SARS-CoV-2 genotyping and sequencing following a simple and economical RNA extraction and storage protocol

Since the beginning of the SARS-CoV-2 pandemic, supply chain shortages have caused major disruptions in sourcing the materials needed for laboratory-based molecular assays. With increasing demand for molecular testing, these disruptions have limited testing capacity and hindered efforts to mitigate spread of the virus and new variants. Here we evaluate an economical and reliable protocol for the extraction and short-term ambient temperature storage of SARS-CoV-2 RNA. Additional objectives of the study were to evaluate RNA from this protocol for 1) detection of single nucleotide polymorphisms (SNPs) in the spike gene and 2) whole genome sequencing of SARS-CoV-2. The RNAES protocol was evaluated with residual nasopharyngeal (NP) samples collected from Emory Healthcare and Emory Student Health services. All RNAES extractions were performed in duplicate and once with a commercial extraction robot for comparison. Following extraction, eluates were immediately tested by rRT-PCR. SARS-CoV-2 RNA was successfully detected in 56/60 (93.3%) RNAES replicates, and Ct values corresponded with comparator results. Upon testing in spike SNP assays, three genotypes were identified, and all variant calls were consistent with those previously obtained after commercial extraction. Additionally, the SARS-RNAES protocol yield eluate pure enough for downstream whole genome sequencing, and results were consistent with SARS-CoV-2 whole genome sequencing of eluates matched for Ct value. With reproducible results across a range of virus concentrations, the SARS-RNAES protocol could help increase SARS-CoV-2 diagnostic testing and monitoring for emerging variants in resource-constrained communities.

Defining the spatial landscape of KRAS mutated congenital pulmonary airway malformations: a distinct entity with a spectrum of histopathologic features

The potential pathogenetic mechanisms underlying the varied morphology of congenital pulmonary airway malformations (CPAMs) have not been molecularly determined, but a subset have been shown to contain clusters of mucinous cells (MCC). These clusters are believed to serve as precursors for potential invasive mucinous adenocarcinoma, and they are associated with KRAS codon 12 mutations. To assess the universality of KRAS mutations in MCCs, we sequenced exon 2 of KRAS in 61 MCCs from 18 patients, and we found a KRAS codon 12 mutation in all 61 MCCs. Furthermore, all MCCs from a single patient always had the same KRAS mutation, and the same KRAS mutation was also found in non-mucinous lesional tissue. Next generation sequencing of seven MCCs showed no other mutations or copy number variations. Sequencing of 46 additional CPAMs with MCCs revealed KRAS mutations in non-mucinous lesional tissue in all cases. RNA in situ hybridization confirmed widespread distribution of cells with mutant KRAS RNA, even extending outside of the bronchiolar type epithelium. We identified 25 additional CPAMs with overall histologic architecture similar to CPAMs with KRAS mutations but without identifiable MCCs, and we found KRAS mutations in 17 (68%). The histologic features of these KRAS mutated CPAMs included type 1 and type 3 morphology, as well as lesions with an intermediate histologic appearance, and analysis revealed a strong correlation between the specific amino acid substitution and histomorphology. These findings, together with previously published model organism data, suggests that the formation of type 1 and 3 CPAMs is driven by mosaic KRAS mutations arising in the lung epithelium early in development and places them within the growing field of mosaic RASopathies. The presence of widespread epithelial mutation explains late metastatic disease in incompletely resected patients and reinforces the recommendation for complete resection of these lesions.

Persistence of β-Cell Responsiveness for Over Two Years in Autoantibody-Positive Children With Marked Metabolic Impairment at Screening

OBJECTIVE

We studied longitudinal differences between progressors and nonprogressors to type 1 diabetes with similar and substantial baseline risk.

RESEARCH DESIGN AND METHODS

Changes in 2-h oral glucose tolerance test indices were used to examine variability in diabetes progression in the Diabetes Prevention Trial-Type 1 (DPT-1) study (n = 246) and Type 1 Diabetes TrialNet Pathway to Prevention study (TNPTP) (n = 503) among autoantibody (Ab)+ children (aged <18.0 years) with similar baseline metabolic impairment (DPT-1 Risk Score [DPTRS] of 6.5-7.5), as well as in TNPTP Ab- children (n = 94).

RESULTS

Longitudinal analyses revealed annualized area under the curve (AUC) of C-peptide increases in nonprogressors versus decreases in progressors (P ≤ 0.026 for DPT-1 and TNPTP). Vector indices for AUC glucose and AUC C-peptide changes (on a two-dimensional grid) also differed significantly (P < 0.001). Despite marked baseline metabolic impairment of nonprogressors, changes in AUC C-peptide, AUC glucose, AUC C-peptide-to-AUC glucose ratio (AUC ratio), and Index60 did not differ from Ab- relatives during follow-up. Divergence between nonprogressors and progressors occurred by 6 months from baseline in both cohorts (AUC glucose, P ≤ 0.007; AUC ratio, P ≤ 0.034; Index60, P < 0.001; vector indices of change, P < 0.001). Differences in 6-month change were positively associated with greater diabetes risk (respectively, P < 0.001, P ≤ 0.019, P < 0.001, and P < 0.001) in DPT-1 and TNPTP, except AUC ratio, which was inversely associated with risk (P < 0.001).

