Echocardiographic heart ageing patterns predict cardiovascular and non-cardiovascular events and reflect biological age: the SardiNIA study

AIMS

Age is a crucial risk factor for cardiovascular (CV) and non-CV diseases. As people age at different rates, the concept of biological age has been introduced as a personalized measure of functional deterioration. Associations of age with echocardiographic quantitative traits were analysed to assess different heart ageing rates and their ability to predict outcomes and reflect biological age.

METHODS AND RESULTS

Associations of age with left ventricular mass, geometry, diastolic function, left atrial volume, and aortic root size were measured in 2614 healthy subjects. Based on the 95% two-sided tolerance intervals of each correlation, three discrete ageing trajectories were identified and categorized as 'slow', 'normal', and 'accelerated' heart ageing patterns. The primary endpoint included fatal and non-fatal CV events, and the secondary endpoint was a composite of CV and non-CV events and all-cause death. The phenotypic age of the heart (HeartPhAge) was estimated as a proxy of biological age. The slow ageing pattern was found in 8.7% of healthy participants, the normal pattern in 76.9%, and the accelerated pattern in 14.4%. Kaplan-Meier curves of the heart ageing patterns diverged significantly (P = 0.0001) for both primary and secondary endpoints, with the event rate being lowest in the slow, intermediate in the normal, and highest in the accelerated pattern. In the Cox proportional hazards model, heart ageing patterns predicted both primary (P = 0.01) and secondary (P = 0.03 to <0.0001) endpoints, independent of chronological age and risk factors. Compared with chronological age, HeartPhAge was 9 years younger in slow, 4 years older in accelerated (both P < 0.0001), and overlapping in normal ageing patterns.

CONCLUSION

Standard Doppler echocardiography detects slow, normal, and accelerated heart ageing patterns. They predict CV and non-CV events, reflect biological age, and provide a new tool to calibrate prevention timing and intensity.

Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error

In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.

Spatial Transcriptomic Analysis of Pituitary Corticotroph Tumors

Context

Spatial transcriptomic (ST) analysis of tumors provides a novel approach to studying gene expression along with the localization of tumor cells in their environment to uncover spatial interactions.

Design

We present ST analysis of corticotroph pituitary neuroendocrine tumors (PitNETs) from formalin-fixed, paraffin-embedded tissues. ST data were compared to immunohistochemistry results. Gene expression profiles were reviewed for cluster annotations, and differentially expressed genes were used for pathway analysis.

Results

Seven tumors were used for ST analysis. In situ annotation of tumor tissue was inferred from the gene expression profiles and was in concordance with the annotation made by a pathologist. Furthermore, relative gene expression in the tumor corresponded to common protein staining used in the evaluation of PitNETs, such as reticulin and Ki-67 index. Finally, we identified intratumor heterogeneity; clusters within the same tumor may present with different transcriptomic profiles, unveiling potential intratumor cell variability.

Conclusion

Together, our results provide the first attempt to clarify the spatial cell profile in PitNETs.

Sex differences in cancer incidence among solid organ transplant recipients

BACKGROUND

Males have 2-3-fold greater risk of cancer than females at most shared anatomic sites, possibly reflecting enhanced immune surveillance against cancer in females. We examined whether these sex differences remained among immunocompromised adults.

METHODS

Using the Transplant Cancer Match (TCM) study, we estimated the male-to-female incidence rate ratio in TCM (M:F IRRTransplant) for 15 cancer sites diagnosed between 1995 and 2017 using Poisson regression. Male to female IRRs in the general population (M:F IRRGP) were calculated using expected cancer counts from the Surveillance, Epidemiology, and End Results Program, standardized to the transplant population on age, race and ethnicity, and diagnosis year. Male to female IRRs were compared using a chi-square test.

RESULTS

Among 343 802 solid organ transplants, 211 206 (61.4%) were among men and 132 596 (38.6%) among women. An excess cancer incidence in males was seen in transplant recipients, but the sex difference was attenuated for cancers of the lip (M:F IRRTransplant: 1.81 vs M:F IRRGP: 3.96; P < .0001), stomach (1.51 vs 2.09; P = .002), colorectum (0.98 vs 1.43; P < .0001), liver (2.39 vs 3.44; P = .002), kidney (1.67 vs 2.24; P < .0001), bladder (2.02 vs 4.19; P < .0001), Kaposi sarcoma (1.79 vs 3.26; P = .0009), and non-Hodgkin lymphoma (1.34 vs 1.64; P < .0001). The M:F IRRTransplant was not statistically different from the M:F IRRGP for other cancer sites.

CONCLUSIONS

Although male solid organ transplant recipients have higher cancer incidence than female recipients, the attenuation in the male to female ratio for many cancers studied relative to the general population might suggest the importance of immunosurveillance, with some loss of advantage in female recipients due to immunosuppression after transplantation.

Autoimmune disease and the risk of anal cancer in the US population aged 66 years and over

BACKGROUND

In the United States, anal squamous cell carcinoma rates have increased rapidly, particularly among women 50 or older than 66 years of age. As immunosuppression is associated with increased risk, autoimmune conditions may be associated with greater risk of anal squamous cell carcinoma.

METHODS

We conducted a population-based, case-control study using Surveillance, Epidemiology, and End Results-Medicare data (2000-2017). Anal squamous cell carcinoma cases (n = 4505) were matched to 200 000 cancer-free controls. Using multivariable logistic regression, we calculated odds ratios (ORs) and 95% confidence intervals (CIs) for associations between 47 autoimmune conditions diagnosed before selection, identified using Medicare claims, and anal squamous cell carcinoma. The Bonferroni threshold was used to correct for multiple comparisons. Population attributable fractions were calculated for conditions nominally associated with anal squamous cell carcinoma.

RESULTS

In total, 18% of anal squamous cell carcinoma cases and 15% of cancer-free controls had a diagnosed autoimmune condition. Any autoimmune condition was associated with an increased risk of anal squamous cell carcinoma (OR = 1.11, 95% CI = 1.02 to 1.21; population attributable fraction = 1.8%). Anal squamous cell carcinoma was associated with systemic lupus erythematosus (OR = 1.79, 95% CI = 1.32 to 2.42; population attributable fraction = 0.4%) and nominally associated (P < .05) with sarcoidosis (OR = 2.09, 95% CI = 1.30 to 3.37; population-attributable fraction = 0.2%) and psoriasis (OR = 1.28, 95% CI = 1.06 to 1.56; population attributable fraction = 0.5%). Stratified by sex, only women showed statistically significant associations for systemic lupus erythematosus (OR = 1.97, 95% CI = 1.46 to 2.68). Statistically significant interaction was observed by sex for psoriasis (men vs women: OR = 1.68 [95% CI = 1.03 to 4.28] vs OR = 1.12 [95% CI = 0.88 to 1.43]) and polymyalgia rheumatica (OR = 0.33 [95% CI = 0.12 to 0.89] vs OR = 0.99 [95% CI = 0.75 to 1.30]).

CONCLUSION

Systemic lupus erythematosus, sarcoidosis, and psoriasis were associated with a moderately increased risk of anal squamous cell carcinoma. Given these conditions' rarity and moderate associations with anal squamous cell carcinoma, autoimmune diseases cannot explain the rising trend in this disease.

Exposure to indoor light at night in relation to multiple dimensions of sleep health: findings from the Sister Study

STUDY OBJECTIVE

To examine the association between light at night (LAN) and multiple sleep health dimensions.

METHODS

Among 47 765 Sister Study participants, indoor LAN (TV on in the room, light(s) on in room, light from outside the room, nightlight, no light) and sleep dimensions were self-reported at baseline (2003-2009). We used Poisson regression with robust variance to estimate adjusted prevalence ratios (PR) and 95% confidence intervals (CI) for the cross-sectional associations between LAN and short sleep duration (<7 hours/night), insomnia symptoms (difficulty falling or staying asleep), frequent napping (≥3 naps/week), inconsistent sleep/wake time (differed day-to-day and week-to-week), sleep debt (≥2 hours between longest and shortest duration), recent sleep medication use, and a cumulative poor sleep score (≥3 poor sleep dimensions). Population-attributable risks (PARs) were determined for any light exposure vs. none by race/ethnicity.

RESULTS

Compared to sleeping with no light in the bedroom, sleeping with a TV on was associated with a higher prevalence of most dimensions of poor sleep (e.g. short sleep duration: PR = 1.38, 95% CI: 1.32 to 1.45; inconsistent sleep/wake time: PR = 1.55, 95% CI: 1.44 to 1.66; sleep debt: PR = 1.36, 95% CI: 1.29 to 1.44; poor sleep score: PR = 1.58, 95% CI: 1.48-1.68). PARs tended to be higher for non-Hispanic black women compared to non-Hispanic white women.

CONCLUSIONS

Sleeping with a TV on was associated with poor sleep health among US women, and non-Hispanic black women may be disproportionately burdened.

