1.02-1.12; P = 0.036) versus higher SES recipients (Q2–Q4). Conclusions. We observed significant socioeconomic disparities in kidney transplant access, dialysis duration, and graft survival. The HOUSES index may be a promising tool for individual-based targeted interventions as it identifies SES on an individual rather than an area-level basis.

Background: Erdheim-Chester disease (ECD) manifests as multi-organ infiltration of clonal histiocytes with mutations primarily in the mitogen-activated protein kinase (MAPK) pathway. The revised classification of histiocytosis (2016) categorizes ECD with typical bilateral, symmetric osteosclerosis of the lower extremity long bones as classical (C) and as non-classical (NC) if otherwise. The clinical and biological significance of this classification is unclear. This study compared the clinical and genotypic findings of the 2 subtypes within a large cohort of ECD patients. Methods: We included patients seen at our institution since 1990 meeting the following criteria: A) had an ECD diagnosis based on the revised criteria by Haroche J, et al. (Blood 2020;135:1311-1318); B) completed whole-body imaging studies including long bones of the legs. Classification as C-ECD required symmetric osteosclerosis of the distal femur and/or proximal tibia/fibula. Results: A total of 145 patients were enrolled, comprising a male-to-female ratio of 2:1 (66.2% male). C-ECD was diagnosed in 77.2% of cases, and NC-ECD in 22.8%. The median age at diagnosis was similar with 58.5 years (range, 18-82) in C-ECD and 55 years (range, 20-81) in NC-ECD, (p=0.65). The most frequently affected systems included skeletal (81.4%), renal (60.0%), vascular (45.5%), cardiac (40.0%), central nervous (38.6%), sinus (37.2%), pulmonary (36.6%), and adrenal (32.4%). The numbers of organs involved were significantly higher in C-ECD compared to NC-ECD (median 5 vs 3, p&lt;0.01). Higher rates of skeletal (100% vs. 18.2%, p&lt;0.01), adrenal gland (37.5% vs. 15.2%, p=0.02), and sinus (44.6% vs. 12.1%, p&lt;0.01) involvement were observed in C-ECD. Arginine vasopressin deficiency (AVP-D) was exclusively observed in C-ECD (20.7% vs. 0%, p&lt;0.01). NC-ECD had a higher rate of cardiac involvement (69.7% vs. 31.3%, p&lt;0.01). No significant differences were found in other systems. The overall median time between onset of the first symptoms/signs to diagnosis was 15 months with no significant difference between C-ECD and NC-ECD (17.5 vs. 12 months, p=0.18). The median time to diagnosis of ECD in patients with AVP-D was 38.5 months, compared to 12 months without AVP-D (p=0.09). Genetic testing was conducted in 86.2% of patients and B-Raf proto-oncogene (BRAF) alterations were identified in 59.2% of the tested cases. BRAFV600E was more prevalent in C-ECD (61.3% vs. 21.9%, p&lt;0.01), whereas non-V600 mutations were more commonly found in NC-ECD (12.5% vs. 1.1%, p&lt;0.01). There was no significant difference in the frequency of BRAF fusions. NC-ECD patients exhibited a higher rate of MAP2K1 mutations (25.0% vs. 5.4%, p&lt;0.01). Other frequently mutated genes included KRAS (4.0%), NRAS (2.4%), and CSF1R (2.4%), although no significant difference was observed in their frequency between C-ECD and NC-ECD. Testicular involvement appeared to be more common in patients with MAP2K1 mutations (23.1% vs. 8%, p=0.08). Two patients with pathogenic CSF1R mutations both had central nervous system (CNS) involvement. Among C-ECD patients, BRAFV600E conferred a higher rate of CNS involvement (50.9% vs. 25%, p=0.01). No significant difference was observed in NC-ECD patients (71.4% vs 36%, p=0.09). Among NC-ECD cases, MAP2K1 mutations conferred a reduced risk of cardiac involvement (37.5% vs. 79.2%, p=0.03) and no such difference was observed in patients with C-ECD (40% vs 34.1%, p=0.79). The median numbers of organs involved in patients with BRAF, MAP2K1, and KRAS/NRAS mutations were 5, 3, and 3, respectively, with no significant difference. Conclusions: C-ECD affects more organs and more frequently involves bones, adrenal glands, and sinuses. AVP-D was exclusively observed in C-ECD. Conversely, NC-ECD showed a higher prevalence of cardiac involvement. BRAFV600E was more commonly identified in C-ECD, whereas non-V600 mutations and MAP2K1 mutations were more prevalent in NC-ECD. Among C-ECD patients, BRAFV600E was correlated with a greater likelihood of CNS involvement. Conversely, NC-ECD patients with MAP2K1 mutations had a reduced risk of cardiac involvement. This study highlights the distinct clinical and molecular features of C-ECD and NC-ECD, underscoring the importance of subclassifying ECD into classical and non-classical forms. Further studies are needed to explore differences in the clinical outcomes between the 2 forms.

Abstract Aspiration-related syndromes comprise a broad spectrum of diseases affecting the airways and lung parenchyma resulting from inadvertent entry of oropharyngeal or gastric contents into the respiratory tract. The diagnosis can be challenging given lack of self-reported symptoms and unwitnessed or silent aspiration events. Aspiration is a common finding in healthy individuals suggesting that host defenses play a critical role in the pathophysiology. In the absence of strict criterion, a high index of suspicion is necessary based on recognition of established risk factors and identification of characteristic imaging findings. Conditions predisposing to altered levels of consciousness and neuromuscular weakness can lead to dysphagia, impaired cough reflux, and subsequent aspiration. The most salient feature on imaging is the anatomic location of the abnormalities, with the superior segments of the lower lobes and posterior segments of upper lobes involved in the recumbent position, and basilar segments of lower lobes in the upright position. Acute syndromes include pneumonia, pneumonitis, and foreign body aspiration. In the more indolent form of aspiration, bronchiectasis, diffuse bronchiolitis, and interstitial lung disease can develop. A detailed understanding of associated radiographic findings for these syndromes can help to implicate aspiration as the cause for imaging abnormalities and ultimately optimize patient management.