Whole-genome sequencing of African Americans implicates differential genetic architecture in inflammatory bowel disease

Whether or not populations diverge with respect to the genetic contribution to risk of specific complex diseases is relevant to understanding the evolution of susceptibility and origins of health disparities. Here, we describe a large-scale whole-genome sequencing study of inflammatory bowel disease encompassing 1,774 affected individuals and 1,644 healthy control Americans with African ancestry (African Americans). Although no new loci for inflammatory bowel disease are discovered at genome-wide significance levels, we identify numerous instances of differential effect sizes in combination with divergent allele frequencies. For example, the major effect at PTGER4 fine maps to a single credible interval of 22 SNPs corresponding to one of four independent associations at the locus in European ancestry individuals but with an elevated odds ratio for Crohn disease in African Americans. A rare variant aggregate analysis implicates C

Large-scale sequencing identifies multiple genes and rare variants associated with Crohn’s disease susceptibility

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Dynamic transcriptional and epigenomic reprogramming from pediatric nasal epithelial cells to induced pluripotent stem cells

BackgroundInduced pluripotent stem cells (iPSCs) hold tremendous potential, both as a biological tool to uncover the pathophysiology of disease by creating relevant human cell models and as a source of cells for cell-based therapeutic applications. Studying the reprogramming process will also provide significant insight into tissue development.ObjectiveWe sought to characterize the derivation of iPSC lines from nasal epithelial cells (NECs) isolated from nasal mucosa samples of children, a highly relevant and easily accessible tissue for pediatric populations.MethodsWe performed detailed comparative analysis on the transcriptomes and methylomes of NECs, iPSCs derived from NECs (NEC-iPSCs), and embryonic stem cells (ESCs).ResultsNEC-iPSCs express pluripotent cell markers, can differentiate into all 3 germ layers in vivo and in vitro, and have a transcriptome and methylome remarkably similar to those of ESCs. However, residual DNA methylation marks exist, which are differentially methylated between NEC-iPSCs and ESCs. A subset of these methylation markers related to epithelium development and asthma and specific to NEC-iPSCs persisted after several passages in vitro, suggesting the retention of an epigenetic memory of their tissue of origin. Our analysis also identified novel candidate genes with dynamic gene expression and DNA methylation changes during reprogramming, which are indicative of possible roles in airway epithelium development.ConclusionNECs are an excellent tissue source to generate iPSCs in pediatric asthmatic patients, and detailed characterization of the resulting iPSC lines would help us better understand the reprogramming process and retention of epigenetic memory

Chronic treatment with rosiglitazone (10–20 mg/kg/day) normalized hyperglycemia and improved glucose tolerance in <i>db</i>/<i>db</i> mice.

<p>(A) Non fasted blood glucose levels in control, control+rosiglitazone, <i>db/db</i> and <i>db/db</i>+rosiglitazone mice. Repeated measures two-way ANOVA using a Bonferroni’s posthoc test showed that treatment with rosiglitazone caused a significant decrease in blood glucose levels of <i>db</i>/<i>db</i> mice [F (3, 54) = 176.04], <i>p</i><0.0001. Similarly, duration of treatment showed a significant decrease in blood glucose levels of <i>db/db</i> mice [F (21, 54) = 16.34], <i>p</i><0.0001. Data are represented as mean ± SEM of group size (n = 6–8). (B) Glucose tolerance test in rosiglitazone treated and untreated lean control and <i>db</i>/<i>db</i> mice. After eight weeks of treatment with rosiglitazone, mice were fasted for 16 hours and dosed with glucose (1.5 g/kg I.P). Blood glucose levels were measured by tail tip bleed at 0, 15, 30, 60, 90 and 120 minutes post administration. *<i>p</i><0.001 Vs age-matched lean control and lean control+rosiglitazone mice. ^#<i>p</i><0.001, ^$<i>p</i><0.01 Vs untreated <i>db/db</i> mice. Data are represented as mean ± SEM of group size (n = 6–8). (C) One-way ANOVA of area under curve showed that rosiglitazone significantly improved the glucose tolerance in <i>db/db</i>+rosiglitazone mice compared to untreated <i>db/db</i> mice. *<i>p</i><0.001 Vs age-matched lean control mice. ^#<i>p</i><0.05 Vs untreated <i>db/db</i> mice. Each bar represents mean ± SEM of group size (n = 6–8).</p

Immunofluorescence of nephrin, ACE2 and ADAM17 after 8 weeks of treatment with rosiglitazone.