Comparison of sleep parameters from wrist-worn ActiGraph and Actiwatch devices

Sleep and physical activity, two important health behaviors, are often studied independently using different accelerometer types and body locations. Understanding whether accelerometers designed for monitoring each behavior can provide similar sleep parameter estimates may help determine whether one device can be used to measure both behaviors. Three hundred and thirty one adults (70.7 ± 13.7 years) from the Baltimore Longitudinal Study of Aging wore the ActiGraph GT9X Link and the Actiwatch 2 simultaneously on the non-dominant wrist for 7.0 ± 1.6 nights. Total sleep time (TST), wake after sleep onset (WASO), sleep efficiency, number of wake bouts, mean wake bout length, and sleep fragmentation index (SFI) were extracted from ActiGraph using the Cole-Kripke algorithm and from Actiwatch using the software default algorithm. These parameters were compared using paired t-tests, Bland-Altman plots, and Deming regression models. Stratified analyses were performed by age, sex, and body mass index (BMI). Compared to the Actiwatch, the ActiGraph estimated comparable TST and sleep efficiency, but fewer wake bouts, longer WASO, longer wake bout length, and higher SFI (all p < .001). Both devices estimated similar 1-min and 1% differences between participants for TST and SFI (β = 0.99, 95% CI: 0.95, 1.03, and 0.91, 1.13, respectively), but not for other parameters. These differences varied by age, sex, and/or BMI. The ActiGraph and the Actiwatch provide comparable absolute and relative estimates of TST, but not other parameters. The discrepancies could result from device differences in movement collection and/or sleep scoring algorithms. Further comparison and calibration is required before these devices can be used interchangeably.

Harnessing the Power of IL-7 to Boost T Cell Immunity in Experimental and Clinical Immunotherapies

The cytokine IL-7 plays critical and nonredundant roles in T cell immunity so that the abundance and availability of IL-7 act as key regulatory mechanisms in T cell immunity. Importantly, IL-7 is not produced by T cells themselves but primarily by non-lymphoid lineage stromal cells and epithelial cells that are limited in their numbers. Thus, T cells depend on cell extrinsic IL-7, and the amount of in vivo IL-7 is considered a major factor in maximizing and maintaining the number of T cells in peripheral tissues. Moreover, IL-7 provides metabolic cues and promotes the survival of both naïve and memory T cells. Thus, IL-7 is also essential for the functional fitness of T cells. In this regard, there has been an extensive effort trying to increase the protein abundance of IL-7 in vivo, with the aim to augment T cell immunity and harness T cell functions in anti-tumor responses. Such approaches started under experimental animal models, but they recently culminated into clinical studies, with striking effects in re-establishing T cell immunity in immunocompromised patients, as well as boosting anti-tumor effects. Depending on the design, glycosylation, and the structure of recombinantly engineered IL-7 proteins and their mimetics, recombinant IL-7 molecules have shown dramatic differences in their stability, efficacy, cellular effects, and overall immune functions. The current review is aimed to summarize the past and present efforts in the field that led to clinical trials, and to highlight the therapeutical significance of IL-7 biology as a master regulator of T cell immunity.

Reevaluating First-line Therapies in Youth-Onset Type 2 Diabetes

The prevalence of youth-onset type 2 diabetes is growing worldwide and current first-line treatment with metformin and intensive behavior and lifestyle changes are suboptimal in over 50% of youth within 2 years of diagnosis. This perspective article is a call to action for reevaluation of existing strategies and critical appraisal of metformin as first-line therapy in youth-onset type 2 diabetes. Increased attention should be given to novel therapeutics approved in youth, including glucagon-like 1 receptor agonists, sodium glucose cotransporter-2, and sociocultural interventions that will promote diabetes self-management.

Occupational Benzene Exposure and Lung Cancer Risk: A Pooled Analysis of 14 Case-Control Studies

Rationale: Benzene has been classified as carcinogenic to humans, but there is limited evidence linking benzene exposure to lung cancer. Objectives: We aimed to examine the relationship between occupational benzene exposure and lung cancer. Methods: Subjects from 14 case-control studies across Europe and Canada were pooled. We used a quantitative job-exposure matrix to estimate benzene exposure. Logistic regression models assessed lung cancer risk across different exposure indices. We adjusted for smoking and five main occupational lung carcinogens and stratified analyses by smoking status and lung cancer subtypes. Measurements and Main Results: Analyses included 28,048 subjects (12,329 cases, 15,719 control subjects). Lung cancer odds ratios ranged from 1.12 (95% confidence interval, 1.03-1.22) to 1.32 (95% confidence interval, 1.18-1.48) (Ptrend = 0.002) for groups with the lowest and highest cumulative occupational exposures, respectively, compared with unexposed subjects. We observed an increasing trend of lung cancer with longer duration of exposure (Ptrend < 0.001) and a decreasing trend with longer time since last exposure (Ptrend = 0.02). These effects were seen for all lung cancer subtypes, regardless of smoking status, and were not influenced by specific occupational groups, exposures, or studies. Conclusions: We found consistent and robust associations between different dimensions of occupational benzene exposure and lung cancer after adjusting for smoking and main occupational lung carcinogens. These associations were observed across different subgroups, including nonsmokers. Our findings support the hypothesis that occupational benzene exposure increases the risk of developing lung cancer. Consequently, there is a need to revisit published epidemiological and molecular data on the pulmonary carcinogenicity of benzene.

Direct interhemispheric cortical communication via thalamic commissures: a new white matter pathway in the primate brain

Cortical neurons of eutherian mammals project to the contralateral hemisphere, crossing the midline primarily via the corpus callosum and the anterior, posterior, and hippocampal commissures. We recently reported and named the thalamic commissures (TCs) as an additional interhemispheric axonal fiber pathway connecting the cortex to the contralateral thalamus in the rodent brain. Here, we demonstrate that TCs also exist in primates and characterize the connectivity of these pathways with high-resolution diffusion-weighted MRI, viral axonal tracing, and fMRI. We present evidence of TCs in both New World (Callithrix jacchus and Cebus apella) and Old World primates (Macaca mulatta). Further, like rodents, we show that the TCs in primates develop during the embryonic period, forming anatomical and functionally active connections of the cortex with the contralateral thalamus. We also searched for TCs in the human brain, showing their presence in humans with brain malformations, although we could not identify TCs in healthy subjects. These results pose the TCs as a vital fiber pathway in the primate brain, allowing for more robust interhemispheric connectivity and synchrony and serving as an alternative commissural route in developmental brain malformations.

Maternal self-reported polycystic ovary syndrome with offspring and maternal cardiometabolic outcomes

STUDY QUESTION

Do children born to mothers with polycystic ovary syndrome (PCOS) have an adverse cardiometabolic profile including arterial stiffness at 9 years of age compared to other children?

SUMMARY ANSWER

Children of mothers with PCOS did not have differing cardiometabolic outcomes than children without exposure.

WHAT IS KNOWN ALREADY

While women with PCOS themselves have higher risk of cardiometabolic conditions such as obesity and diabetes, the evidence on intergenerational impact is unclear. Given in utero sequalae of PCOS (e.g. hyperandrogenism, insulin resistance), the increased risk could be to both boys and girls.

STUDY DESIGN, SIZE, DURATION

The Upstate KIDS cohort is a population-based birth cohort established in 2008-2010 to prospectively study the impact of infertility treatment on children's health. After ∼10 years of follow-up, 446 mothers and their 556 children attended clinical visits to measure blood pressure (BP), heart rate, arterial stiffness by pulse wave velocity (PWV), mean arterial pressure, lipids, high-sensitivity C-reactive protein (hsCRP), hemoglobin A1c (HbA1c), and anthropometrics.

PARTICIPANTS/MATERIALS, SETTING, METHODS

Women self-reported ever diagnoses of PCOS ∼4 months after delivery of their children in 2008-2010. Linear regression models applying generalized estimating equations to account for correlation within twins were used to examine associations with each childhood cardiometabolic outcome.

MAIN RESULTS AND THE ROLE OF CHANCE

In this cohort with women oversampled on infertility treatment, ∼14% of women reported a PCOS diagnosis (n = 61). We observed similarities in BP, heart rate, PWV, lipids, hsCRP, HbA1c, and anthropometry (P-values >0.05) among children born to mothers with and without PCOS. Associations did not differ by child sex.

LIMITATIONS, REASONS FOR CAUTION

The sample size of women with PCOS precluded further separation of subgroups (e.g. by hirsutism). The population-based approach relied on self-reported diagnosis of maternal PCOS even though self-report has been found to be valid. Participants were predominantly non-Hispanic White and a high proportion were using fertility treatment due to the original design. Differences in cardiometabolic health may be apparent later in age, such as after puberty.

WIDER IMPLICATIONS OF THE FINDINGS

Our results provide some reassurance that cardiometabolic factors do not differ in children of women with and without self-reported PCOS during pregnancy.

STUDY FUNDING/COMPETING INTEREST(S)

Supported by the Intramural Research Program of the Eunice Kennedy Shriver National Institute of Child Health and Human Development, United States (contracts #HHSN275201200005C, #HHSN267200700019C, #HHSN275201400013C, #HHSN275201300026I/27500004, #HHSN275201300023I/27500017). The authors have no conflicts of interest.

REGISTRATION NUMBER

NCT03106493.

Development of a computed tomography calcium scoring technique for assessing calcinosis distribution, pattern and burden in dermatomyositis

OBJECTIVES

To utilize whole-body CT imaging and calcium scoring techniques as tools for calcinosis assessment in a prospective cohort of patients with adult and juvenile dermatomyositis (DM and JDM, respectively).