CONCLUSIONS

Novel findings show that even with similarly abnormal baseline risk, progressors had appreciably more metabolic impairment than nonprogressors within 6 months and that the measures showing impairment were predictive of type 1 diabetes. Longitudinal metabolic patterns did not differ between nonprogressors and Ab- relatives, suggesting persistent β-cell responsiveness in nonprogressors.

The origins of skin diversity: lessons from dermal fibroblasts

Skin is largely composed of an epidermis that overlies a supporting dermis. Recent advancements in our understanding of how diverse groups of dermal fibroblasts regulate epidermal and hair follicle growth and differentiation have been fueled by tools capable of resolving molecular heterogeneity at a single-cell level. Fibroblast heterogeneity can be traced back to their developmental origin before their segregation into spatially distinct fibroblast subtypes. The mechanisms that drive this lineage diversification during development are being unraveled, with studies showing that both large- and small-scale positional signals play important roles during dermal development. Here, we first delineate what is known about the origins of the dermis and the central role of Wnt/β-catenin signaling in its specification across anatomical locations. We then discuss how one of the first morphologically recognizable fibroblast subtypes, the hair follicle dermal condensate lineage, emerges. Leveraging the natural variation of skin and its appendages between species and between different anatomical locations, these collective studies have identified shared and divergent factors that contribute to the extraordinary diversity of skin.

Fibromuscular Dysplasia and Abdominal Aortic Aneurysms Are Dimorphic Sex-Specific Diseases With Shared Complex Genetic Architecture

BACKGROUND

The risk of arterial diseases may be elevated among family members of individuals having multifocal fibromuscular dysplasia (FMD). We sought to investigate the risk of arterial diseases in families of individuals with FMD.

METHODS

Family histories for 73 probands with FMD were obtained, which included an analysis of 463 total first-degree relatives focusing on FMD and related arterial disorders. A polygenic risk score for FMD (PRSFMD) was constructed from prior genome-wide association findings of 584 FMD cases and 7139 controls and evaluated for association with an abdominal aortic aneurysm (AAA) in a cohort of 9693 AAA cases and 294 049 controls. A previously published PRSAAA was also assessed among the FMD cases and controls.

RESULTS

Of all first degree relatives of probands, 9.3% were diagnosed with FMD, aneurysms, and dissections. Aneurysmal disease occurred in 60.5% of affected relatives and 5.6% of all relatives. Among 227 female first-degree relatives of probands, 4.8% (11) had FMD, representing a relative risk (RR)FMD of 1.5 ([95% CI, 0.75-2.8]; P=0.19) compared with the estimated population prevalence of 3.3%, though not of statistical significance. Of all fathers of FMD probands, 11% had AAAs resulting in a RRAAA of 2.3 ([95% CI, 1.12-4.6]; P=0.014) compared with population estimates. The PRSFMD was found to be associated with an AAA (odds ratio, 1.03 [95% CI, 1.01-1.05]; P=2.6×10-3), and the PRSAAA was found to be associated with FMD (odds ratio, 1.53 [95% CI, 1.2-1.9]; P=9.0×10-5) as well.

CONCLUSIONS

FMD and AAAs seem to be sex-dimorphic manifestations of a heritable arterial disease with a partially shared complex genetic architecture. Excess risk of having an AAA according to a family history of FMD may justify screening in family members of individuals having FMD.

Utility of plasma beta-hydroxybutyrate to define resolution of diabetic ketoacidosis

BACKGROUND

Diabetic ketoacidosis (DKA) is a common, life-threatening complication of type 1 diabetes (T1D) characterized by unregulated ketogenesis caused by relative or absolute insulin deficiency. DKA management requires frequent biochemical monitoring. Plasma ß-hydroxybutyrate (BOHB) has not been included in traditional definitions of DKA resolution.

OBJECTIVE

The aim of this study was to determine a cut-point level of BOHB to define DKA resolution in patients with T1D treated with intravenous (IV) insulin.

SUBJECTS

We identified patients with T1D receiving IV insulin for DKA treatment at a quaternary children's hospital from January 1, 2017 through December 31, 2020 who had plasma measurements of BOHB after DKA onset and whose DKA resolved by traditional laboratory criteria (venous pH (vpH) ≥ 7.3, serum bicarbonate (HCO3 ) ≥ 15 mmol/L, and/or anion gap (AG) ≤ 14 mmol/L).

METHODS

Associations between plasma BOHB and vpH, HCO3 , and AG were evaluated via scatterplots. Receiver operating characteristic (ROC) curves and area under the curve (AUC) were used to evaluate BOHB cut-points to predict DKA resolution.

RESULTS

We analyzed 403 patients with 471 unique encounters. Plasma BOHB showed the most robust relationship with AG. The ROC curve comparing plasma BOHB to the accepted definition of DKA resolution, AG ≤14 mmol/L, had an AUC of 0.92. A BOHB value of <1.5 mmol/L had a sensitivity of 83% and specificity of 87%; this cut-point correctly classified 86% of the observations.

CONCLUSIONS

A plasma BOHB value of <1.5 mmol/L can be used to define resolution of DKA.