<p>(A) Immunofluorescence staining for nephrin in the glomeruli of control, untreated and rosiglitazone treated <i>db/db</i> mice at 20× magnification. Nephrin expression was significantly decreased in <i>db/db</i> mice. After eight weeks of treatment with rosiglitazone there was a significant increase in nephrin expression compared to untreated <i>db/db</i> mice. *<i>p</i><0.01 Vs control mice.^#<i>p</i><0.05 Vs untreated <i>db/db</i> mice. Each bar represents mean ± SEM of group size (n = 11–18). (B) Immunofluorescence staining for ACE2 in cortical tubules and glomeruli of control, untreated and rosiglitazone treated <i>db/db</i> mice at 20× magnification. White arrows indicate glomeruli. While tubular ACE2 expression was increased, glomerular ACE2 expression was significantly decreased in <i>db/db</i> mice. After eight weeks of treatment with rosiglitazone there was a significant increase in glomerular ACE2 expression while tubular ACE2 expression was unchanged compared to untreated <i>db/db</i> mice. *<i>p</i><0.001 Vs control mice.^#<i>p</i><0.01 Vs untreated <i>db/db</i> mice. Each bar represents mean ± SEM of group size (n = 11–18). (C) Immunofluorescence staining for ADAM17 in cortical tubules of control, untreated and rosiglitazone treated <i>db/db</i> mice at 20× magnification. (D) Immunofluorescence double staining for ACE2 and ADAM17 in cortical tubules of <i>db/db</i> mice at 60× magnification.</p

ACE2 and ACE activity in urine, plasma and kidney of control, <i>db/db</i> and <i>db/db</i>+rosiglitazone mice using a fluorometric enzyme assay.

<p>(A) Urinary ACE2 activity in control, <i>db/db</i> and <i>db/db</i>+rosiglitazone mice before and after the commencement of treatment. Two-way ANOVA showed an increase in urinary ACE2 activity of <i>db/db</i> mice compared to control mice. Four and eight weeks after treatment commenced there was a significant decrease in urinary ACE2 activity of the <i>db/db</i>+rosiglitazone mice compared to untreated <i>db/db</i> mice. *<i>p</i><0.001 Vs control mice.^#<i>p</i><0.001 Vs untreated <i>db/db</i> mice. Each bar represents mean ± SEM of group size (n = 6–7). (B) Plasma and renal ACE2 activity in control, <i>db/db</i> and <i>db/db+</i>rosiglitazone mice. There was no plasma ACE2 activity in control and <i>db/db</i> mice but a significant increase in renal ACE2 activity of <i>db/db</i> mice compared to control mice was observed. Treatment with rosiglitazone had no significant effect on renal ACE2 activity of treated <i>db/db</i> mice compared to untreated <i>db/db</i> mice.*<i>p</i><0.05 Vs control kidney. Each bar represents mean ± SEM of group size (n = 5–8). (C) Plasma ACE activity in control, <i>db/db</i> and <i>db/db</i>+rosiglitazone mice 8 wks after the commencement of treatment. One-way ANOVA showed an increase in plasma ACE activity of <i>db/db</i> mice compared to control mice. Eight weeks after treatment commenced there was a significant decrease in plasma ACE activity of the <i>db/db</i>+rosiglitazone mice compared to untreated <i>db/db</i> mice. *<i>p</i><0.05, **<i>p</i><0.001 Vs control mice.^#<i>p</i><0.05 Vs untreated <i>db/db</i> mice. Each bar represents mean ± SEM of group size (n = 6–7).</p

Mass spectrometric analysis of ACE2 activity in urine from control, <i>db/db</i> and <i>db/db</i>+rosiglitazone mice.

<p>Urine (2 µl) was incubated for 1.5 h at 37°C in 50 mM MES buffer pH 6.75 containing 0.5 µM Ang II, 2 mM PMSF and 20 µM bestatin. Shown is the conversion of Ang II (<i>m/z</i> 1046) to Ang-(1–7) (<i>m/z</i> 899). (A) Urinary ACE2 activity in control mice. (B) Urinary ACE2 activity in <i>db/db</i> mice. (C) Urinary ACE2 activity in <i>db/db</i> mice treated with rosiglitazone. (D) Urinary ACE2 activity in <i>db/db</i> mice in incubations with the ACE2 inhibitor, MLN-4760. (E) MS/MS of enzymatically generated Ang-(1–7) (upper panel) and synthetic Ang-(1–7) (lower panel).</p

DNA methylation dynamics during ex vivo differentiation and maturation of human dendritic cells.

BackgroundDendritic cells (DCs) are important mediators of innate and adaptive immune responses, but the gene networks governing their lineage differentiation and maturation are poorly understood. To gain insight into the mechanisms that promote human DC differentiation and contribute to the acquisition of their functional phenotypes, we performed genome-wide base-resolution mapping of 5-methylcytosine in purified monocytes and in monocyte-derived immature and mature DCs.ResultsDC development and maturation were associated with a great loss of DNA methylation across many regions, most of which occurs at predicted enhancers and binding sites for known transcription factors affiliated with DC lineage specification and response to immune stimuli. In addition, we discovered novel genes that may contribute to DC differentiation and maturation. Interestingly, many genes close to demethylated CG sites were upregulated in expression. We observed dynamic changes in the expression of TET2, DNMT1, DNMT3A and DNMT3B coupled with temporal locus-specific demethylation, providing possible mechanisms accounting for the dramatic loss in DNA methylation.ConclusionsOur study is the first to map DNA methylation changes during human DC differentiation and maturation in purified cell populations and will greatly enhance the understanding of DC development and maturation and aid in the development of more efficacious DC-based therapeutic strategies