METHODS

Thirty-one patients (14 DM and 17 JDM) who fulfilled Bohan and Peter Classification criteria as probable or definite DM, the EULAR-ACR criteria for definite DM, and with calcinosis identified by physical examination or prior imaging studies were included. Non-contrast whole-body CT scans were obtained using low-dose radiation procedures. Scans were read qualitatively and quantitated. We calculated the sensitivity and specificity of calcinosis detection of physician physical exam against CT. We quantified calcinosis burden using the Agatston scoring technique.

RESULTS

We identified five distinct calcinosis patterns: Clustered, Disjoint, Interfascial, Confluent and Fluid-filled. Novel locations of calcinosis were observed, including the cardiac tissue, pelvic and shoulder bursa, and the spermatic cord. Quantitative measures using Agatston scoring for calcinosis were used in regional distributions across the body. Physician physical exams had a sensitivity of 59% and a specificity of 90% compared with CT detection. A higher calcium score correlated with higher Physician Global Damage, Calcinosis Severity scores, and disease duration.

CONCLUSION

Whole-body CT scans and the Agatston scoring metric define distinct calcinosis patterns and provide novel insights relating to calcinosis in DM and JDM patients. Physicians' physical examinations underrepresented the presence of calcium. Calcium scoring of CT scans correlated with clinical measures, which suggests that this method may be used to assess calcinosis and follow its progression.

Neuropsychiatric lupus in late- and early-onset systemic lupus erythematosus patients: a systematic review and meta-analysis

OBJECTIVES

Late-onset SLE is usually milder and associated with lower frequency of LN and neuropsychiatric manifestations. The diagnosis of NPSLE is especially challenging in older patients because of increased incidence of neurological comorbidities. We performed a systematic review and meta-analysis to evaluate the differences in NPSLE manifestations in early-onset (<50-year-old) vs late-onset (≥50-year-old) SLE patients.

METHODS

A literature search was performed using the PubMed, Web of Science and Cochrane Library databases. Studies available in English (1959-2022) including a late-onset SLE comparison group and evaluating the frequency of NPSLE were eligible. A forest plot was used to compare odds ratios (95% CI) of incidence and manifestations of NPSLE by age groups. Study heterogeneity was assessed using I2 statistics.

RESULTS

A total of 44 studies, including 17 865 early-onset and 2970 late-onset SLE patients, fulfilled our eligibility criteria. CNS involvement was reported in 3326 patients. Cumulative NPSLE frequency was higher in the early-onset group than in the late-onset group (OR: 1.41, 95% CI: 1.24, 1.59, P < 0.0001). In early-onset SLE patients, seizures (OR: 1.68, 95% CI: 1.27, 2.22) and psychosis (OR: 1.72, 95% CI: 1.23, 2.41) were more common than in late-onset SLE patients (P values, 0.0003 and 0.0014, respectively). Peripheral neuropathy was more commonly reported in the late-onset SLE group than in the early-onset SLE group (OR: 0.64, 95% CI: 0.47, 0.86, P = 0.004).

CONCLUSION

Our meta-analysis revealed that the frequencies of overall NPSLE, seizures, and psychosis were less common in late-onset SLE patients than in early-onset SLE patients. In contrast, peripheral neuropathy was more common in the late-onset SLE group.

Non-invasive pressure-volume loops using the elastance model and CMR: a porcine validation at transient pre-loads

Aims

Pressure-volume (PV) loops have utility in the evaluation of cardiac pathophysiology but require invasive measurements. Recently, a time-varying elastance model to derive PV loops non-invasively was proposed, using left ventricular (LV) volume by cardiovascular magnetic resonance (CMR) and brachial cuff pressure as inputs. Validation was performed using CMR and pressure measurements acquired on the same day, but not simultaneously, and without varying pre-loads. This study validates the non-invasive elastance model used to estimate PV loops at varying pre-loads, compared with simultaneous measurements of invasive pressure and volume from real-time CMR, acquired concurrent to an inferior vena cava (IVC) occlusion.

Methods and results

We performed dynamic PV loop experiments under CMR guidance in 15 pigs (n = 7 naïve, n = 8 with ischaemic cardiomyopathy). Pre-load was altered by IVC occlusion, while simultaneously acquiring invasive LV pressures and volumes from real-time CMR. Pairing pressure and volume signals yielded invasive PV loops, and model-based PV loops were derived using real-time LV volumes. Haemodynamic parameters derived from invasive and model-based PV loops were compared. Across 15 pigs, 297 PV loops were recorded. Intra-class correlation coefficient (ICC) agreement was excellent between model-based and invasive parameters: stroke work (bias = 0.007 ± 0.03 J, ICC = 0.98), potential energy (bias = 0.02 ± 0.03 J, ICC = 0.99), ventricular energy efficiency (bias = -0.7 ± 2.7%, ICC = 0.98), contractility (bias = 0.04 ± 0.1 mmHg/mL, ICC = 0.97), and ventriculoarterial coupling (bias = 0.07 ± 0.15, ICC = 0.99). All haemodynamic parameters differed between naïve and cardiomyopathy animals (P < 0.05). The invasive vs. model-based PV loop dice similarity coefficient was 0.88 ± 0.04.

Conclusion

An elastance model-based estimation of PV loops and associated haemodynamic parameters provided accurate measurements at transient loading conditions compared with invasive PV loops.

Clustering rare diseases within an ontology-enriched knowledge graph

OBJECTIVE

Identifying sets of rare diseases with shared aspects of etiology and pathophysiology may enable drug repurposing. Toward that aim, we utilized an integrative knowledge graph to construct clusters of rare diseases.

MATERIALS AND METHODS

Data on 3242 rare diseases were extracted from the National Center for Advancing Translational Science Genetic and Rare Diseases Information center internal data resources. The rare disease data enriched with additional biomedical data, including gene and phenotype ontologies, biological pathway data, and small molecule-target activity data, to create a knowledge graph (KG). Node embeddings were trained and clustered. We validated the disease clusters through semantic similarity and feature enrichment analysis.

RESULTS

Thirty-seven disease clusters were created with a mean size of 87 diseases. We validate the clusters quantitatively via semantic similarity based on the Orphanet Rare Disease Ontology. In addition, the clusters were analyzed for enrichment of associated genes, revealing that the enriched genes within clusters are highly related.

DISCUSSION

We demonstrate that node embeddings are an effective method for clustering diseases within a heterogenous KG. Semantically similar diseases and relevant enriched genes have been uncovered within the clusters. Connections between disease clusters and drugs are enumerated for follow-up efforts.

CONCLUSION

We lay out a method for clustering rare diseases using graph node embeddings. We develop an easy-to-maintain pipeline that can be updated when new data on rare diseases emerges. The embeddings themselves can be paired with other representation learning methods for other data types, such as drugs, to address other predictive modeling problems.

Association of cardiovascular disease management drugs with Lewy body dementia: a case-control study

Lewy body dementia is the second most common neurodegenerative dementia after Alzheimer's disease. Disease-modifying therapies for this disabling neuropsychiatric condition are critically needed. To identify drugs associated with the risk of developing Lewy body dementia, we performed a population-based case-control study of 148 170 US Medicare participants diagnosed with Lewy body dementia between 1 January 2008 and 31 December 2014 and of 1 253 043 frequency-matched controls. We estimated odds ratios and 95% confidence intervals for the association of Lewy body dementia risk with 1017 prescription drugs overall and separately for the three major racial groups (Black, Hispanic and White Americans). We identified significantly reduced Lewy body dementia risk associated with drugs used to treat cardiovascular diseases (anti-hypertensives: odds ratio = 0.72, 95% confidence interval = 0.70-0.74, P-value = 0; cholesterol-lowering agents: odds ratio = 0.85, 95% confidence interval = 0.83-0.87, P-value = 0; anti-diabetics: odds ratio = 0.83, 95% confidence interval = 0.62-0.72, P-value = 0). Notably, anti-diabetic medications were associated with a larger risk reduction among Black Lewy body dementia patients compared with other racial groups (Black: odds ratio = 0.67, 95% confidence interval = 0.62-0.72, P-value = 0; Hispanic: odds ratio = 0.86, 95% = 0.80-0.92, P-value = 5.16 × 10-5; White: odds ratio = 0.85, 95% confidence interval = 0.82-0.88, P-value = 0). To independently confirm the epidemiological findings, we looked for evidence of genetic overlap between Lewy body dementia and cardiovascular traits using whole-genome sequence data generated for 2591 Lewy body dementia patients and 4027 controls. Bivariate mixed modelling identified shared genetic risk between Lewy body dementia and low-density lipoprotein cholesterol levels, Type 2 diabetes and hypertension. By combining epidemiological and genomic data, we demonstrated that drugs treating cardiovascular diseases are associated with reduced Lewy body dementia risk, and these associations varied across racial groups. Future randomized clinical trials need to confirm our findings, but our data suggest that assiduous management of cardiovascular diseases may be beneficial in this understudied form of dementia.

