Clonal dynamics in early human embryogenesis inferred from somatic mutation.

Cellular dynamics and fate decision in early human embryogenesis remain largely unknown owing to the challenges of performing studies in human embryos1. Here, we explored whole-genomes of 334 single-cell colonies and targeted deep sequences of 379 bulk tissues obtained from various anatomical locations of seven recently deceased adult human donors. Using somatic mutations as an intrinsic barcode, we reconstructed early cellular phylogenies that demonstrate (1) an endogenous mutational rate that is higher in the first cell division but decreases to approximately one per cell per cell division later in life; (2) universal unequal contribution of early cells to embryo proper, resulting from early cellular bottlenecks that stochastically set aside epiblast cells within the embryo; (3) examples of varying degrees of early clonal imbalances between tissues on the left and right sides of the body, different germ layers and specific anatomical parts and organs; (4) emergence of a few ancestral cells that will substantially contribute to adult cell pools in blood and liver; and (5) presence of mitochondrial DNA heteroplasmy in the fertilized egg. Our approach also provides insights into the age-related mutational processes and loss of sex chromosomes in normal somatic cells. In sum, this study provides a foundation for future studies to complete cellular phylogenies in human embryogenesis.

Comprehensive analysis of somatic mutations and structural variations in domestic pig.

Understanding somatic mutations and structural variations in domestic pigs (Sus scrofa domestica) is critical due to their increasing importance as model organisms in biomedical research. In this study, we conducted a comprehensive analysis through whole-genome sequencing of skin, organs, and blood samples. By examining two pig pedigrees, we investigated the inheritance and sharedness of structural variants among fathers, mothers, and offsprings. Utilizing single-cell clonal expansion techniques, we observed significant variations in the number of somatic mutations across different tissues. An in-house developed pipeline enabled precise filtering and analysis of these mutations, resulting in the construction of individual phylogenetic trees for two pigs. These trees explored the developmental relationships between different tissues, revealing insights into clonal expansions from various anatomical locations. This study enhances the understanding of pig genomes, affirming their increasing value in clinical and genomic research, and provides a foundation for future studies in other animals, paralleling previous studies in mice and humans. This approach not only deepens our understanding of mammalian genomic variations but also strengthens the role of pigs as a crucial model in human health and disease research.

Ara h2 levels in dust from homes of individuals with peanut allergy and individuals with peanut tolerance.

BACKGROUND: Approximately 1% of the U.S. population has a peanut allergy. Previous studies that measured peanut protein in house dust support the hypothesis that household peanut consumption may lead to clinical sensitization through transdermal exposure. OBJECTIVE: The aim of this pilot study was to characterize Ara h2 levels in house dust from homes with and without individuals with peanut allergy. METHODS: Household dust was obtained from homes with an individual with peanut allergy and from homes with no individual with peanut allergy. Ara h2 levels were determined by using a monoclonal antibody-based immunoassay with a level of determination of 150 ng per gram of dust. Peanut consumption information was obtained by questionnaire. RESULTS: A total of 85 dust samples were collected: 38 from homes with a individual with peanut allergy and 47 from control homes. The median Ara h2 level in homes with an individual with peanut allergy was 1236 ng/g (interquartile range [IQR], 256-1342 ng/g), whereas the median Ara h2 level in homes without an individual with peanut allergy was 650 ng/g (IQR, 163-2201 ng/g). Ara h2 levels in dust from homes of individuals with peanut allergy were not significantly lower than in dust from control homes. Of the homes with an individual with peanut allergy, 15 reported complete avoidance of peanut in the home (39%). Ara h2 levels in homes that completely avoided peanuts were not significantly lower than Ara h2 levels in homes that did not restrict peanuts (p = 0.531). CONCLUSION: Although families may restrict peanuts and peanut products in the home, there was still detectable Ara h2 levels found in homes. Each subject's definition of restriction may vary, there seemed to be peanut protein entering the home, although the protein origin is not known. Possibilities include cross-reactivity with another antigen or transport into the home on some vector. Further investigation of hypotheses regarding cross-reactivity and environmental exposure to Ara h2 is necessary.

Association of tree nut and coconut sensitizations.

