Prioritization of Randomized Clinical Trial Questions for Children Hospitalized With Common Conditions: A Consensus Statement.

Importance: There is a lack of randomized clinical trial (RCT) data to guide many routine decisions in the care of children hospitalized for common conditions. A first step in addressing the shortage of RCTs for this population is to identify the most pressing RCT questions for children hospitalized with common conditions. Objective: To identify the most important and feasible RCT questions for children hospitalized with common conditions. Design, Setting, and Participants: For this consensus statement, a 3-stage modified Delphi process was used in a virtual conference series spanning January 1 to September 29, 2022. Forty-six individuals from 30 different institutions participated in the process. Stage 1 involved construction of RCT questions for the 10 most common pediatric conditions leading to hospitalization. Participants used condition-specific guidelines and reviews from a structured literature search to inform their development of RCT questions. During stage 2, RCT questions were refined and scored according to importance. Stage 3 incorporated public comment and feasibility with the prioritization of RCT questions. Main Outcomes and Measures: The main outcome was RCT questions framed in a PICO (population, intervention, control, and outcome) format and ranked according to importance and feasibility; score choices ranged from 1 to 9, with higher scores indicating greater importance and feasibility. Results: Forty-six individuals (38 who shared demographic data; 24 women [63%]) from 30 different institutions participated in our modified Delphi process. Participants included children's hospital (n = 14) and community hospital (n = 13) pediatricians, parents of hospitalized children (n = 4), other clinicians (n = 2), biostatisticians (n = 2), and other researchers (n = 11). The process yielded 62 unique RCT questions, most of which are pragmatic, comparing interventions in widespread use for which definitive effectiveness data are lacking. Overall scores for importance and feasibility of the RCT questions ranged from 1 to 9, with a median of 5 (IQR, 4-7). Six of the top 10 selected questions focused on determining optimal antibiotic regimens for 3 common infections (pneumonia, urinary tract infection, and cellulitis). Conclusions and Relevance: This consensus statementhas identified the most important and feasible RCT questions for children hospitalized with common conditions. This list of RCT questions can guide investigators and funders in conducting impactful trials to improve care and outcomes for hospitalized children.

Global O-glycoproteome enrichment and analysis enabled by a combinatorial enzymatic workflow.

A comprehensive analysis of site-specific protein O-glycosylation is hindered by the absence of a consensus O-glycosylation motif, the diversity of O-glycan structures, and the lack of a universal enzyme that cleaves attached O-glycans. Here, we report the development of a robust O-glycoproteomic workflow for analyzing complex biological samples by combining four different strategies: removal of N-glycans, complementary digestion using O-glycoprotease (IMPa) with/without another protease, glycopeptide enrichment, and mass spectrometry with fragmentation of glycopeptides using stepped collision energy. Using this workflow, we cataloged 474 O-glycopeptides on 189 O-glycosites derived from 79 O-glycoproteins from human plasma. These data revealed O-glycosylation of several abundant proteins that have not been previously reported. Because many of the proteins that contained unannotated O-glycosylation sites have been extensively studied, we wished to confirm glycosylation at these sites in a targeted fashion. Thus, we analyzed selected purified proteins (kininogen-1, fetuin-A, fibrinogen, apolipoprotein E, and plasminogen) in independent experiments and validated the previously unknown O-glycosites.

A complement C4-derived glycopeptide is a biomarker for PMM2-CDG.