Model-based evaluation of spatiotemporal data reduction methods with unknown ground truth through optimal visualization and interpretability metrics

Optimizing and benchmarking data reduction methods for dynamic or spatial visualization and interpretation (DSVI) face challenges due to many factors, including data complexity, lack of ground truth, time-dependent metrics, dimensionality bias and different visual mappings of the same data. Current studies often focus on independent static visualization or interpretability metrics that require ground truth. To overcome this limitation, we propose the MIBCOVIS framework, a comprehensive and interpretable benchmarking and computational approach. MIBCOVIS enhances the visualization and interpretability of high-dimensional data without relying on ground truth by integrating five robust metrics, including a novel time-ordered Markov-based structural metric, into a semi-supervised hierarchical Bayesian model. The framework assesses method accuracy and considers interaction effects among metric features. We apply MIBCOVIS using linear and nonlinear dimensionality reduction methods to evaluate optimal DSVI for four distinct dynamic and spatial biological processes captured by three single-cell data modalities: CyTOF, scRNA-seq and CODEX. These data vary in complexity based on feature dimensionality, unknown cell types and dynamic or spatial differences. Unlike traditional single-summary score approaches, MIBCOVIS compares accuracy distributions across methods. Our findings underscore the joint evaluation of visualization and interpretability, rather than relying on separate metrics. We reveal that prioritizing average performance can obscure method feature performance. Additionally, we explore the impact of data complexity on visualization and interpretability. Specifically, we provide optimal parameters and features and recommend methods, like the optimized variational contractive autoencoder, for targeted DSVI for various data complexities. MIBCOVIS shows promise for evaluating dynamic single-cell atlases and spatiotemporal data reduction models.

Clinical and Immunologic Correlates of Vasodilatory Shock Among Ebola Virus-Infected Nonhuman Primates in a Critical Care Model

BACKGROUND

Existing models of Ebola virus infection have not fully characterized the pathophysiology of shock in connection with daily virologic, clinical, and immunologic parameters. We implemented a nonhuman primate critical care model to investigate these associations.

METHODS

Two rhesus macaques received a target dose of 1000 plaque-forming units of Ebola virus intramuscularly with supportive care initiated on day 3. High-dimensional spectral cytometry was used to phenotype neutrophils and peripheral blood mononuclear cells daily.

RESULTS

We observed progressive vasodilatory shock with preserved cardiac function following viremia onset on day 5. Multiorgan dysfunction began on day 6 coincident with the nadir of circulating neutrophils. Consumptive coagulopathy and anemia occurred on days 7 to 8 along with irreversible shock, followed by death. The monocyte repertoire began shifting on day 4 with a decline in classical and expansion of double-negative monocytes. A selective loss of CXCR3-positive B and T cells, expansion of naive B cells, and activation of natural killer cells followed viremia onset.

CONCLUSIONS

Our model allows for high-fidelity characterization of the pathophysiology of acute Ebola virus infection with host innate and adaptive immune responses, which may advance host-targeted therapy design and evaluation for use after the onset of multiorgan failure.

Large-scale rare variant burden testing in Parkinson's disease

Parkinson's disease has a large heritable component and genome-wide association studies have identified over 90 variants with disease-associated common variants, providing deeper insights into the disease biology. However, there have not been large-scale rare variant analyses for Parkinson's disease. To address this gap, we investigated the rare genetic component of Parkinson's disease at minor allele frequencies <1%, using whole genome and whole exome sequencing data from 7184 Parkinson's disease cases, 6701 proxy cases and 51 650 healthy controls from the Accelerating Medicines Partnership Parkinson's disease (AMP-PD) initiative, the National Institutes of Health, the UK Biobank and Genentech. We performed burden tests meta-analyses on small indels and single nucleotide protein-altering variants, prioritized based on their predicted functional impact. Our work identified several genes reaching exome-wide significance. Two of these genes, GBA1 and LRRK2, have variants that have been previously implicated as risk factors for Parkinson's disease, with some variants in LRRK2 resulting in monogenic forms of the disease. We identify potential novel risk associations for variants in B3GNT3, AUNIP, ADH5, TUBA1B, OR1G1, CAPN10 and TREML1 but were unable to replicate the observed associations across independent datasets. Of these, B3GNT3 and TREML1 could provide new evidence for the role of neuroinflammation in Parkinson's disease. To date, this is the largest analysis of rare genetic variants in Parkinson's disease.

Standardized In Vitro Models of Human Adipose Tissue Reveal Metabolic Flexibility in Brown Adipocyte Thermogenesis

Functional human brown and white adipose tissue (BAT and WAT) are vital for thermoregulation and nutritional homeostasis, while obesity and other stressors lead, respectively, to cold intolerance and metabolic disease. Understanding BAT and WAT physiology and dysfunction necessitates clinical trials complemented by mechanistic experiments at the cellular level. These require standardized in vitro models, currently lacking, that establish references for gene expression and function. We generated and characterized a pair of immortalized, clonal human brown (hBA) and white (hWA) preadipocytes derived from the perirenal and subcutaneous depots, respectively, of a 40-year-old male individual. Cells were immortalized with hTERT and confirmed to be of a mesenchymal, nonhematopoietic lineage based on fluorescence-activated cell sorting and DNA barcoding. Functional assessments showed that the hWA and hBA phenocopied primary adipocytes in terms of adrenergic signaling, lipolysis, and thermogenesis. Compared to hWA, hBA were metabolically distinct, with higher rates of glucose uptake and lactate metabolism, and greater basal, maximal, and nonmitochondrial respiration, providing a mechanistic explanation for the association between obesity and BAT dysfunction. The hBA also responded to the stress of maximal respiration by using both endogenous and exogenous fatty acids. In contrast to certain mouse models, hBA adrenergic thermogenesis was mediated by several mechanisms, not principally via uncoupling protein 1 (UCP1). Transcriptomics via RNA-seq were consistent with the functional studies and established a molecular signature for each cell type before and after differentiation. These standardized cells are anticipated to become a common resource for future physiological, pharmacological, and genetic studies of human adipocytes.

Associations Between Circulating Levels of Myostatin and Plasma β-Amyloid 42/40 in a Biracial Cohort of Older Adults

BACKGROUND

Myostatin, a cytokine produced by skeletal muscle, may influence Alzheimer's disease (AD) pathogenesis, but sparse evidence exists in humans. We assessed the association between circulating levels of myostatin at Year 1 and plasma levels of β-amyloid 42/40 at Year 2, a marker of AD pathology, in a biracial cohort of older adults.

METHODS

We studied 403 community-dwelling older adults enrolled in the Health, Aging and Body Composition Study from Memphis, Tennessee, and Pittsburgh, PA. Mean age was 73.8 ± 3 years; 54% were female; and 52% were Black. Serum myostatin levels were measured at Year 1, plasma β-amyloid 42/40 levels in Year 2 (higher ratio indicating lower amyloid load). Multivariable linear regression analyses tested the association of serum myostatin with plasma levels of β-amyloid 42/40 adjusted for computed-tomography-derived thigh muscle cross-sectional area, demographics, APOe4 allele, and risk factors for dementia. We tested for 2-way.interactions between myostatin and race or sex; results were stratified by race and sex.

RESULTS

In multivariable models, myostatin was positively associated with plasma levels of β-amyloid 42/40 (standardized regression coefficient: 0.145, p = .004). Results were significant for white men and women (0.279, p = .009, and 0.221, p = .035, respectively) but not for Black men or women; interactions by race and gender were not statistically significant.

CONCLUSIONS

Higher serum myostatin was associated with lower amyloid burden, independently of APOe4 alleles, muscle area and other established risk factors for dementia. The role of myostatin in AD pathogenesis and the influence of race should be further investigated.

Cumulative incidence of anal cancer since HIV or AIDS diagnosis in the United States

Treatment of screen-detected anal high-grade squamous intraepithelial lesions has been shown to effectively reduce the incidence of invasive anal cancer in people with HIV. We provide population-based estimates of cumulative incidence of anal cancer by risk group and age at HIV or AIDS diagnosis. The 0- to 10-year cumulative incidence of anal cancer for men who have sex with men and are younger than 30 years of age at HIV diagnosis was 0.17% (95% confidence interval [CI] = 0.13% to 0.20%) compared with 0.04% (95% CI = 0.02% to 0.06%) in other men and 0.03% (95% CI = 0.01% to 0.04%) in women. For men who have sex with men and have a diagnosis of AIDS and are younger than 30 years of age, the 0- to 10-year cumulative incidence was 0.35% (95% CI = 0.28% to 0.41%). Among people with HIV, men who have sex with men are at the greatest risk of anal cancer, and those with a diagnosis of AIDS had higher risk than those without AIDS. These estimates may inform recommendations for priority populations that could benefit most from anal cancer screening and treatment.