BACKGROUND: Coconut (Cocos nucifera), despite being a drupe, was added to the US Food and Drug Administration list of tree nuts in 2006, causing potential confusion regarding the prevalence of coconut allergy among tree nut allergic patients. OBJECTIVE: To determine whether sensitization to tree nuts is associated with increased odds of coconut sensitization. METHODS: A single-center retrospective analysis of serum specific IgE levels to coconut, tree nuts (almond, Brazil nut, cashew, chestnut, hazelnut, macadamia, pecan, pistachio, and walnut), and controls (milk and peanut) was performed using deidentified data from January 2000 to August 2012. Spearman correlation (ρ) between coconut and each tree nut was determined, followed by hierarchical clustering. Sensitization was defined as a nut specific IgE level of 0.35 kU/L or higher. Unadjusted and adjusted associations between coconut and tree nut sensitization were tested by logistic regression. RESULTS: Of 298 coconut IgE values, 90 (30%) were considered positive results, with a mean (SD) of 1.70 (8.28) kU/L. Macadamia had the strongest correlation (ρ = 0.77), whereas most other tree nuts had significant (P < .05) but low correlation (ρ < 0.5) with coconut. The adjusted odds ratio between coconut and macadamia was 7.39 (95% confidence interval, 2.60-21.02; P < .001) and 5.32 (95% confidence interval, 2.18-12.95; P < .001) between coconut and almond, with other nuts not being statistically significant. CONCLUSION: Our findings suggest that although sensitization to most tree nuts appears to correlate with coconut, this is largely explained by sensitization to almond and macadamia. This finding has not previously been reported in the literature. Further study correlating these results with clinical symptoms is planned.

A cross-sectional questionnaire assessing patient and physician use of short-term prophylaxis for hereditary angioedema.

BACKGROUND: Current guidelines recommend short-term prophylaxis (STP) before invasive procedures to prevent hereditary angioedema (HAE) attacks; however, adherence to these guidelines may be variable because this indication lacks Food and Drug Administration approval in the United States. OBJECTIVE: To ascertain the STP experiences of patients with HAE and HAE-treating physicians. METHODS: Online questionnaires focusing on STP experiences were distributed by the US Hereditary Angioedema Association to the first 250 patients with HAE and to registered HAE-treating physicians. SAS 9.3 was used to perform descriptive statistics and to test the difference between patients who underwent procedures and those who did not using Pearson χ(2) test, Fisher exact test, and 2-sample t test. RESULTS: For the patient survey, 219 respondents met the criteria for HAE type 1 and 2; 37 (17%) underwent 66 invasive procedures, and all reported receiving STP. Eight patients (22%) reported failed STP, but only 3 required on-demand therapy. For STP, anabolic steroids and plasma-derived C1 inhibitor were the most and second-most commonly used, respectively. For the physician survey, 37 physicians reported caring for 433 patients with HAE. Depending on the procedure, 19% to 54% of physicians used STP and 30% to 86% prescribed on-demand therapy; 69% and 78% of physicians prescribed plasma-derived C1 inhibitor as STP for minimally invasive and invasive procedures, respectively. Physicians reported excellent efficacy for the STP treatments used. CONCLUSION: Physicians reported excellent outcomes using primarily newer STP therapies, namely plasma-derived C1 inhibitor, which was discordant to patient-reported outcomes using older STP therapies, namely anabolic steroids. Well-controlled STP studies are needed to clarify use for patients with HAE in the United States.

Restoration of Immune Privilege in Human Dermal Papillae Controlling Epithelial-Mesenchymal Interactions in Hair Formation.

BACKGROUND: Hair follicles are among a handful of organs that exhibit immune privilege. Dysfunction of the hair follicle immune system underlies the development of inflammatory diseases, such as alopecia areata. METHODS: Quantitative reverse transcription PCR and immunostaining was used to confirm the expression of major histocompatibility complex class I in human dermal papilla cells. Through transcriptomic analyses of human keratinocyte stem cells, major histocompatibility complex class I was identified as differentially expressed genes. Organ culture and patch assay were performed to assess the ability of WNT3a conditioned media to rescue immune privilege. Lastly, CD8+ T cells were detected near the hair bulb in alopecia areata patients through immunohistochemistry. RESULTS: Inflammatory factors such as tumor necrosis factor alpha and interferon gamma were verified to induce the expression of major histocompatibility complex class I proteins in dermal papilla cells. Additionally, loss of immune privilege of hair follicles was rescued following treatment with conditioned media from outer root sheath cells. Transcriptomic analyses found 58 up-regulated genes and 183 down-regulated genes related in MHC class I+ cells. Using newborn hair patch assay, we demonstrated that WNT3a conditioned media with epidermal growth factor can restore hair growth. In alopecia areata patients, CD8+ T cells were increased during the transition from mid-anagen to late catagen. CONCLUSION: Identification of mechanisms governing epithelial and mesenchymal interactions of the hair follicle facilitates an improved understanding of the regulation of hair follicle immune privilege.

Asymmetric Contribution of Blastomere Lineages of First Division of the Zygote to Entire Human Body Using Post-Zygotic Variants.