BACKGROUNDDiagnosis of PMM2-CDG, the most common congenital disorder of glycosylation (CDG), relies on measuring carbohydrate-deficient transferrin (CDT) and genetic testing. CDT tests have false negatives and may normalize with age. Site-specific changes in protein N-glycosylation have not been reported in sera in PMM2-CDG.METHODSUsing multistep mass spectrometry-based N-glycoproteomics, we analyzed sera from 72 individuals to discover and validate glycopeptide alterations. We performed comprehensive tandem mass tag-based discovery experiments in well-characterized patients and controls. Next, we developed a method for rapid profiling of additional samples. Finally, targeted mass spectrometry was used for validation in an independent set of samples in a blinded fashion.RESULTSOf the 3,342 N-glycopeptides identified, patients exhibited decrease in complex-type N-glycans and increase in truncated, mannose-rich, and hybrid species. We identified a glycopeptide from complement C4 carrying the glycan Man5GlcNAc2, which was not detected in controls, in 5 patients with normal CDT results, including 1 after liver transplant and 2 with a known genetic variant associated with mild disease, indicating greater sensitivity than CDT. It was detected by targeted analysis in 2 individuals with variants of uncertain significance in PMM2.CONCLUSIONComplement C4-derived Man5GlcNAc2 glycopeptide could be a biomarker for accurate diagnosis and therapeutic monitoring of patients with PMM2-CDG and other CDGs.FUNDINGU54NS115198 (Frontiers in Congenital Disorders of Glycosylation: NINDS; NCATS; Eunice Kennedy Shriver NICHD; Rare Disorders Consortium Disease Network); K08NS118119 (NINDS); Minnesota Partnership for Biotechnology and Medical Genomics; Rocket Fund; R01DK099551 (NIDDK); Mayo Clinic DERIVE Office; Mayo Clinic Center for Biomedical Discovery; IA/CRC/20/1/600002 (Center for Rare Disease Diagnosis, Research and Training; DBT/Wellcome Trust India Alliance).

Dysregulated proteome and N-glycoproteome in ALG1-deficient fibroblasts.

Asparagine-linked glycosylation 1 protein is a ß-1,4-mannosyltransferase, is encoded by the ALG1 gene, which catalyzes the first step of mannosylation in N-glycosylation. Pathogenic variants in ALG1 cause a rare autosomal recessive disorder termed as ALG1-CDG. We performed a quantitative proteomics and N-glycoproteomics study in fibroblasts derived from patients with one homozygous and two compound heterozygous pathogenic variants in ALG1. Several proteins that exhibited significant upregulation included insulin-like growth factor II and pleckstrin, whereas hyaluronan and proteoglycan link protein 1 was downregulated. These proteins are crucial for cell growth, survival and differentiation. Additionally, we observed a decrease in the expression of mitochondrial proteins and an increase in autophagy-related proteins, suggesting mitochondrial and cellular stress. N-glycoproteomics revealed the reduction in high-mannose and complex/hybrid glycopeptides derived from numerous proteins in patients explaining that defect in ALG1 has broad effects on glycosylation. Further, we detected an increase in several short oligosaccharides, including chitobiose (HexNAc2 ) trisaccharides (Hex-HexNAc2 ) and novel tetrasaccharides (NeuAc-Hex-HexNAc2 ) derived from essential proteins including LAMP1, CD44 and integrin. These changes in glycosylation were observed in all patients irrespective of their gene variants. Overall, our findings not only provide novel molecular insights into understanding ALG1-CDG but also offer short oligosaccharide-bearing peptides as potential biomarkers.

Metabolomic biomarkers for (R, S)-ketamine and (S)-ketamine in treatment-resistant depression and healthy controls: A systematic review.

BACKGROUND: Ketamine is increasingly used for treatment-resistant depression (TRD) while its mechanism of action is still being investigated. In this systematic review, we appraise the current evidence of metabolomic biomarkers for racemic ketamine and esketamine in patients with TRD and healthy controls (HCs). METHODS: A comprehensive search of several databases (Ovid MEDLINE®, Embase, and Epub Ahead of Print) was performed from each database's inception to June 29, 2022, in any language, was conducted. We included studies wherein the metabolomic biomarkers for racemic ketamine or esketamine were investigated in TRD or HCs. Our main outcomes were to examine changes in metabolites among patients treated with ketamine/esketamine and explore the association with response to ketamine/esketamine. RESULTS: A total of 1859 abstracts were screened of which 11 were included for full-text review. Of these, a total of five articles were included (N = 147), including three RCTs (n = 129) and two open-label trials (n = 18). All studies used racemic ketamine; one study additionally used esketamine. The included studies evaluated patients with treatment-resistant bipolar depression (n = 22), unipolar depression (n = 91), and HCs (n = 34). The included studies reported alteration in several metabolites including acylcarnitines, lipids, kynurenine (KYN), and arginine with ketamine in TRD. Studies suggest the involvement of energy metabolism, KYN, and arginine pathways. In HCs, acetylcarnitine decreased post-infusion, whereas inconsistent findings were observed after the ketamine infusion in TRD patients. CONCLUSIONS: This systematic review provides preliminary evidence that ketamine may cause changes in several important pathways involved in energy metabolism and inflammation. Larger and more rigorous studies are needed.