Adverse childhood experiences and binge-eating disorder in early adolescents

BACKGROUND

Adverse childhood experiences (ACEs) are common and linked to negative health outcomes. Previous studies have found associations between ACEs and binge-eating disorder (BED), though they have mainly focused on adults and use cross-sectional data. The objective of this study was to examine the associations between ACEs and BED in a large, national cohort of 9-14-year-old early adolescents in the US.

METHODS

We analyzed prospective cohort data from the Adolescent Brain Cognitive Development (ABCD) Study (N = 10,145, 2016-2020). Logistic regression analyses were used to determine the associations between self-reported ACEs and BED based on the Kiddie Schedule for Affective Disorders and Schizophrenia at two-year follow-up, adjusting for sex, race/ethnicity, baseline household income, parental education, site, and baseline binge-eating disorder.

RESULTS

In the sample, (49% female, 46% racial/ethnic minority), 82.8% of adolescents reported at least one ACE and 1.2% had a diagnosis of BED at two-year follow-up. The mean number of ACEs was higher in those with a diagnosis of BED compared to those without (2.6 ± 0.14 vs 1.7 ± 0.02). The association between number of ACEs and BED in general had a dose-response relationship. One ACE (adjusted odds ratio [aOR] 3.48, 95% confidence interval [CI] 1.11-10.89), two ACEs (aOR 3.88, 95% CI 1.28-11.74), and three or more ACEs (aOR 8.94, 95% CI 3.01-26.54) were all associated with higher odds of BED at two-year follow-up. When stratified by types of ACEs, history of household mental illness (aOR 2.18, 95% 1.31-3.63), household violence (aOR 2.43, 95% CI 1.42-4.15), and criminal household member (aOR 2.14, 95% CI 1.23-3.73) were most associated with BED at two-year follow-up.

CONCLUSIONS

Children and adolescents who have experienced ACEs, particularly household challenges, have higher odds of developing BED. Clinicians may consider screening for ACEs and providing trauma-focused care when evaluating patients for BED.

Diagnostic accuracy of handheld fundus photography: A comparative study of three commercially available cameras

The objective of this study was to compare the sensitivity and specificity of handheld fundus cameras in detecting diabetic retinopathy (DR), diabetic macular edema (DME), and macular degeneration. Participants in the study, conducted at Maharaj Nakorn Hospital in Northern Thailand between September 2018 and May 2019, underwent an ophthalmologist examination as well as mydriatic fundus photography with three handheld fundus cameras (iNview, Peek Retina, Pictor Plus). Photographs were graded and adjudicated by masked ophthalmologists. Outcome measures included the sensitivity and specificity of each fundus camera for detecting DR, DME, and macular degeneration, relative to ophthalmologist examination. Fundus photographs of 355 eyes from 185 participants were captured with each of the three retinal cameras. Of the 355 eyes, 102 had DR, 71 had DME, and 89 had macular degeneration on ophthalmologist examination. The Pictor Plus was the most sensitive camera for each of the diseases (73-77%) and also achieved relatively high specificity (77-91%). The Peek Retina was the most specific (96-99%), although in part due to its low sensitivity (6-18%). The iNview had slightly lower estimates of sensitivity (55-72%) and specificity (86-90%) compared to the Pictor Plus. These findings demonstrated that the handheld cameras achieved high specificity but variable sensitivities in detecting DR, DME, and macular degeneration. The Pictor Plus, iNview, and Peek Retina would have distinct advantages and disadvantages when applied for utilization in tele-ophthalmology retinal screening programs.

Longitudinal Immune Cell Profiling in Patients With Early Systemic Lupus Erythematosus

OBJECTIVES

To investigate the immune cell profiles of patients with systemic lupus erythematosus (SLE), and to identify longitudinal changes in those profiles over time.

METHODS

We employed mass cytometry with 3 different panels of 38-39 markers (an immunophenotyping panel, a T cell/monocyte panel, and a B cell panel) in cryopreserved peripheral blood mononuclear cells (PBMCs) from 9 patients with early SLE, 15 patients with established SLE, and 14 controls without autoimmune disease. We used machine learning-driven clustering, flow self-organizing maps, and dimensional reduction with t-distributed stochastic neighbor embedding to identify unique cell populations in early SLE and established SLE. We used mass cytometry data of PBMCs from 19 patients with early rheumatoid arthritis (RA) and 23 controls to compare levels of specific cell populations in early RA and SLE. For the 9 patients with early SLE, longitudinal mass cytometry analysis was applied to PBMCs at enrollment, 6 months after enrollment, and 1 year after enrollment. Serum samples were also assayed for 65 cytokines using Luminex multiplex assay, and associations between cell types and cytokines/chemokines were assessed.

RESULTS

Levels of peripheral helper T cells, follicular helper T (Tfh) cells, and several Ki-67+ proliferating subsets (ICOS+Ki-67+ CD8 T cells, Ki-67+ regulatory T cells, CD19intermediate Ki-67high plasmablasts, and PU.1high Ki-67high monocytes) were increased in patients with early SLE, with more prominent alterations than were seen in patients with early RA. Longitudinal mass cytometry and multiplex serum cytokine assays of samples from patients with early SLE revealed that levels of Tfh cells and CXCL10 had decreased 1 year after enrollment. Levels of CXCL13 were positively correlated with levels of several of the expanded cell populations in early SLE.