Correspondence of mean apparent propagator MRI metrics with phosphorylated tau and astrogliosis in chronic traumatic encephalopathy

Chronic traumatic encephalopathy is a neurodegenerative disease that is diagnosed and staged based on the localization and extent of phosphorylated tau pathology. Although its identification remains the primary diagnostic criteria to distinguish chronic traumatic encephalopathy from other tauopathies, the hyperphosphorylated tau that accumulates in neurofibrillary tangles in cortical grey matter and perivascular regions is often accompanied by concomitant pathology such as astrogliosis. Mean apparent propagator MRI is a clinically feasible diffusion MRI method that is suitable to characterize microstructure of complex biological media efficiently and comprehensively. We performed quantitative correlations between propagator metrics and underlying phosphorylated tau and astroglial pathology in a cross-sectional study of 10 ex vivo human tissue specimens with 'high chronic traumatic encephalopathy' at 0.25 mm isotropic voxels. Linear mixed effects analysis of regions of interest showed significant relationships of phosphorylated tau with propagator-estimated non-Gaussianity in cortical grey matter (P = 0.002) and of astrogliosis with propagator anisotropy in superficial cortical white matter (P = 0.0009). The positive correlation between phosphorylated tau and non-Gaussianity was found to be modest but significant (R2 = 0.44, P = 6.0 × 10-5) using linear regression. We developed an unsupervised clustering algorithm with non-Gaussianity and propagator anisotropy as inputs, which was able to identify voxels in superficial cortical white matter that corresponded to astrocytes that were accumulated at the grey-white matter interface. Our results suggest that mean apparent propagator MRI at high spatial resolution provides a means to not only identify phosphorylated tau pathology but also detect regions with astrocytic pathology and may therefore prove diagnostically valuable in the evaluation of concomitant pathology in cortical tissue with complex microstructure.

A Single-Arm, Open-Label Phase II Study of ONC201 in Recurrent/Refractory Metastatic Breast Cancer and Advanced Endometrial Carcinoma

BACKGROUND

ONC201 is a small molecule that can cause nonapoptotic cell death through loss of mitochondrial function. Results from the phase I/II trials of ONC201 in patients with refractory solid tumors demonstrated tumor responses and prolonged stable disease in some patients.

METHODS

This single-arm, open-label, phase II clinical trial evaluated the efficacy of ONC201 at the recommended phase II dose (RP2D) in patients with recurrent or refractory metastatic breast or endometrial cancer. Fresh tissue biopsies and blood were collected at baseline and at cycle 2 day 2 for correlative studies.

RESULTS

Twenty-two patients were enrolled; 10 patients with endometrial cancer, 7 patients with hormone receptor-positive breast cancer, and 5 patients with triple-negative breast cancer. The overall response rate was 0%, and the clinical benefit rate, defined by complete response (CR) + partial response (PR) + stable disease (SD), was 27% (n = 3/11). All patients experienced an adverse event (AE), which was primarily low grade. Grade 3 AEs occurred in 4 patients; no grade 4 AEs occurred. Tumor biopsies did not show that ONC201 consistently induced mitochondrial damage or alterations in tumor necrosis factor-related apoptosis-inducing ligand (TRAIL) or the TRAIL death receptors. ONC201 treatment caused alterations in peripheral immune cell subsets.

CONCLUSION

ONC201 monotherapy did not induce objective responses in recurrent or refractory metastatic breast or endometrial cancer at the RP2D dose of 625 mg weekly but had an acceptable safety profile (ClinicalTrials.gov Identifier: NCT03394027).

Differential Expression and Diagnostic Value of MUC5AC Glycoforms in Pancreatic Ductal Adenocarcinoma

We explored the differential expression and diagnostic value of two significant Mucin 5AC (MUC5AC) glycoforms, less-glycosylated immature (IM) and heavily-glycosylated mature (MM), in neoplastic diseases (NpD), including pancreatic ductal adenocarcinoma (PDA) and neuroendocrine tumors (NET), and non-neoplastic (non-NpD) diseases. Commercially available tissue microarray (TMA) was constructed from 96 patients, including 38 primary PDA (PT), 5 metastatic lesions (ML), 11 NET, and the rest being non-NpD tissues. Immunohistochemistry for MUC5AC was performed using CHL2 and 45M1 clones for IM and MM isoforms, respectively. MUC5AC (both glycoforms) are not detected in non-NpD. In MUC5AC-positive neoplastic tissues, IM was localized to the cytoplasm (Cy) while MM was identified in apical (Ap) and extracellular (Ec) regions too. One ML positive (omentum) in the TMA expressed both. For PDA vs. non-PDA, the sensitivity (SN) was higher with MM ± IM (71%) than MM (47%) or IM (65%)-alone. The specificity (SP) was 100% with MM-alone, which dropped with the addition of IM (96%) or IM-alone (93%). For NpD vs. non-NpD, the SN (MM + IM-59%, IM-55%, MM-37%) was inferior, and SP was 100% for both glycoforms (MM ± IM). The combination of MUC5AC glycoforms has high SP and reasonable SN to diagnose PDA. They have the potential to be a reliable diagnostic marker and should be investigated further in more extensive studies.

A practical strategy to use the ICD-11 for morbidity coding in the United States without a clinical modification

OBJECTIVE

The aim of this study was to derive and evaluate a practical strategy of replacing ICD-10-CM codes by ICD-11 for morbidity coding in the United States, without the creation of a Clinical Modification.

MATERIALS AND METHODS

A stepwise strategy is described, using first the ICD-11 stem codes from the Mortality and Morbidity Statistics (MMS) linearization, followed by exposing Foundation entities, then adding postcoordination (with existing codes and adding new stem codes if necessary), with creating new stem codes as the last resort. The strategy was evaluated by recoding 2 samples of ICD-10-CM codes comprised of frequently used codes and all codes from the digestive diseases chapter.

RESULTS

Among the 1725 ICD-10-CM codes examined, the cumulative coverage at the stem code, Foundation, and postcoordination levels are 35.2%, 46.5% and 89.4% respectively. 7.1% of codes require new extension codes and 3.5% require new stem codes. Among the new extension codes, severity scale values and anatomy are the most common categories. 5.5% of codes are not one-to-one matches (1 ICD-10-CM code matched to 1 ICD-11 stem code or Foundation entity) which could be potentially challenging.

CONCLUSION

Existing ICD-11 content can achieve full representation of almost 90% of ICD-10-CM codes, provided that postcoordination can be used and the coding guidelines and hierarchical structures of ICD-10-CM and ICD-11 can be harmonized. The various options examined in this study should be carefully considered before embarking on the traditional approach of a full-fledged ICD-11-CM.

RNA helicase DDX6 and scaffold protein GW182 in P-bodies promote biogenesis of stress granules

Two prominent cytoplasmic RNA granules, ubiquitous RNA-processing bodies (PB) and inducible stress granules (SG), regulate mRNA translation and are intimately related. In this study, we found that arsenite (ARS)-induced SG formed in a stepwise process is topologically and mechanically linked to PB. Two essential PB components, GW182 and DDX6, are repurposed under stress to play direct but distinguishable roles in SG biogenesis. By providing scaffolding activities, GW182 promotes the aggregation of SG components to form SG bodies. DEAD-box helicase DDX6 is also essential for the proper assembly and separation of PB from SG. DDX6 deficiency results in the formation of irregularly shaped 'hybrid' PB/SG granules with accumulated components of both PB and SG. Wild-type DDX6, but not its helicase mutant E247A, can rescue the separation of PB from SG in DDX6KO cells, indicating a requirement of DDX6 helicase activity for this process. DDX6 activity in biogenesis of both PB and SG in the cells under stress is further modulated by its interaction with two protein partners, CNOT1 and 4E-T, of which knockdown affects the formation of both PB and also SG. Together, these data highlight a new functional paradigm between PB and SG biogenesis during the stress.

Identification of neoepitope reactive T-cell receptors guided by HLA-A*03:01 and HLA-A*11:01 immunopeptidomics

BACKGROUND

Tumor-specific mutated proteins can create immunogenic non-self, mutation-containing 'neoepitopes' that are attractive targets for adoptive T-cell therapies. To avoid the complexity of defining patient-specific, private neoepitopes, there has been major interest in targeting common shared mutations in driver genes using off-the-shelf T-cell receptors (TCRs) engineered into autologous lymphocytes. However, identifying the precise naturally processed neoepitopes to pursue is a complex and challenging process. One method to definitively demonstrate whether an epitope is presented at the cell surface is to elute peptides bound to a specific major histocompatibility complex (MHC) allele and analyze them by mass spectrometry (MS). These MS data can then be prospectively applied to isolate TCRs specific to the neoepitope.

METHODS

We created mono-allelic cell lines expressing one class I HLA allele and one common mutated oncogene in order to eliminate HLA deconvolution requirements and increase the signal of recovered peptides. MHC-bound peptides on the surface of these cell lines were immunoprecipitated, purified, and analyzed using liquid chromatography-tandem mass spectrometry, producing a list of mutation-containing minimal epitopes. To validate the immunogenicity of these neoepitopes, HLA-transgenic mice were vaccinated using the minimal peptides identified by MS in order to generate neoepitope-reactive TCRs. Specificity of these candidate TCRs was confirmed by peptide titration and recognition of transduced targets.

RESULTS

We identified precise neoepitopes derived from mutated isoforms of KRAS, EGFR, BRAF, and PIK3CA presented by HLA-A*03:01 and/or HLA-A*11:01 across multiple biological replicates. From our MS data, we were able to successfully isolate murine TCRs that specifically recognize four HLA-A*11:01 restricted neoepitopes (KRAS G13D, PIK3CA E545K, EGFR L858R and BRAF V600E) and three HLA-A*03:01 restricted neoepitopes (KRAS G12V, EGFR L858R and BRAF V600E).