Recent progress in mass spectrometry-based urinary proteomics.

Serum or plasma is frequently utilized in biomedical research; however, its application is impeded by the requirement for invasive sample collection. The non-invasive nature of urine collection makes it an attractive alternative for disease characterization and biomarker discovery. Mass spectrometry-based protein profiling of urine has led to the discovery of several disease-associated biomarkers. Proteomic analysis of urine has not only been applied to disorders of the kidney and urinary bladder but also to conditions affecting distant organs because proteins excreted in the urine originate from multiple organs. This review provides a progress update on urinary proteomics carried out over the past decade. Studies summarized in this review have expanded the catalog of proteins detected in the urine in a variety of clinical conditions. The wide range of applications of urine analysis-from characterizing diseases to discovering predictive, diagnostic and prognostic markers-continues to drive investigations of the urinary proteome.

Resource Utilization and Costs Associated with Approaches to Identify Infants with Early-Onset Sepsis.

Objective. To compare resource utilization and costs associated with 3 alternative screening approaches to identify early-onset sepsis (EOS) in infants born at ≥35 wk of gestational age, as recommended by the American Academy of Pediatrics (AAP) in 2018. Study Design. Decision tree-based cost analysis of the 3 AAP-recommended approaches: 1) categorical risk assessment (categorization by chorioamnionitis exposure status), 2) neonatal sepsis calculator (a multivariate prediction model based on perinatal risk factors), and 3) enhanced clinical observation (assessment based on serial clinical examinations). We evaluated resource utilization and direct costs (2022 US dollars) to the health system. Results. Categorical risk assessment led to the greatest neonatal intensive care unit usage (210 d per 1,000 live births) and antibiotic exposure (6.8%) compared with the neonatal sepsis calculator (112 d per 1,000 live births and 3.6%) and enhanced clinical observation (99 d per 1,000 live births and 3.1%). While the per-live birth hospital costs of the 3 approaches were similar-categorical risk assessment cost $1,360, the neonatal sepsis calculator cost $1,317, and enhanced clinical observation cost $1,310-the cost of infants receiving intervention under categorical risk assessment was approximately twice that of the other 2 strategies. Results were robust to variations in data parameters. Conclusion. The neonatal sepsis calculator and enhanced clinical observation approaches may be preferred to categorical risk assessment as they reduce the number of infants receiving intervention and thus antibiotic exposure and associated costs. All 3 approaches have similar costs over all live births, and prior literature has indicated similar health outcomes. Inclusion of downstream effects of antibiotic exposure in the neonatal period should be evaluated within a cost-effectiveness analysis. Highlights: Of the 3 approaches recommended by the American Academy of Pediatrics in 2018 to identify early-onset sepsis in infants born at ≥35 weeks, the categorical risk assessment approach leads to about twice as many infants receiving evaluation to rule out early-onset sepsis compared with the neonatal sepsis calculator and enhanced clinical observation approaches.While the hospital costs of the 3 approaches were similar over the entire population of live births, the neonatal sepsis calculator and enhanced clinical observation approaches reduce antibiotic exposure, neonatal intensive care unit admission, and hospital costs associated with interventions as part of the screening approach compared with the categorical risk assessment approach.

Changes in perceptions of antibiotic stewardship among neonatal intensive care unit providers over the course of a learning collaborative: a prospective, multisite, mixed-methods evaluation.