CONCLUSION

Two major helper T cell subsets and unique Ki-67+ proliferating immune cell subsets were expanded in patients in the early phase of SLE, and the immunologic features characteristic of early SLE evolved over time.

Cardiac microstructural alterations measured by echocardiography identify sex-specific risk for heart failure

OBJECTIVE

Established preclinical imaging assessments of heart failure (HF) risk are based on macrostructural cardiac remodelling. Given that microstructural alterations may also influence HF risk, particularly in women, we examined associations between microstructural alterations and incident HF.

METHODS

We studied N=2511 adult participants (mean age 65.7±8.8 years, 56% women) of the Framingham Offspring Study who were free of cardiovascular disease at baseline. We employed texture analysis of echocardiography to quantify microstructural alteration, based on the high spectrum signal intensity coefficient (HS-SIC). We examined its relations to incident HF in sex-pooled and sex-specific Cox models accounting for traditional HF risk factors and macrostructural alterations.

RESULTS

We observed 94 new HF events over 7.4±1.7 years. Individuals with higher HS-SIC had increased risk for incident HF (HR 1.67 per 1-SD in HS-SIC, 95% CI 1.31 to 2.13; p<0.0001). Adjusting for age and antihypertensive medication use, this association was significant in women (p=0.02) but not men (p=0.78). Adjusting for traditional risk factors (including body mass index, total/high-density lipoprotein cholesterol, blood pressure traits, diabetes and smoking) attenuated the association in women (HR 1.30, p=0.07), with mediation of HF risk by the HS-SIC seen for a majority of these risk factors. However, the HS-SIC association with HF in women remained significant after adjusting for relative wall thickness (representing macrostructure alteration) in addition to these risk factors (HR 1.47, p=0.02).

CONCLUSIONS

Cardiac microstructural alterations are associated with elevated risk for HF, particularly in women. Microstructural alteration may identify sex-specific pathways by which individuals progress from risk factors to clinical HF.

Health professionals' readiness to implement electronic medical recording system and associated factors in public general hospitals of Sidama region, Ethiopia

BACKGROUND

Electronic medical recording system is one of the information technologies that has a proven benefit to improve the quality of health service. Readiness assessment is one of the recommended steps to be taken prior to implementing electronic medical recording system to reduce the probability of failure.

OBJECTIVE

To determine the level of health professional readiness to implement Electronic medical recording system and associated factors in public general hospitals of Sidama region, 2022.

METHODOLOGY

A cross-sectional study design complemented with qualitative study was employed at three public general hospitals in Sidama region on a sample of 306 participants. A pretested self-administered questionnaire was used to collect quantitative data and in-depth interview was used for the qualitative study. Bivariate and multivariate Binary logistics regression was performed to determine predictors of readiness at α = 0.05, using an odds ratio and 95% confidence interval. Thematic analysis was done for qualitative data collected through in-depth interview.

RESULT

The overall readiness for health professionals was 36.5%. Of the study participants, 201 (73.4%) were computer literate, 176(64.23%) had good knowledge, and 204 (74.45%) had favorable attitude towards EMR. Only 31 participants had previous training (11.3%), while 64 (23%) had previous experience. EMR knowledge (AOR = 3.332; 95%CI: (1.662, 6.682)) and attitude towards electronic medical recording (AOR = 2.432; 95%CI: (1.146, 5.159)) were statistically significant predictors of readiness to implement electronic medical recording. Qualitative analysis has revealed lack of training, ease of use concerns, information security concerns, and perceived inadequacy of infrastructures including internet connectivity and electricity as common barriers for health professional readiness to implement EMR.

CONCLUSION

Health professionals' readiness in this study was low. Capacity building efforts to increase the awareness and skills of health professionals should be done before implementing the system.

Cardiovascular and hepatic disease associations by magnetic resonance imaging: A retrospective cohort study

Background

Hepatic disease is linked to cardiovascular events but the independent association between hepatic and cardiovascular disease remains unclear, given shared risk factors.

Methods

This was a retrospective study of consecutive patients with a clinical cardiac MRI (CMR) and a serological marker of hepatic fibrosis, the FIB-4 score, within one year of clinical imaging. We assessed the relations between FIB-4 scores grouped based on prior literature: low (< 1.3), moderate (1.3–3.25), and high (>3.25), and abnormalities detected by comprehensive CMR grouped into 4 domains: cardiac structure (end diastolic volumes, atrial dimensions, wall thickness); cardiac function (ejection fractions, wall motion abnormalities, cardiac output); vascular structure (ascending aortic and pulmonary arterial sizes); and cardiac composition (late gadolinium enhancement, T1 and T2 times). We used Poisson regression to examine the association between the conventionally defined FIB-4 category (low <1.3, moderate 1.3–3.25, and high >3.25) and any CMR abnormality while adjusting for demographics and traditional cardiovascular risk factors.