CONCLUSIONS

Our data show that an MS approach can be used to demonstrate which shared oncogene-derived neoepitopes are processed and presented by common HLA alleles, and those MS data can rapidly be used to develop TCRs against these common tumor-specific antigens. Although further characterization of these neoepitope-specific murine TCRs is required, ultimately, they have the potential to be used clinically for adoptive cell therapy.

Longitudinal Bile Acid Composition Changes Following Faecal Microbiota Transplantation for Clostridioides difficile Infection in Children With and Without Underlying Inflammatory Bowel Disease

BACKGROUND AND AIMS

Faecal microbiota transplant [FMT] is effective in treating recurrent Clostridioides difficile infection [CDI] and restores gut microbiota composition. This is unlikely to account for its entire mechanism of efficacy, as studies have shown that factors such as bile acids influence the risk of infection by affecting Clostridioides difficile germination. We therefore aimed to investigate longitudinal changes in the gut bile acid composition after FMT performed for recurrent CDI, in children with and without inflammatory bowel disease [IBD].

METHODS

Eight children received FMT; five had underlying IBD. Primary and secondary faecal bile acids were measured by liquid chromatography-mass spectrometry in recipients [pre-FMT and longitudinally post-FMT for up to 6 months] and donors.

RESULTS

Pre-FMT, recipients had higher primary and lower secondary bile acid proportions compared with donors. Post-FMT, there was a gradual increase of secondary and decrease of primary bile acids. Whereas gut bacterial diversity had been shown to be restored in all children shortly after FMT, normalisation of bile acids to donor levels occurred only by 6 months. In children with IBD, although microbiota diversity returned to pre-FMT levels within 6 months, secondary bile acids remained at donor levels.

CONCLUSIONS

The differences in bile acid profiles compared with gut bacterial diversity post-FMT suggests that interactions between the two may be more complex than previously appreciated and may contribute to FMT efficacy in different ways. This initial finding demonstrates the need to further investigate gut metabolites in larger cohorts, with longitudinal sampling to understand the mechanisms of FMT effectiveness.

Context-dependent role of Pho binding sites in Polycomb complex recruitment in Drosophila

Polycomb group (PcG) proteins maintain the silenced state of key developmental genes, but how these proteins are recruited to specific regions of the genome is still not completely understood. In Drosophila, PcG proteins are recruited to Polycomb response elements (PREs) comprised of a flexible array of sites for sequence-specific DNA binding proteins, "PcG recruiters," including Pho, Spps, Cg, and GAF. Pho is thought to play a central role in PcG recruitment. Early data showed that mutation of Pho binding sites in PREs in transgenes abrogated the ability of those PREs to repress gene expression. In contrast, genome-wide experiments in pho mutants or by Pho knockdown showed that PcG proteins can bind to PREs in the absence of Pho. Here, we directly addressed the importance of Pho binding sites in 2 engrailed (en) PREs at the endogenous locus and in transgenes. Our results show that Pho binding sites are required for PRE activity in transgenes with a single PRE. In a transgene, 2 PREs together lead to stronger, more stable repression and confer some resistance to the loss of Pho binding sites. Making the same mutation in Pho binding sites has little effect on PcG-protein binding at the endogenous en gene. Overall, our data support the model that Pho is important for PcG binding but emphasize how multiple PREs and chromatin environment increase the ability of PREs to function in the absence of Pho. This supports the view that multiple mechanisms contribute to PcG recruitment in Drosophila.

Precision diagnosis and staging of TDP-43 proteinopathies: harnessing the power of artificial intelligence

This scientific commentary refers to ‘Data-driven neuropathological staging and subtyping of TDP-43 proteinopathies’ by Young et al. (https://doi.org/10.1093/brain/awad145).

Early Discontinuation of Antibiotics in Patients Admitted With Clinically Suspected Serious Infection but Negative Cultures: Retrospective Cohort Study of Practice Patterns and Outcomes at 111 US Hospitals

Background

The optimal duration for antibiotics in patients hospitalized with culture-negative serious infection (CNSI) is unknown. We compared outcomes in patients with CNSI treated with 3 or 4 vs ≥5 days of antibiotics.

Methods

CNSI was identified among adults admitted to 111 US hospitals between 2009 and 2014 via electronic health record data, defined as suspected serious infection (blood cultures drawn and ≥3 days of antibiotics) and negative culture- and nonculture-based tests for infection. Patients treated with antibiotics on their last hospital day and patients with diagnosis codes for sepsis-mimicking conditions were excluded. Among patients without fevers/hypothermia or vasopressors by day 3, we calculated odds ratios for in-hospital mortality or discharge to hospice associated with 3 or 4 vs ≥5 days of antibiotics, adjusting for confounders.

Results

Antibiotics were discontinued in 3 or 4 days in 1862 (9%) of 20 714 patients with CNSI. Early discontinuation was not associated with higher mortality odds overall (adjusted odds ratio [aOR], 1.27; 95% CI, .98-1.65), in patients presenting with (1.39; .88-2.22) and without sepsis (1.17; .81-1.69), and in those with pulmonary (1.23; .65-2.34) and nonpulmonary CNSI (1.30; .99-1.72). Early discontinuation appeared detrimental with propensity score weighting (aOR, 1.36; 95% CI, 1.03-1.80) and when retaining patients with sepsis mimics (1.38; 1.16-1.65), but it was protective (0.48; .37-.64]) when retaining patients who received antibiotics on their last hospital day.

Conclusions

Early discontinuation of antibiotics in CNSI was not associated with significant harm in our primary analysis, but different conclusions based on alternative analytic decisions, as well as risk of residual confounding, indicate that randomized controlled trials are needed.

Hysterectomy, bilateral oophorectomy, and breast cancer risk in a racially diverse prospective cohort study

BACKGROUND

Gynecologic surgery is hypothesized to reduce risk of breast cancer; however, associations may be modified by subsequent hormone use. Our objective was to examine the association between gynecologic surgery and breast cancer incidence considering the use of hormone therapy.

METHODS

The Sister Study is a prospective cohort of initially breast cancer-free women aged 35-74 years with a sister who had breast cancer. We used Cox proportional hazards models to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) for the association between gynecologic surgery (no surgery, hysterectomy only, bilateral oophorectomy with or without hysterectomy) and incident breast cancer among 50 701 women.

RESULTS

History of gynecologic surgery was common, with 13.8% reporting hysterectomy only and 18.1% reporting bilateral oophorectomy with or without hysterectomy. During follow-up (median = 11.4 years), 3948 cases were diagnosed. Compared with no surgery, bilateral oophorectomy was inversely associated with breast cancer (HR = 0.91, 95% CI = 0.83 to 1.00), and hysterectomy alone was positively associated (HR = 1.12, 95% CI = 1.02 to 1.23). Compared with no surgery and no hormone therapy, bilateral oophorectomy combined with estrogen only therapy (HR = 0.83, 95% CI = 0.74 to 0.94) was inversely associated with breast cancer, while hysterectomy combined with estrogen plus progestin therapy was positively associated with breast cancer (HR = 1.25, 95% CI = 1.01 to 1.55).

CONCLUSIONS

We observed an inverse association between bilateral oophorectomy and breast cancer risk. The positive association between hysterectomy and breast cancer may be due to concomitant estrogen plus progestin therapy.

Key questions for the evaluation of anti-amyloid immunotherapies for Alzheimer's disease

The clinical benefit associated with anti-amyloid immunotherapies, a new class of drugs for the treatment of Alzheimer's disease, is predicated on their ability to modify disease course by lowering brain amyloid levels. At the time of writing, two amyloid-lowering antibodies, aducanumab and lecanemab, have obtained United States Food and Drug Administration accelerated approval, with further agents of this class in the Alzheimer's disease treatment pipeline. Based on limited published clinical trial data to date, regulators, payors and physicians will need to assess their efficacy, clinical effectiveness and safety, as well as cost and accessibility. We propose that attention to three important questions related to treatment efficacy, clinical effectiveness and safety should guide evidence-based consideration of this important class of drugs. These are: (1) Were trial statistical analyses appropriate and did they convincingly support claims of efficacy? (2) Do reported treatment effects outweigh safety concerns and are they generalizable to a representative clinical population of people with Alzheimer's disease? and (3) Do the data convincingly demonstrate disease course modification, suggesting that increasing clinical benefits beyond the duration of the trials are likely? We suggest specific approaches to interpreting trial results for these drugs and highlight important areas of uncertainty where additional data and a cautious interpretation of existing results is warranted. Safe, effective and accessible treatments for Alzheimer's disease are eagerly awaited by millions of patients and their caregivers worldwide. While amyloid-targeting immunotherapies may be promising disease-modifying Alzheimer's disease treatments, rigorous and unbiased assessment of clinical trial data is critical to regulatory decision-making and subsequently determining their provision and utility in routine clinical practice. Our recommendations provide a framework for evidence-based appraisal of these drugs by regulators, payors, physicians and patients.