BACKGROUND: In humans, after fertilization, the zygote divides into two 2n diploid daughter blastomeres. During this division, DNA is replicated, and the remaining mutually exclusive genetic mutations in the genome of each cell are called post-zygotic variants. Using these somatic mutations, developmental lineages can be reconstructed. How these two blastomeres are contributing to the entire body is not yet identified. This study aims to evaluate the cellular contribution of two blastomeres of 2-cell embryos to the entire body in humans using post-zygotic variants based on whole genome sequencing. METHODS: Tissues from different anatomical areas were obtained from five donated cadavers for use in single-cell clonal expansion and bulk target sequencing. After conducting whole genome sequencing, computational analysis was applied to find the early embryonic mutations of each clone. We developed our in-house bioinformatics pipeline, and filtered variants using strict criteria, composed of mapping quality, base quality scores, depth, soft-clipped reads, and manual inspection, resulting in the construction of embryological phylogenetic cellular trees. RESULTS: Using our in-house pipeline for variant filtering, we could extract accurate true positive variants, and construct the embryological phylogenetic trees for each cadaver. We found that two daughter blastomeres, L1 and L2 (lineage 1 and 2, respectively), derived from the zygote, distribute unequally to the whole body at the clonal level. From bulk target sequencing data, we validated asymmetric contribution by means of the variant allele frequency of L1 and L2. The asymmetric contribution of L1 and L2 varied from person to person. CONCLUSION: We confirmed that there is asymmetric contribution of two daughter blastomeres from the first division of the zygote across the whole human body.

Neutrophil-derived trail is a proinflammatory subtype of neutrophil-derived extracellular vesicles.

Aims: Extracellular vesicles (EVs) are membrane-derived vesicles that mediate intercellular communications. Neutrophils produce different subtypes of EVs during inflammatory responses. Neutrophil-derived trails (NDTRs) are generated by neutrophils migrating toward inflammatory foci, whereas neutrophil-derived microvesicles (NDMVs) are thought to be generated by neutrophils that have arrived at the inflammatory foci. However, the physical and functional characteristics of neutrophil-derived EVs are incompletely understood. In this study, we aimed to investigate the differences between NDTRs and NDMVs. Methods: The generation of neutrophil-derived EVs were visualized by live-cell fluorescence images and the physical characteristics were further analyzed using nanotracking analysis assay, scanning electron microscopic analysis, and marker expressions. Functional characteristics of neutrophil-derived EVs were analyzed using assays for bactericidal activity, monocyte chemotaxis, phenotype polarization of macrophages, and miRNA sequencing. Finally, the effects of neutrophil-derived EVs on the acute and chronic inflammation were examined in vivo. Results: Both EVs share similar characteristics including stimulators, surface marker expression, bactericidal activity, and chemoattractive effect on monocytes via MCP-1. However, the integrin-mediated physical interaction was required for generation of NDTRs whereas NDMV generation was dependent on PI3K pathway. Interestingly, NDTRs contained proinflammatory miRNAs such as miR-1260, miR-1285, miR-4454, and miR-7975, while NDMVs contained anti-inflammatory miRNAs such as miR-126, miR-150, and miR-451a. Although both EVs were easily uptaken by monocytes, NDTRs enhanced proinflammatory macrophage polarization whereas NDMVs induced anti-inflammatory macrophage polarization. Moreover, NDTRs showed protective effects against lethality in a murine sepsis model and pathological changes in a murine chronic colitis model. Conclusion: These results suggest that NDTR is a proinflammatory subtype of neutrophil-derived EVs distinguished from NDMV.

A multi-scale model for hair follicles reveals heterogeneous domains driving rapid spatiotemporal hair growth patterning.

The control principles behind robust cyclic regeneration of hair follicles (HFs) remain unclear. Using multi-scale modeling, we show that coupling inhibitors and activators with physical growth of HFs is sufficient to drive periodicity and excitability of hair regeneration. Model simulations and experimental data reveal that mouse skin behaves as a heterogeneous regenerative field, composed of anatomical domains where HFs have distinct cycling dynamics. Interactions between fast-cycling chin and ventral HFs and slow-cycling dorsal HFs produce bilaterally symmetric patterns. Ear skin behaves as a hyper-refractory domain with HFs in extended rest phase. Such hyper-refractivity relates to high levels of BMP ligands and WNT antagonists, in part expressed by ear-specific cartilage and muscle. Hair growth stops at the boundaries with hyper-refractory ears and anatomically discontinuous eyelids, generating wave-breaking effects. We posit that similar mechanisms for coupled regeneration with dominant activator, hyper-refractory, and wave-breaker regions can operate in other actively renewing organs.