Results

Of the 1668 patients studied (mean age: 55.971 ± 7.28, 901 [54%] male), 85.9% had ≥1 cardiac abnormality with increasing prevalence seen within the low (82.0%) to moderate (88.8%) to high (92.3%) FIB-4 categories. Multivariable analyses demonstrated the presence of any cardiac abnormality was significantly associated with having a high-range FIB-4 (prevalence ratio 1.07, 95% CI: 1.01–1.13); notably, the presence of functional cardiac abnormalities were associated with being in the high FIB-4 range (1.41, 1.21–1.65) and any vascular abnormalities with being in the moderate FIB-4 range (1.22, 1.01–1.47).

Conclusions

Elevated FIB-4 was associated with cardiac functional and vascular abnormalities even after adjustment for shared risk factors in a cohort of patients with clinically referred CMR. These CMR findings indicate that cardiovascular abnormalities exist in the presence of subclinical hepatic fibrosis, irrespective of shared risk factors, underscoring the need for further studies of the heart-liver axis.

Clinical implementation of artificial intelligence in neuroradiology with development of a novel workflow-efficient picture archiving and communication system-based automated brain tumor segmentation and radiomic feature extraction

Purpose

Personalized interpretation of medical images is critical for optimum patient care, but current tools available to physicians to perform quantitative analysis of patient’s medical images in real time are significantly limited. In this work, we describe a novel platform within PACS for volumetric analysis of images and thus development of large expert annotated datasets in parallel with radiologist performing the reading that are critically needed for development of clinically meaningful AI algorithms. Specifically, we implemented a deep learning-based algorithm for automated brain tumor segmentation and radiomics extraction, and embedded it into PACS to accelerate a supervised, end-to- end workflow for image annotation and radiomic feature extraction.

Materials and methods

An algorithm was trained to segment whole primary brain tumors on FLAIR images from multi-institutional glioma BraTS 2021 dataset. Algorithm was validated using internal dataset from Yale New Haven Health (YHHH) and compared (by Dice similarity coefficient [DSC]) to radiologist manual segmentation. A UNETR deep-learning was embedded into Visage 7 (Visage Imaging, Inc., San Diego, CA, United States) diagnostic workstation. The automatically segmented brain tumor was pliable for manual modification. PyRadiomics (Harvard Medical School, Boston, MA) was natively embedded into Visage 7 for feature extraction from the brain tumor segmentations.

Results

UNETR brain tumor segmentation took on average 4 s and the median DSC was 86%, which is similar to published literature but lower than the RSNA ASNR MICCAI BRATS challenge 2021. Finally, extraction of 106 radiomic features within PACS took on average 5.8 ± 0.01 s. The extracted radiomic features did not vary over time of extraction or whether they were extracted within PACS or outside of PACS. The ability to perform segmentation and feature extraction before radiologist opens the study was made available in the workflow. Opening the study in PACS, allows the radiologists to verify the segmentation and thus annotate the study.

Conclusion

Integration of image processing algorithms for tumor auto-segmentation and feature extraction into PACS allows curation of large datasets of annotated medical images and can accelerate translation of research into development of personalized medicine applications in the clinic. The ability to use familiar clinical tools to revise the AI segmentations and natively embedding the segmentation and radiomic feature extraction tools on the diagnostic workstation accelerates the process to generate ground-truth data.

Drivers of variation in telemedicine use during the COVID-19 pandemic: The experience of a large academic cardiovascular practice

BACKGROUND

COVID-19 spurred rapid adoption and expansion of telemedicine. We investigated the factors driving visit modality (telemedicine vs. in-person) for outpatient visits at a large cardiovascular center.

METHODS

We used electronic health record data from March 2020 to February 2021 from four cardiology subspecialties (general cardiology, electrophysiology, heart failure, and interventional cardiology) at a large academic health system in Northern California. There were 21,912 new and return visits with 69% delivered by telemedicine. We used hierarchical logistic regression and cross-validation methods to estimate the variation in visit modality explained by patient, clinician, and visit factors as measured by the mean area under the curve.

RESULTS

Across all subspecialties, the clinician seen was the strongest predictor of telemedicine usage, while primary visit diagnosis was the next most predictive. In general cardiology, the model based on clinician seen had a mean area under the curve of 0.83, the model based on the primary diagnosis had a mean area under the curve of 0.69, and the model based on all patient characteristics combined had a mean area under the curve of 0.56. There was significant variation in telemedicine use across clinicians within each subspecialty, even for visits with the same primary visit diagnosis.

CONCLUSION

Individual clinician practice patterns had the largest influence on visit modality across subspecialties in a large cardiovascular medicine practice, while primary diagnosis was less predictive, and patient characteristics even less so. Cardiovascular clinics should reduce variability in visit modality selection through standardized processes that integrate clinical factors and patient preference.

Gut dysbiosis and inflammatory blood markers precede HIV with limited changes after early seroconversion

BACKGROUND

Alterations in the gut microbiome have been associated with HIV infection, but the relative impact of HIV versus other factors on the gut microbiome has been difficult to determine in cross-sectional studies.

METHODS

To address this, we examined the gut microbiome, serum metabolome, and cytokines longitudinally within 27 individuals before and during acute HIV using samples collected from several ongoing cohort studies. Matched control participants (n=28) from the same cohort studies without HIV but at similar behavioral risk were used for comparison.