A tiered testing strategy based on in vitro phenotypic and transcriptomic data for selecting representative petroleum UVCBs for toxicity evaluation in vivo

Hazard evaluation of substances of "unknown or variable composition, complex reaction products and biological materials" (UVCBs) remains a major challenge in regulatory science because their chemical composition is difficult to ascertain. Petroleum substances are representative UVCBs and human cell-based data have been previously used to substantiate their groupings for regulatory submissions. We hypothesized that a combination of phenotypic and transcriptomic data could be integrated to make decisions as to selection of group-representative worst-case petroleum UVCBs for subsequent toxicity evaluation in vivo. We used data obtained from 141 substances from 16 manufacturing categories previously tested in 6 human cell types (induced pluripotent stem cell [iPSC]-derived hepatocytes, cardiomyocytes, neurons, and endothelial cells, and MCF7 and A375 cell lines). Benchmark doses for gene-substance combinations were calculated, and both transcriptomic and phenotype-derived points of departure (PODs) were obtained. Correlation analysis and machine learning were used to assess associations between phenotypic and transcriptional PODs and to determine the most informative cell types and assays, thus representing a cost-effective integrated testing strategy. We found that 2 cell types-iPSC-derived-hepatocytes and -cardiomyocytes-contributed the most informative and protective PODs and may be used to inform selection of representative petroleum UVCBs for further toxicity evaluation in vivo. Overall, although the use of new approach methodologies to prioritize UVCBs has not been widely adopted, our study proposes a tiered testing strategy based on iPSC-derived hepatocytes and cardiomyocytes to inform selection of representative worst-case petroleum UVCBs from each manufacturing category for further toxicity evaluation in vivo.

Inborn errors of human IKAROS: LOF and GOF variants associated with primary immunodeficiency

IKAROS/IKZF1 plays a pivotal role in lymphocyte differentiation and development. Germline mutations in IKZF1, which have been shown to be associated with primary immunodeficiency, can be classified through four different mechanisms of action depending on the protein expression and its functional defects: haploinsufficiency, dimerization defective, dominant negative, and gain of function. These different mechanisms are associated with variable degrees of susceptibility to infectious diseases, autoimmune disorders, allergic diseases, and malignancies. To date, more than 30 heterozygous IKZF1 germline variants have been reported in patients with primary immunodeficiency. Here we review recent discoveries and clinical/immunological characterization of IKAROS-associated diseases that are linked to different mechanisms of action in IKAROS function.

Epigenetic gestational age and the relationship with developmental milestones in early childhood

Shorter gestational age (GA) is a risk factor of developmental delay. GA is usually estimated clinically from last menstrual period and ultrasound. DNA methylation (DNAm) estimates GA using sets of cytosine-guanine-sites coupled with a clock algorithm. Therefore, DNAm-estimated GA may better reflect biological maturation. A DNAm GA greater than clinical GA, known as gestational age acceleration (GAA), may indicate epigenetic maturity and holds potential as an early biomarker for developmental delay risk. We used data from the Upstate KIDS Study to examine associations of DNAm GA and developmental delay within the first 3 years based on the Ages & Stages Questionnaire® (n = 1010). We estimated DNAm GA using two clocks specific to the Illumina Methylation EPIC 850K, the Haftorn clock and one developed from the Effects of Aspirin in Gestation and Reproduction study, in which women were followed to detect pregnancy at the earliest time possible. Among singletons, each week increase in DNAm GA was protective for overall delay (odds ratio:0.74; 95% confidence interval:0.61-0.90) and delay in all domains except for problem-solving skills. Among twins, we observed similar point estimates but lower precision. Results were similar for clinical GA. GAA was largely not associated with developmental delays. In summary, either DNAm GA or clinical GA at birth, but not epigenetic maturity (i.e. GAA), was associated with decreased odds of developmental delay in early childhood. Our study does not support using DNAm GA or GAA as separate risk factors for future risk of developmental delay within the first 3 years of age.

Visual recognition in rhesus monkeys requires area TE but not TEO

The primate visual system is often described as a hierarchical feature-conjunction pathway, whereby each level represents an increasingly complex combination of image elements, culminating in the representation of whole coherent images in anterior inferior temporal cortex. Although many models of the ventral visual stream emphasize serial feedforward processing ((Poggio T, Mutch J, Leibo J, Rosasco L, Tacchetti A. The computationalmagic of the ventral stream: sketch of a theory (and why some deep architectures work). TechRep MIT-CSAIL-TR-2012-035. MIT CSAIL, Cambridge, MA. 2012); (Yamins DLK, DiCarlo JJ. Eight open questions in the computational modeling of higher sensory cortex. Curr Opin Neurobiol. 2016:37:114-120.)), anatomical studies show connections that bypass intermediate areas and that feedback to preceding areas ((Distler C, Boussaoud D, Desimone R, Ungerleider LG. Cortical connections of inferior temporal area TEO in macaque monkeys. J Comp Neurol. 1993:334(1):125-150.); (Kravitz DJ, Saleem KS, Baker CI, Mishkin M. A new neural framework for visuospatial processing. Nat Rev Neurosci. 2011:12(4):217-230.)). Prior studies on visual discrimination and object transforms also provide evidence against a strictly feed-forward serial transfer of information between adjacent areas ((Kikuchi R, Iwai E. The locus of the posterior subdivision of the inferotemporal visual learning area in the monkey. Brain Res. 1980:198(2):347-360.); (Weiskrantz L, Saunders RC. Impairments of visual object transforms in monkeys. Brain. 1984:107(4):1033-1072.); (Kar K, DiCarlo JJ. Fast recurrent processing via ventrolateral prefrontal cortex is needed by the primate ventral stream for robust Core visual object recognition. Neuron. 2021:109(1):164-176.e5.)). Thus, we sought to investigate whether behaviorally relevant propagation of visual information is as strictly sequential as sometimes supposed. We compared the accuracy of visual recognition after selective removal of specific subregions of inferior temporal cortex-area TEO, area TE, or both areas combined. Removal of TEO alone had no detectable effect on recognition memory, whereas removal of TE alone produced a large and significant impairment. Combined removal of both areas created no additional deficit relative to removal of TE alone. Thus, area TE is critical for rapid visual object recognition, and detailed image-level visual information can reach area TE via a route other than through TEO.

Associations Between Objectively Measured Sleep and Cognition: Main Effects and Interactions With Race in Adults Aged ≥50 Years

BACKGROUND

This study examined associations of actigraphy-estimated sleep parameters with concurrent and future cognitive performance in adults aged ≥ 50 years and explored interactions with race.

METHODS

Participants were 435 cognitively normal adults in the Baltimore Longitudinal Study of Aging who completed wrist actigraphy at baseline (mean = 6.6 nights) and underwent longitudinal testing of memory, attention, executive function, language, and visuospatial ability. On average, participants with follow-up data were followed for 3.1 years. Primary predictors were baseline mean total sleep time, sleep onset latency, sleep efficiency (SE), and wake after sleep onset (WASO). Fully adjusted linear mixed-effects models included demographics, baseline health-related characteristics, smoking status, sleep medication use, APOE e4 carrier status, and interactions of each covariate with time.

RESULTS

In adjusted models, higher SE (per 10%; B = 0.11, p = .012) and lower WASO (per 30 minutes; B = -0.12, p = .007) were associated with better memory cross-sectionally. In contrast, higher SE was associated with greater visuospatial ability decline longitudinally (B = -0.02, p = .004). Greater WASO was associated with poorer visuospatial ability cross-sectionally (B = -0.09, p = .019) but slower declines in visuospatial abilities longitudinally (B = 0.02, p = .002). Several sleep-cognition cross-sectional and longitudinal associations were stronger in, or limited to, Black participants (compared to White participants).

CONCLUSIONS

This study suggests cross-sectional sleep-cognition associations differ across distinct objective sleep parameters and cognitive domains. This study also provides preliminary evidence for racial differences across some sleep-cognition relationships. Unexpected directions of associations between baseline sleep and cognitive performance over time may be attributable to the significant proportion of participants without follow-up data and require further investigation.

SP7 gene silencing dampens bone marrow stromal cell hypertrophy, but it also dampens chondrogenesis

For bone marrow stromal cells (BMSC) to be useful in cartilage repair their propensity for hypertrophic differentiation must be overcome. A single day of TGF-β1 stimulation activates intrinsic signaling cascades in BMSCs which subsequently drives both chondrogenic and hypertrophic differentiation. TGF-β1 stimulation upregulates SP7, a transcription factor known to contribute to hypertrophic differentiation, and SP7 remains upregulated even if TGF-β1 is subsequently withdrawn from the chondrogenic induction medium. Herein, we stably transduced BMSCs to express an shRNA designed to silence SP7, and assess the capacity of SP7 silencing to mitigate hypertrophy. SP7 silencing dampened both hypertrophic and chondrogenic differentiation processes, resulting in diminished microtissue size, impaired glycosaminoglycan production and reduced chondrogenic and hypertrophic gene expression. Thus, while hypertrophic features were dampened by SP7 silencing, chondrogenic differentation was also compromised. We further investigated the role of SP7 in monolayer osteogenic and adipogenic cultures, finding that SP7 silencing dampened characteristic mineralization and lipid vacuole formation, respectively. Overall, SP7 silencing affects the trilineage differentiation of BMSCs, but is insufficient to decouple BMSC hypertrophy from chondrogenesis. These data highlight the challenge of promoting BMSC chondrogenesis whilst simultaneously reducing hypertrophy in cartilage tissue engineering strategies.