OBJECTIVE: To assess clinician perceptions towards the value and implementation of antibiotic stewardship (AS) in neonatal intensive care units (NICU). STUDY DESIGN: We performed a mixed-methods study of AS perceptions (prescribing appropriateness, importance, activity, capacity) using surveys and interviews in 30 California NICUs before and after a multicenter collaborative (Optimizing Antibiotic Use in California NICUs [OASCN]). RESULTS: Pre-OASCN, 24% of respondents felt there was "a lot of" or "some" inappropriate prescribing, often driven by fear of a bad outcome or reluctance to change existing practice. Clinicians reported statistically significant increases in AS importance (71 v 79%), perceived AS activity (67 v 87%), and more openness to change after OASCN (59 v 70%). We identified other concerns that lessen AS effort. CONCLUSION: OASCN increased perceived AS activity and openness to change in AS practices among NICU prescribers. Greater attention to subjective concerns should augment AS improvement.

Maternal physical activity, sitting, and risk of non-cardiac birth defects.

BACKGROUND: The relationship between maternal physical activity (PA)/sitting and birth defects is largely unexplored. We examined whether pre-pregnancy PA/sitting were associated with having a pregnancy affected by a birth defect. METHODS: We used data from two United States population-based case-control studies: 2008-2011 deliveries from the National Birth Defects Prevention Study (NBDPS; 9 states) and 2014-2018 deliveries from the Birth Defects Study To Evaluate Pregnancy exposureS (BD-STEPS; 7 states). Cases with one of 12 non-cardiac birth defects (n = 3798) were identified through population-based registries. Controls (n = 2682) were live-born infants without major birth defects randomly sampled using vital/hospital records. Mothers self-reported pre-pregnancy PA/sitting. Unconditional logistic regression models estimated associations between PA/sitting categories and the 12 birth defects. RESULTS: Mothers engaging in pre-pregnancy PA was associated with a reduced odds of five (spina bifida, cleft palate, anorectal atresia, hypospadias, transverse limb deficiency) and a higher odds of two (anencephaly, gastroschisis) birth defects. Mothers spending less time sitting in pre-pregnancy was associated with a reduced odds of two (anorectal atresia, hypospadias) and a higher odds of one (cleft lip with or without cleft palate) birth defect. CONCLUSIONS: Reasonable next steps include replication of these findings, improved exposure assessment, and elucidation of biologic mechanisms. IMPACT: Using data from two population-based case-control studies, we found that mothers engaging in different types of physical activity in the 3 months before pregnancy had an infant with a reduced odds of five and a higher odds of two birth defects. Mothers spending less time sitting in the 3 months before pregnancy had an infant with a reduced odds of two and a higher odds of one birth defect. Clarification and confirmation from additional studies are needed using more precise exposure measures, distinguishing occupational from leisure-time physical activity, and elucidation of mechanisms supporting these associations.

Evaluating Epidemiologic Trends and Variations in NICU Admissions in California, 2008 to 2018.

OBJECTIVE: Previous research suggests increasing numbers of and variation in NICU admissions. We explored whether these trends were reflected in California by examining NICU admissions and birth data in aggregate and among patient and hospital subpopulations more susceptible to variations in care. METHODS: In this retrospective cohort study, we evaluated NICU utilization between 2008 and 2018 for all live births at hospitals that provide data to the California Perinatal Quality Care Collaborative. We compared hospital- and admission-level data across birth weight (BW), gestational age (GA), and illness acuity categories. Trends were analyzed by using linear regression models. RESULTS: We identified 472 402 inborn NICU admissions and 3 960 441 live births across 144 hospitals. Yearly trends in NICU admissions remained stable among all births and higher acuity births (mean admission rates 11.9% and 4.1%, respectively). However, analysis of the higher acuity births revealed significant increases in NICU admission rates for neonates with higher BW and GA (BW ≥ 2500g: 1.8% in 2008, 2.1% in 2018; GA ≥ 37 weeks: 1.5% in 2010, 1.8% in 2018). Kaiser hospitals had a decreasing trend of NICU admissions compared to non-Kaiser hospitals (Kaiser: 13.9% in 2008, 10.1% in 2018; non-Kaiser: 11.3% in 2008, 12.3% in 2018). CONCLUSIONS: Overall NICU admission rates in California were stable from 2008-2018. However, trends similar to national patterns emerged when stratified by infant GA, BW, and illness acuity as well as Kaiser or non-Kaiser hospitals, with increasing admission rates for infants born at higher BW and GA and within non-Kaiser hospitals.