FINDINGS

We identified few changes in the microbiome during acute HIV infection, but did find alterations in serum metabolites involving secondary bile acid (lithocholate sulfate, glycocholenate sulfate) and amino acid metabolism (3-methyl-2-oxovalerate, serine, cysteine, N-acetylputrescine). Greater microbiome differences, including decreased Bacteroides spp and increased Megasphaera elsdenii, were seen when comparing pre-HIV infection visits to matched at-risk controls. Those who acquired HIV also had elevated inflammatory cytokines (TNF-α, B cell activating factor, IL-8) and bioactive lipids (palmitoyl-sphingosine-phosphoethanolamide and glycerophosphoinositol) prior to HIV acquisition compared to matched controls.

INTERPRETATION

Longitudinal sampling identified pre-existing microbiome differences in participants with acute HIV compared to matched control participants observed over the same period. These data highlight the importance of increasing understanding of the role of the microbiome in HIV susceptibility.

FUNDING

This work was supported by NIH/NIAID (K08AI124979; P30AI117943), NIH/NIDA (U01DA036267; U01DA036939; U01DA036926; U24DA044554), and NIH/NIMH (P30MH058107; R34MH105272).

A Practical Guide to Genetic Testing for Kidney Disorders of Unknown Etiology

Genetic testing is increasingly used in the workup and diagnosis of kidney disease and kidney-related disorders of undetermined cause. Out-of-pocket costs for clinical genetic testing have become affordable, and logistical hurdles overcome. The interest in genetic testing may stem from the need to make or confirm a diagnosis, guide management, or the patient's desire to have a more informed explanation or prognosis. This poses a challenge for providers who do not have formal training in the selection, interpretation, and limitations of genetic tests. In this manuscript, we provide detailed discussion of relevant cases in which clinical genetic testing using a kidney gene panel was applied. The cases demonstrate identification of pathogenic variants for monogenic diseases-contrasting them from genetic risk alleles-and bring up diagnostic limitations and diagnostic utility of these tests in nephrology. This review aims to guide clinicians in formulating pretest conversations with their patients, interpreting genetic variant nomenclature, and considering follow-up investigations. Although providers are gaining experience, there is still risk of testing causing more anxiety than benefit. However, with provider education and support, clinical genetic testing applied to otherwise unexplained kidney-related disorders will increasingly serve as a valuable diagnostic tool with the potential to reshape how we consider and treat many kidney-related diagnoses.

Islet primary cilia motility controls insulin secretion

Primary cilia are specialized cell-surface organelles that mediate sensory perception and, in contrast to motile cilia and flagella, are thought to lack motility function. Here, we show that primary cilia in human and mouse pancreatic islets exhibit movement that is required for glucose-dependent insulin secretion. Islet primary cilia contain motor proteins conserved from those found in classic motile cilia, and their three-dimensional motion is dynein-driven and dependent on adenosine 5'-triphosphate and glucose metabolism. Inhibition of cilia motion blocks beta cell calcium influx and insulin secretion. Human beta cells have enriched ciliary gene expression, and motile cilia genes are altered in type 2 diabetes. Our findings redefine primary cilia as dynamic structures having both sensory and motile function and establish that pancreatic islet cilia movement plays a regulatory role in insulin secretion.

Why maternal continuum of care remains low in Northwest Ethiopia? A multilevel logistic regression analysis

BACKGROUND

Non-adherence to the maternal continuum of care remains a significant challenge. Though early initiation and continuum of care are recommended for mothers' and newborns' well-being, there is a paucity of evidence that clarify this condition in resource-limited settings. This study aimed to assess the level of women's completion of the maternal continuum of care and factors affecting it in Northwest Ethiopia.

METHODS

A community-based cross-sectional study was conducted from October to November, 2020. Data were collected from 811 women who had a recent history of birth within the past one year. The random and fixed effects were reported using an adjusted odds ratio with a 95% confidence interval. The p-value of 0.05 was used to declare significantly associated factors with women's completion of the maternal continuum of care.

RESULTS

The study revealed that 6.9% (95%CI: 5.3-8.9%) of women were retained fully on the continuum of maternal care, while 7.89% of women did not receive any care from the existing healthcare system. Attending secondary and above education (AOR = 3.15; 95%CI: 1.25,7.89), membership in the women's development army (AOR = 2.91; 95%CI: 1.56,5.44); being insured (AOR = 2.59; 95%CI: 1.33,5.01); getting health education (AOR = 2.44; 95%CI: 1.33,4.45); short distance to health facility (AOR = 4.81; 95%CI: 1.55,14.95); and mass-media exposure (AOR = 2.39; 95%CI: 1.11,5.15) were significantly associated with maternal continuum of care.

CONCLUSIONS

The maternal continuum of care is low in rural northwest Ethiopia compared to findings from most resource-limited settings. Therefore, the existing health system should consider multilevel intervention strategies that focus on providing maternal health education, facilitating insurance mechanisms, encouraging women's participation in health clubs, and ensuring physical accessibility to healthcare facilities to be more effective in improving maternal health services.