Allergic Diseases and Internalizing Behaviors in Early Childhood.

BACKGROUND AND OBJECTIVES: The relationship between allergic diseases and internalizing disorders has not been well characterized with regard to multiple allergic diseases or longitudinal study. The objective of this study was to examine the association between multiple allergic diseases in early childhood with validated measures of internalizing disorders in the school-age years. METHODS: Children enrolled in the Cincinnati Childhood Allergy and Air Pollution Study underwent skin testing and examinations at ages 1, 2, 3, 4, and 7 years. At age 7, parents completed the Behavior Assessment System for Children, Second Edition (BASC-2), a validated measure of childhood behavior and emotion. The association between allergic diseases at age 4, including allergic rhinitis, allergic persistent wheezing, atopic dermatitis, and allergic sensitization, and BASC-2 internalizing, anxiety, and depression T scores at age 7 was examined by logistic and linear regression, adjusting for covariates. RESULTS: The cohort included 546 children with complete information on allergic disease and BASC-2 outcomes. Allergic rhinitis at age 4 was significantly associated with elevated internalizing (adjusted odds ratio [aOR]: 3.2; 95% confidence interval [CI]: 1.8-5.8), anxiety (aOR: 2.0; 95% CI: 1.2-3.6), and depressive scores (aOR: 3.2; 95% CI: 1.7-6.5) at age 7. Allergic persistent wheezing was significantly associated with elevated internalizing scores (aOR: 2.7; 95% CI: 1.2-6.3). The presence of >1 allergic disease (aOR: 3.6; 95% CI: 1.7-7.6) and allergic rhinitis with comorbid allergic disease(s) (aOR: 4.3; 95% CI: 2.0-9.2) at age 4 had dose-dependent associations with internalizing scores. CONCLUSIONS: Children with allergic rhinitis and allergic persistent wheezing at age 4 are at increased risk of internalizing behaviors at age 7. Furthermore, multiple allergic diseases had a dose-dependent association with elevated internalizing scores.

Clinical features of pediatric hereditary angioedema.

BACKGROUND: There is a paucity of data that describe the clinical course of hereditary angioedema (HAE) in children. OBJECTIVE: The purpose of this study was to examine the clinical features of children with HAE. METHODS: Electronic medical records from the past 10 years at Cincinnati Children's Hospital Medical Center and an outpatient allergy community practice were searched for ICD-9 code 277.6 (Other deficiencies of circulating enzyme). Exclusion criteria included laboratory data not supportive of type I or II HAE diagnosis or age at diagnosis greater than 18 years. Chart review was performed and missing data were collected by telephone interviews with patient families. Descriptive statistics were performed using SAS version 9.4. RESULTS: Twenty-one children were identified. The median age was 13.2 years (interquartile range [IQR], 9.1-18.8), 71% were male, 86% had an HAE family history, and 95% were Caucasian. The median age of symptom onset and diagnosis was 5.7 (IQR, 5-9 years) and 5.0 (IQR, 4-8 years), respectively. Five children diagnosed were asymptomatic. Three children without a family history had a 6.0-year delay in diagnosis. The most common angioedema attack sites were abdominal, peripheral, and laryngeal, which occurred at least once in 93%, 73%, and 27%, respectively. Of the 15 children with onset of symptoms, only 6 children received on-demand therapy for an acute attack, whereas 13 children were administered either short-term or long-term prophylaxis therapy. CONCLUSIONS: In this pediatric HAE population, symptom onset and diagnosis occurred at a median age of 5 years with a delay in diagnosis in those without a family history. Abdominal attacks were more common than peripheral attacks in this population.

Utility of post-urinary tract infection imaging in patients with normal prenatal renal ultrasound.

The American Academy of Pediatrics recommends renal ultrasound (RUS) and voiding cystourethrography (VCUG) for all infants after a first urinary tract infection (UTI). However, many congenital renal anomalies are identified by a prenatal US. At the present time, there are no data regarding the yield of post-UTI imaging among infants who have a documented normal prenatal US. We retrospectively reviewed the charts of all patients <1 year of age with a first UTI who had normal kidneys noted on prenatal US to determine the frequency of abnormal findings. Abnormal RUS and VCUG results were noted in 5.1% (24 of 471) and 20.4% (75 of 368) of infants, respectively. While the abnormal US rate is significantly less than what has been previously reported, the frequency of abnormal VCUGs is similar. These results suggest that a post-UTI RUS may not be needed if the prenatal US was normal. However, a VCUG continues to be indicated.