Life-space Mobility in Older Men: The Role of Perceived Physical and Mental Fatigability

BACKGROUND

Physical performance and fatigue can limit mobility within the larger environment (life-space mobility). It is unknown whether perceived fatigability, self-reported fatigue anchored to activity intensity and duration, is independently associated with life-space.

METHODS

We assessed this cross-sectionally in Visit 4 (2014-2016) of the Osteoporotic Fractures in Men Study (MrOS; N = 1 672, Age: Mean = 84.2 ± 4.0 years). The Pittsburgh Fatigability Scale (PFS, range: 0-50; higher = greater fatigability) measured physical (Mean = 16.1 ± 9.4) and mental fatigability (Mean = 7.5 ± 7.9). Life Space Assessment scores incorporated level, frequency, and assistance used for life-space mobility (range: 0-120, higher = greater life-space mobility; life-space constriction: inability to leave neighborhood without assistance). Separate multiple linear and logistic regressions for physical and mental fatigability were sequentially adjusted for demographic, health/lifestyle, and performance measures.

RESULTS

The mean life-space mobility score was 84.6 ± 21.8, and 18% (n = 296) of men had life-space constriction. Higher physical and mental fatigability were both associated with lower life-space mobility in models adjusted for health and lifestyle factors (Physical PFS: B = -2.37, 95% confidence interval [CI]: [-3.39, -1.35]; Mental PFS: B = -1.79, 95% CI: [-2.73, -0.84]). Men with higher fatigability also had increased risk of life-space constriction (Physical PFS: OR = 1.59, 95% CI: [1.32, 1.92]; Mental PFS: OR = 1.25, 95% CI: [1.08, 1.46]). Associations were larger in magnitude for physical versus mental fatigability. Adjusting for physical performance measures more strongly attenuated associations for physical compared to mental fatigability.

CONCLUSIONS

Fatigability is linked with real-world mobility in older men, independent of their physical health. This association may be driven by separate physical and cognitive mechanisms worth examining further in longitudinal studies.

The Estrogen Receptor α Cistrome in Human Endometrium and Epithelial Organoids

Endometrial health is affected by molecular processes that underlie estrogen responses. We assessed estrogen regulation of endometrial function by integrating the estrogen receptor α (ESR1) cistromes and transcriptomes of endometrial biopsies taken from the proliferative and mid-secretory phases of the menstrual cycle together with hormonally stimulated endometrial epithelial organoids. The cycle stage-specific ESR1 binding sites were determined by chromatin immunoprecipitation and next-generation sequencing and then integrated with changes in gene expression from RNA sequencing data to infer candidate ESR1 targets in normal endometrium. Genes with ESR1 binding in whole endometrium were enriched for chromatin modification and regulation of cell proliferation. The distribution of ESR1 binding sites in organoids was more distal from gene promoters when compared to primary endometrium and was more similar to the proliferative than the mid-secretory phase ESR1 cistrome. Inferred organoid estrogen/ESR1 candidate target genes affected formation of cellular protrusions and chromatin modification. Comparison of signaling effected by candidate ESR1 target genes in endometrium vs organoids reveals enrichment of both overlapping and distinct responses. Our analysis of the ESR1 cistromes and transcriptomes from endometrium and organoids provides important resources for understanding how estrogen affects endometrial health and function.

Recessive inborn errors of type I IFN immunity in children with COVID-19 pneumonia

Recessive or dominant inborn errors of type I interferon (IFN) immunity can underlie critical COVID-19 pneumonia in unvaccinated adults. The risk of COVID-19 pneumonia in unvaccinated children, which is much lower than in unvaccinated adults, remains unexplained. In an international cohort of 112 children (<16 yr old) hospitalized for COVID-19 pneumonia, we report 12 children (10.7%) aged 1.5-13 yr with critical (7 children), severe (3), and moderate (2) pneumonia and 4 of the 15 known clinically recessive and biochemically complete inborn errors of type I IFN immunity: X-linked recessive TLR7 deficiency (7 children) and autosomal recessive IFNAR1 (1), STAT2 (1), or TYK2 (3) deficiencies. Fibroblasts deficient for IFNAR1, STAT2, or TYK2 are highly vulnerable to SARS-CoV-2. These 15 deficiencies were not found in 1,224 children and adults with benign SARS-CoV-2 infection without pneumonia (P = 1.2 × 10-11) and with overlapping age, sex, consanguinity, and ethnicity characteristics. Recessive complete deficiencies of type I IFN immunity may underlie ∼10% of hospitalizations for COVID-19 pneumonia in children.

Abnormal urinary loss of vitamin C in diabetes: prevalence and clinical characteristics of a vitamin C renal leak

BACKGROUND

Diabetes is associated with low plasma vitamin C concentrations.

OBJECTIVES

We investigated the contribution of dysregulated vitamin C renal physiology, its prevalence, and associated clinical characteristics.

METHODS

An essential prerequisite was determination of normal vitamin C renal threshold, the plasma concentration at which vitamin C first appears in urine. Using data from 17 healthy participants who underwent vitamin C depletion-repletion studies with a vitamin C dose range of 15-1250 mg daily, renal threshold was estimated using physiology-based pharmacokinetics modeling. Applying renal threshold 95% CIs, we estimated the minimal elimination threshold, the plasma concentration below which no vitamin C was expected in urine of healthy people. Renal leak was defined as abnormal presence of vitamin C in urine with plasma concentrations below the minimal elimination threshold. Criteria were tested in a cross-sectional cohort study of individuals with diabetes (82) and nondiabetic controls (80) using matched plasma and urine samples.

RESULTS

Vitamin C renal thresholds in healthy men and women were [mean (SD)] 48.5 (5.2) µM and 58.3 (7.5) µM, respectively. Compared with nondiabetic controls, participants with diabetes had significantly higher prevalence of vitamin C renal leak (9% compared with 33%; OR: 5.07; 95% CI: 1.97, 14.83; P < 0.001) and 30% lower mean plasma vitamin C concentrations (53.1 µM compared with 40.9 µM, P < 0.001). Fasting plasma glucose, glycosylated hemoglobin A1c, BMI, micro/macrovascular complications, and protein/creatinine ratio were predictive of vitamin C renal leak.

CONCLUSIONS

Increased prevalence of vitamin C renal leak in diabetes is associated with reduced plasma vitamin C concentrations. Glycemic control, microvascular complications, obesity, and proteinuria are predictive of renal leak.

Graft-Versus-Solid-Tumor Effect: From Hematopoietic Stem Cell Transplantation to Adoptive Cell Therapies

After allogeneic hematopoietic stem cell transplantation (HSCT), donor lymphocytes may contribute to the regression of hematological malignancies and select solid tumors, a phenomenon referred to as the graft-versus-tumor effect (GVT). However, this immunologic reaction is frequently limited by either poor specificity resulting in graft-versus-host disease or the frequency of tumor-specific T cells being too low to induce a complete and sustained anti-tumor response. Over the past 2 decades, it has become clear that the driver of GVT following allogeneic HSCT is T-cell-mediated recognition of antigens presented on tumor cells. With that regard, even though the excitement for using HSCT in solid tumors has declined, clinical trials of HSCT in solid tumors provided proof of concept and valuable insights leading to the discovery of tumor antigens and the development of targeted adoptive cell therapies for cancer. In this article, we review the results of clinical trials of allogeneic HSCT in solid tumors. We focus on lessons learned from correlative studies of these trials that hold the potential for the creation of tumor-specific immunotherapies with greater efficacy and safety for the treatment of malignancies.

Lung function impairment and risk of incident heart failure: the NHLBI Pooled Cohorts Study

AIMS

The aim is to evaluate associations of lung function impairment with risk of incident heart failure (HF).

METHODS AND RESULTS

Data were pooled across eight US population-based cohorts that enrolled participants from 1987 to 2004. Participants with self-reported baseline cardiovascular disease were excluded. Spirometry was used to define obstructive [forced expiratory volume in 1 s/forced vital capacity (FEV1/FVC) <0.70] or restrictive (FEV1/FVC ≥0.70, FVC <80%) lung physiology. The incident HF was defined as hospitalization or death caused by HF. In a sub-set, HF events were sub-classified as HF with reduced ejection fraction (HFrEF; EF <50%) or preserved EF (HFpEF; EF ≥50%). The Fine-Gray proportional sub-distribution hazards models were adjusted for sociodemographic factors, smoking, and cardiovascular risk factors. In models of incident HF sub-types, HFrEF, HFpEF, and non-HF mortality were treated as competing risks. Among 31 677 adults, there were 3344 incident HF events over a median follow-up of 21.0 years. Of 2066 classifiable HF events, 1030 were classified as HFrEF and 1036 as HFpEF. Obstructive [adjusted hazard ratio (HR) 1.17, 95% confidence interval (CI) 1.07-1.27] and restrictive physiology (adjusted HR 1.43, 95% CI 1.27-1.62) were associated with incident HF. Obstructive and restrictive ventilatory defects were associated with HFpEF but not HFrEF. The magnitude of the association between restrictive physiology and HFpEF was similar to associations with hypertension, diabetes, and smoking.

CONCLUSION

Lung function impairment was associated with increased risk of incident HF, and particularly incident HFpEF, independent of and to a similar extent as major known cardiovascular risk factors.