Secretory Cells Are the Primary Source of pIgR in Small Airways

Loss of secretory IgA (SIgA) is common in chronic obstructive pulmonary disease (COPD) small airways and likely contributes to disease progression. We hypothesized that loss of SIgA results from reduced expression of pIgR (polymeric immunoglobulin receptor), a chaperone protein needed for SIgA transcytosis, in the COPD small airway epithelium. pIgR-expressing cells were defined and quantified at single-cell resolution in human airways using RNA in situ hybridization, immunostaining, and single-cell RNA sequencing. Complementary studies in mice used immunostaining, primary murine tracheal epithelial cell culture, and transgenic mice with secretory or ciliated cell-specific knockout of pIgR. SIgA degradation by human neutrophil elastase or secreted bacterial proteases from nontypeable Haemophilus influenzae was evaluated in vitro. We found that secretory cells are the predominant cell type responsible for pIgR expression in human and murine airways. Loss of SIgA in small airways was not associated with a reduction in secretory cells but rather a reduction in pIgR protein expression despite intact PIGR mRNA expression. Neutrophil elastase and nontypeable H. influenzae-secreted proteases are both capable of degrading SIgA in vitro and may also contribute to a deficient SIgA immunobarrier in COPD. Loss of the SIgA immunobarrier in small airways of patients with severe COPD is complex and likely results from both pIgR-dependent defects in IgA transcytosis and SIgA degradation.

Thromboxane-Prostanoid Receptor Signaling Drives Persistent Fibroblast Activation in Pulmonary Fibrosis

Rationale: Although persistent fibroblast activation is a hallmark of idiopathic pulmonary fibrosis (IPF), mechanisms regulating persistent fibroblast activation in the lungs have not been fully elucidated. Objectives: On the basis of our observation that lung fibroblasts express TBXA2R (thromboxane-prostanoid receptor) during fibrosis, we investigated the role of TBXA2R signaling in fibrotic remodeling. Methods: We identified TBXA2R expression in lungs of patients with IPF and mice and studied primary mouse and human lung fibroblasts to determine the impact of TBXA2R signaling on fibroblast activation. We used TBXA2R-deficient mice and small-molecule inhibitors to investigate TBXA2R signaling in preclinical lung fibrosis models. Measurements and Main Results: TBXA2R expression was upregulated in fibroblasts in the lungs of patients with IPF and in mouse lungs during experimental lung fibrosis. Genetic deletion of TBXA2R, but not inhibition of thromboxane synthase, protected mice from bleomycin-induced lung fibrosis, thereby suggesting that an alternative ligand activates profibrotic TBXA2R signaling. In contrast to thromboxane, F2-isoprostanes, which are nonenzymatic products of arachidonic acid induced by reactive oxygen species, were persistently elevated during fibrosis. F2-isoprostanes induced TBXA2R signaling in fibroblasts and mediated a myofibroblast activation profile due, at least in part, to potentiation of TGF-β (transforming growth factor-β) signaling. In vivo treatment with the TBXA2R antagonist ifetroban reduced profibrotic signaling in the lungs, protected mice from lung fibrosis in three preclinical models (bleomycin, Hermansky-Pudlak mice, and radiation-induced fibrosis), and markedly enhanced fibrotic resolution after bleomycin treatment. Conclusions: TBXA2R links oxidative stress to fibroblast activation during lung fibrosis. TBXA2R antagonists could have utility in treating pulmonary fibrosis.

The GH/IGF-1 Axis Is Associated With Intrahepatic Lipid Content and Hepatocellular Damage in Overweight/Obesity

CONTEXT

Obesity is a state of relative growth hormone (GH) deficiency, and GH has been identified as a candidate disease-modifying target in nonalcoholic fatty liver disease (NAFLD) because of its lipolytic and anti-inflammatory properties. However, the GH/IGF-1 axis has not been well characterized in NAFLD.

OBJECTIVE

We aimed to investigate serum GH and IGF-1 levels in relation to intrahepatic lipid content (IHL) and markers of hepatocellular damage and fibrosis in NAFLD.

METHODS

This cross-sectional study included 102 adults (43% women; age 19-67; BMI ≥ 25 kg/m2) without type 2 diabetes. IHL was measured by magnetic resonance spectroscopy; NAFLD was defined by ≥ 5% IHL. Peak-stimulated GH in response to GH releasing hormone and arginine was assessed as was serum IGF-1 (LC/MS).

RESULTS

There was no difference in mean age, BMI, or sex distribution in NAFLD vs controls. Mean (± SD) IHL was higher in NAFLD vs controls (21.8 ± 13.3% vs 2.9 ± 1.1%, P < 0.0001). Mean peak-stimulated GH was lower in NAFLD vs controls (9.0 ± 6.3 vs 15.4 ± 11.2 ng/mL, P = 0.003), including after controlling for age, sex, visceral adipose tissue, and fasting glucose. In a stepwise model, peak-stimulated GH predicted 14.6% of the variability in IHL (P = 0.004). Higher peak-stimulated GH was also associated with lower ALT. Higher serum IGF-1 levels were associated with lower risk of liver fibrosis by Fibrosis-4 scores.

CONCLUSION

Individuals with NAFLD have lower peak-stimulated GH levels but similar IGF-1 levels as compared to controls. Higher peak-stimulated GH levels are associated with lower IHL and less hepatocellular damage. Higher IGF-1 levels are associated with more favorable fibrosis risk scores. These data implicate GH and IGF-1 as potential disease modifiers in the development and progression of NAFLD.

