Phylogenetic and Metabolic Tracking of Gut Microbiota during Perinatal Development

The colonization and development of gut microbiota immediately after birth is highly variable and depends on several factors, such as delivery mode and modality of feeding during the first months of life. A cohort of 31 mother and neonate pairs, including 25 at-term caesarean (CS) and 6 vaginally (V) delivered neonates (DNs), were included in this study and 121 meconium/faecal samples were collected at days 1 through 30 following birth. Operational taxonomic units (OTUs) were assessed in 69 stool samples by phylogenetic microarray HITChip and inter- and intra-individual distributions were established by inter-OTUs correlation matrices and OTUs co-occurrence or co-exclusion networks. ¹H-NMR metabolites were determined in 70 stool samples, PCA analysis was performed on 55 CS DNs samples, and metabolome/OTUs co-correlations were assessed in 45 CS samples, providing an integrated map of the early microbiota OTUs-metabolome. A microbiota “core” of OTUs was identified that was independent of delivery mode and lactation stage, suggesting highly specialized communities that act as seminal colonizers of microbial networks. Correlations among OTUs, metabolites, and OTUs-metabolites revealed metabolic profiles associated with early microbial ecological dynamics, maturation of milk components, and host physiology.     

Combined test for UGT1A1 -3279T-->G and A(TA)nTAA polymorphisms best predicts Gilbert's syndrome in Italian pediatric patients

Gilbert's syndrome is a common hereditary chronic or recurrent, mild unconjugated hyperbilirubinemia. Polymorphisms in the bilirubin uridine diphosphate glucuronosyl transferase gene (UGT1A1) causing a decreased enzyme activity are associated with susceptibility to the syndrome. Homozygosity for TA(7) allele of the A(TA)(n)TAA promoter polymorphism is found in the majority of Caucasian patients. We sought to investigate the role of three UGT1A1 polymorphisms (A[TA](n)TAA, -3279T-->G, and G71R) in the susceptibility to Gilbert's syndrome in 53 Italian pediatric subjects compared to 83 unaffected controls. Carriage of two TA(n) risk alleles (TA(7) and TA(8)) and -3279G homozygosity were similarly associated with hyperbilirubinemia (odds ratio [OR] = 11.59, 95% confidence interval [CI] = 4.80-27.98; p < 0.001, and OR = 11.51, 95% CI = 5.06-26.19; p < 0.001, respectively). Homozygosity for both TA7 and -3279G was associated with the highest relative risk estimate (OR = 19.23, 95% CI = 7.34-50.4; p < 0.001), but a significant association was found also for TA7 heterozygosity combined with -3279G/G genotype (OR = 7.98, 95% CI = 2.54-25.06; p < 0.001). The G71R variant was found only in two controls. Our results demonstrate that genotyping of both UGT1A1 A(TA)(n)TAA and -3279T-->G polymorphisms best defines genetic susceptibility to Gilbert's syndrome in Caucasian pediatric patients, and the TA7 heterozygous genotype combined with homozygosity for the -3279G allele can also be associated with pediatric mild hyperbilirubinemia.     

Copy-number variations involving the IHH locus are associated with syndactyly and craniosynostosis

Indian hedgehog (IHH) is a secreted signaling molecule of the hedgehog family known to play important roles in the regulation of chondrocyte differentiation, cortical bone formation, and the development of joints. Here, we describe that copy-number variations of the IHH locus involving conserved noncoding elements (CNEs) are associated with syndactyly and craniosynostosis. These CNEs are able to drive reporter gene expression in a pattern highly similar to wild-type Ihh expression. We postulate that the observed duplications lead to a misexpression and/or overexpression of IHH and by this affect the complex regulatory signaling network during digit and skull development.     

The Q121/Q121 genotype of ENPP1/PC-1 is associated with lower BMI in non-diabetic whites

This study investigated the role of the ENPP1/PC-1 gene K121Q polymorphism in predicting BMI (kg/m2) in non-diabetic individuals. Three independent samples (n = 631, n = 304, and n = 505) of adult whites were analyzed. Selection criteria were fasting plasma glucose level <126 mg/dL, absence of severe obesity (BMI > or =40 kg/m2), and lack of treatment known to modulate BMI. In Sample 1, BMI values were different in individuals carrying the K121/K121 (KK), K121/Q121 (KQ), and Q121/Q121 (QQ) genotypes (25.5 +/- 4.3, 25.3 +/- 4.1, and 22.8 +/- 2.5 kg/m2, respectively (adjusted p = 0.022); BMI values in Samples 2 and 3 also tended to be different, although the differences, after adjustment for age and sex, did not reach statistical significance. When data were pooled, BMI values were 25.8 +/- 4.4, 25.6 +/- 4.4, and 23.6 +/- 3.3 kg/m2 in KK, KQ, and QQ individuals (adjusted p = 0.029). According to a recessive model, QQ individuals had lower BMI values than KK and KQ individuals combined (23.6 +/- 3.3 kg/m2 vs. 25.7 +/- 4.4 kg/m2; adjusted p = 0.008). These data suggest that the QQ genotype of the ENPP1/PC-1 gene is associated with lower BMI. If similar results are confirmed in prospective studies, the K121Q polymorphism may help identify people at risk for obesity.     

Cost-effectiveness of exome sequencing: an Italian pilot study on undiagnosed patients

Recent advances in genomic sequencing and their implementation in clinical practice are widely recognized as diagnostic milestones, and are influencing considerably medical decision making in term of patients’ management. The cost-effectiveness of genomic analysis as first-tier tests has been documented. However, only a few studies have assessed systematically the economic impact of a revised diagnostic trajectory based on exome sequencing in the health system for undiagnosed patients. We report on the assessment of diagnostic costs referred to a large cohort of patients enrolled in the Bambino Gesù Children’s Hospital’s “Undiagnosed Patients Program”, supporting the cost-effectiveness of exome sequencing in a universalistic health care service compared to the traditional multi-step diagnostic workup. Our data provide evidence that revision of health policy to promote genomic sequencing of patients with suspected Mendelian disorders would allow reallocation of resources for rare diseases from diagnostics to patient care. At a social level, diagnosis is crucial to receive the social “sick role” and establish an effective doctor-patient relationship. The application of genomic sequencing as first-tier diagnostic test does improve this process speeding up the diagnosis and management of undiagnosed patients.     

Protein carbonyl group content in patients affected by familiar chronic nail candidiasis

Familiar chronic nail candidiasis (FCNC) is a rare disorder characterized by early-onset infections caused by different species of Candida, restricted to the nail of the hands and feet, and associated with a low serum concentration of intercellular adhesion molecule 1. Host defense mechanisms against candidiasis require the cooperation of many immune cells through several candidacidal mechanisms, including oxygen-dependent killing mechanisms, mediated by a superoxide anion radical myeloperoxidase--H2O2--halide system, and reactive nitrogen intermediates. We analyzed protein carbonyl groups (considered a useful marker of oxidative stress) in the serum of patients belonging to a five-generation Italian family with an isolated form of FCNC. Serum protein carbonyl groups in FCNC patients were significantly lower than those measured in healthy donors. Also, if this hypothesis is merely speculative, we could suggest that the decreased circulating level of protein carbonyl groups in these patients is not a marker of a lower oxidative stress condition, but might be linked to a lower protease activity.