Automated Sample Preparation Workflow for Tandem Mass Tag-Based Proteomics.

Although tandem mass tag (TMT)-based isobaric labeling has become a powerful approach for multiplexed protein quantitation, automating the workflow for this technique has not been easy to achieve for widespread adoption. This is because preparation of TMT-labeled peptide samples involves multiple steps ranging from protein extraction, denaturation, reduction, and alkylation to tryptic digestion, desalting, labeling, and cleanup, all of which require a high level of proficiency. The variability resulting from multiple processing steps is inherently problematic, especially with large-scale clinical studies that involve hundreds of samples where reproducibility is critical for quantitation. Here, we sought to compare the performance of a recently introduced platform, AccelerOme, for an automated proteomic workflow employing TMT labeling with the manual processing of samples. Cell pellets were prepared and subjected to a 16-plex experiment using an automated platform and a conventional manual protocol. Single-shot liquid chromatography with tandem mass spectrometry analysis revealed a higher number of proteins and peptides identified using the automated platform. Efficiency of tryptic digestion, alkylation, and TMT labeling were similar in both manual and automated processes. In addition, comparison of quantitation accuracy and precision showed similar performance in an automated workflow compared to manual sample preparation by an expert. Overall, we demonstrated that the automated platform performs at a level similar to a manual process performed by an expert for TMT-based proteomics. We anticipate that this automated workflow will increasingly replace manual pipelines and has the potential to be applied to large-scale TMT-based studies, providing robust results and high sample throughput.

"A living lab within a lab": approaches and challenges for scaling digital public health in resource-constrained settings.

A living lab is an emerging concept, particularly in Europe, as a vehicle to develop digital innovations through a process of co-produced design and development, which takes place, physically and socially, in real-life use contexts. However, there is limited research relating to guiding our understanding of the process by which such labs are established, and digital innovations are co-created and scaled to other settings requiring similar solutions. Furthermore, beyond Europe, the concept of a living lab has not found widespread application in low- and middle-income countries (LMICs), particularly in their public health contexts. Public health systems offer the unique scaling challenge of "all or nothing", implying that data are required from the whole population rather than isolated pilot settings. The living lab approach promises the rich potential to strengthen public systems but comes with twin interconnected challenges. First, for building appropriate digital solutions to address local public health challenges, and second, in scaling them to other public health facilities. This article investigates these twin challenges through ongoing empirical work in India and identifies three key domains of analysis, which are as follows: the first concerns the process of establishing an enabling structure of a "living lab within a lab"; the second concerns leveraging the capabilities offered by free and open-source digital technologies; and the third concerns the driving impetus to scaling through agile and co-constructed technical support.

Urinary Proteomics for Discovery of Gastric Cancer Biomarkers to Enable Precision Clinical Oncology.

For precision in clinical oncology practice, detection of tumor-derived peptides and proteins in urine offers an attractive and noninvasive alternative for diagnostic or screening purposes. In this study, we report comparative quantitative proteomic profiling of urine samples from patients with gastric cancer and healthy controls using tandem mass tags-based multiplexed mass spectrometry approach. We identified 1504 proteins, of which 246 were differentially expressed in gastric cancer cases. Notably, ephrin A1 (EFNA1), pepsinogen A3 (PGA3), sortilin 1 (SORT1), and vitronectin (VTN) were among the upregulated proteins, which are known to play crucial roles in the progression of gastric cancer. We also found other overexpressed proteins, including shisa family member 5 (SHISA5), mucin like 1 (MUCL1), and leukocyte cell derived chemotaxin 2 (LECT2), which had not previously been linked to gastric cancer. Using a novel approach for targeted proteomics, SureQuant, we validated changes in abundance of a subset of proteins discovered in this study. We confirmed the overexpression of vitronectin and sortilin 1 in an independent set of urine samples. Altogether, this study provides molecular candidates for biomarker development in gastric cancer, and the findings also support the promise of urinary proteomics for noninvasive diagnostics and personalized/precision medicine in the oncology clinic.