Association of GLP1R Polymorphisms With the Incretin Response

CONTEXT

Polymorphisms in the gene encoding the glucagon-like peptide-1 receptor (GLP1R) are associated with type 2 diabetes but their effects on incretin levels remain unclear.

OBJECTIVE

We evaluated the physiologic and hormonal effects of GLP1R genotypes before and after interventions that influence glucose physiology.

DESIGN

Pharmacogenetic study conducted at 3 academic centers in Boston, Massachusetts.

PARTICIPANTS

A total of 868 antidiabetic drug-naïve participants with type 2 diabetes or at risk for developing diabetes.

INTERVENTIONS

We analyzed 5 variants within GLP1R (rs761387, rs10305423, rs10305441, rs742762, and rs10305492) and recorded biochemical data during a 5-mg glipizide challenge and a 75-g oral glucose tolerance test (OGTT) following 4 doses of metformin 500 mg over 2 days.

MAIN OUTCOMES

We used an additive mixed-effects model to evaluate the association of these variants with glucose, insulin, and incretin levels over multiple timepoints during the OGTT.

RESULTS

During the OGTT, the G-risk allele at rs761387 was associated with higher total GLP-1 (2.61 pmol/L; 95% CI, 1.0.72-4.50), active GLP-1 (2.61 pmol/L; 95% CI, 0.04-5.18), and a trend toward higher glucose (3.63; 95% CI, -0.16 to 7.42 mg/dL) per allele but was not associated with insulin. During the glipizide challenge, the G allele was associated with higher insulin levels per allele (2.01 IU/mL; 95% CI, 0.26-3.76). The other variants were not associated with any of the outcomes tested.

CONCLUSIONS

GLP1R variation is associated with differences in GLP-1 levels following an OGTT load despite no differences in insulin levels, highlighting altered incretin signaling as a potential mechanism by which GLP1R variation affects T2D risk.

Immunotherapy of Neuroblastoma: Facts and Hopes

While the adoption of multimodal therapy including surgery, radiation, and aggressive combination chemotherapy has improved outcomes for many children with high-risk neuroblastoma, we appear to have reached a plateau in what can be achieved with cytotoxic therapies alone. Most children with cancer, including high-risk neuroblastoma, do not benefit from treatment with immune checkpoint inhibitors (ICI) that have revolutionized the treatment of many highly immunogenic adult solid tumors. This likely reflects the low tumor mutation burden as well as the downregulated MHC-I that characterizes most high-risk neuroblastomas. For these reasons, neuroblastoma represents an immunotherapeutic challenge that may be a model for the creation of effective immunotherapy for other "cold" tumors in children and adults that do not respond to ICI. The identification of strong expression of the disialoganglioside GD2 on the surface of nearly all neuroblastoma cells provided a target for immune recognition by anti-GD2 mAbs that recruit Fc receptor-expressing innate immune cells that mediate cytotoxicity or phagocytosis. Adoption of anti-GD2 antibodies into both upfront and relapse treatment protocols has dramatically increased survival rates and altered the landscape for children with high-risk neuroblastoma. This review describes how these approaches have been expanded to additional combinations and forms of immunotherapy that have already demonstrated clear clinical benefit. We also describe the efforts to identify additional immune targets for neuroblastoma. Finally, we summarize newer approaches being pursued that may well help both innate and adaptive immune cells, endogenous or genetically engineered, to more effectively destroy neuroblastoma cells, to better induce complete remission and prevent recurrence.

The coronal plane maximum diameter of deep intracerebral hemorrhage predicts functional outcome more accurately than hematoma volume

BACKGROUND

Among prognostic imaging variables, the hematoma volume on admission computed tomography (CT) has long been considered the strongest predictor of outcome and mortality in intracerebral hemorrhage.

AIMS

To examine whether different features of hematoma shape are associated with functional outcome in deep intracerebral hemorrhage.

METHODS

We analyzed 790 patients from the ATACH-2 trial, and 14 shape features were quantified. We calculated Spearman's Rho to assess the correlation between shape features and three-month modified Rankin scale (mRS) score, and the area under the receiver operating characteristic curve (AUC) to quantify the association between shape features and poor outcome defined as mRS>2 as well as mRS > 3.

RESULTS

Among 14 shape features, the maximum intracerebral hemorrhage diameter in the coronal plane was the strongest predictor of functional outcome, with a maximum coronal diameter >∼3.5 cm indicating higher three-month mRS scores. The maximum coronal diameter versus hematoma volume yielded a Rho of 0.40 versus 0.35 (p = 0.006), an AUC_[mRS>2] of 0.71 versus 0.68 (p = 0.004), and an AUC_[mRS>3] of 0.71 versus 0.69 (p = 0.029). In multiple regression analysis adjusted for known outcome predictors, the maximum coronal diameter was independently associated with three-month mRS (p < 0.001).

CONCLUSIONS

A coronal-plane maximum diameter measurement offers greater prognostic value in deep intracerebral hemorrhage than hematoma volume. This simple shape metric may expedite assessment of admission head CTs, offer a potential biomarker for hematoma size eligibility criteria in clinical trials, and may substitute volume in prognostic intracerebral hemorrhage scoring systems.