Lactate-dependent transcriptional regulation controls mammalian eye morphogenesis.

Mammalian retinal metabolism favors aerobic glycolysis. However, the role of glycolytic metabolism in retinal morphogenesis remains unknown. We report that aerobic glycolysis is necessary for the early stages of retinal development. Taking advantage of an unbiased approach that combines the use of eye organoids and single-cell RNA sequencing, we identify specific glucose transporters and glycolytic genes in retinal progenitors. Next, we determine that the optic vesicle territory of mouse embryos displays elevated levels of glycolytic activity. At the functional level, we show that removal of Glucose transporter 1 and Lactate dehydrogenase A gene activity from developing retinal progenitors arrests eye morphogenesis. Surprisingly, we uncover that lactate-mediated upregulation of key eye-field transcription factors is controlled by the epigenetic modification of histone H3 acetylation through histone deacetylase activity. Our results identify an unexpected bioenergetic independent role of lactate as a signaling molecule necessary for mammalian eye morphogenesis.

split-intein Gal4 provides intersectional genetic labeling that is repressible by Gal80.

The split-Gal4 system allows for intersectional genetic labeling of highly specific cell types and tissues in Drosophila. However, the existing split-Gal4 system, unlike the standard Gal4 system, cannot be repressed by Gal80, and therefore cannot be controlled temporally. This lack of temporal control precludes split-Gal4 experiments in which a genetic manipulation must be restricted to specific timepoints. Here, we describe a split-Gal4 system based on a self-excising split-intein, which drives transgene expression as strongly as the current split-Gal4 system and Gal4 reagents, yet which is repressible by Gal80. We demonstrate the potent inducibility of "split-intein Gal4" in vivo using both fluorescent reporters and via reversible tumor induction in the gut. Further, we show that our split-intein Gal4 can be extended to the drug-inducible GeneSwitch system, providing an independent method for intersectional labeling with inducible control. We also show that the split-intein Gal4 system can be used to generate highly cell type-specific genetic drivers based on in silico predictions generated by single-cell RNAseq (scRNAseq) datasets, and we describe an algorithm ("Two Against Background" or TAB) to predict cluster-specific gene pairs across multiple tissue-specific scRNA datasets. We provide a plasmid toolkit to efficiently create split-intein Gal4 drivers based on either CRISPR knock-ins to target genes or using enhancer fragments. Altogether, the split-intein Gal4 system allows for the creation of highly specific intersectional genetic drivers that are inducible/repressible.

Sporadic SNCA mutations A18T and A29S exhibit variable effects on protein aggregation, cell viability and oxidative stress.

BACKGROUND: α-synuclein aggregation is the hallmark feature of Parkinson's disease. Both familial and sporadic forms of the disease exhibit this feature. Several mutations have been identified in patients and are associated with the disease pathology. METHODS AND RESULTS: We have used site-directed mutagenesis to generate α-synuclein mutant variants tagged with GFP. Fluorescence microscopy, flow cytometry, western blotting, cell viability and oxidative stress analysis were performed to investigate the effect of two less studied α-synuclein variants. In this study we characterized two less studied α-synuclein mutations, A18T and A29S, in the well-established yeast model. Our data shows variable expression, distribution and toxicity of the protein in the mutant variants A18T, A29S, A53T and WT. The cells expressing the double mutant variant A18T/A53T showed the most increase in the aggregation phenotype and also depicted reduced viability suggesting a more substantial effect of this variant. CONCLUSION: The outcome of our study highlights the variable localization, aggregation phenotype and toxicity of the studied α-synuclein variants. This underscores the importance of in-depth analysis of every disease-associated mutation which may result in variable cellular phenotype.