Benchmarking omics-based prediction of asthma development in children.

BACKGROUND: Asthma is a heterogeneous disease with high morbidity. Advancement in high-throughput multi-omics approaches has enabled the collection of molecular assessments at different layers, providing a complementary perspective of complex diseases. Numerous computational methods have been developed for the omics-based patient classification or disease outcome prediction. Yet, a systematic benchmarking of those methods using various combinations of omics data for the prediction of asthma development is still lacking. OBJECTIVE: We aimed to investigate the computational methods in disease status prediction using multi-omics data. METHOD: We systematically benchmarked 18 computational methods using all the 63 combinations of six omics data (GWAS, miRNA, mRNA, microbiome, metabolome, DNA methylation) collected in The Vitamin D Antenatal Asthma Reduction Trial (VDAART) cohort. We evaluated each method using standard performance metrics for each of the 63 omics combinations. RESULTS: Our results indicate that overall Logistic Regression, Multi-Layer Perceptron, and MOGONET display superior performance, and the combination of transcriptional, genomic and microbiome data achieves the best prediction. Moreover, we find that including the clinical data can further improve the prediction performance for some but not all the omics combinations. CONCLUSIONS: Specific omics combinations can reach the optimal prediction of asthma development in children. And certain computational methods showed superior performance than other methods.

Clinical epigenetics settings for cancer and cardiovascular diseases: real-life applications of network medicine at the bedside.

Despite impressive efforts invested in epigenetic research in the last 50 years, clinical applications are still lacking. Only a few university hospital centers currently use epigenetic biomarkers at the bedside. Moreover, the overall concept of precision medicine is not widely recognized in routine medical practice and the reductionist approach remains predominant in treating patients affected by major diseases such as cancer and cardiovascular diseases. By its' very nature, epigenetics is integrative of genetic networks. The study of epigenetic biomarkers has led to the identification of numerous drugs with an increasingly significant role in clinical therapy especially of cancer patients. Here, we provide an overview of clinical epigenetics within the context of network analysis. We illustrate achievements to date and discuss how we can move from traditional medicine into the era of network medicine (NM), where pathway-informed molecular diagnostics will allow treatment selection following the paradigm of precision medicine.

Faslodex inhibits estradiol-induced extracellular matrix dynamics and lung metastasis in a model of lymphangioleiomyomatosis.

Lymphangioleiomyomatosis (LAM) is a destructive lung disease primarily affecting women. Genetic studies indicate that LAM cells carry inactivating tuberous sclerosis complex (TSC)-2 mutations, and metastasize to the lung. We previously discovered that estradiol increases the metastasis of TSC2-deficient cells in mice carrying xenograft tumors. Here, we investigate the molecular basis underlying the estradiol-induced lung metastasis of TSC2-deficient cells, and test the efficacy of Faslodex (an estrogen receptor antagonist) in a preclinical model of LAM. We used a xenograft tumor model in which estradiol induces the lung metastasis of TSC2-deficient cells. We analyzed the impact of Faslodex on tumor size, the extracellular matrix organization, the expression of matrix metalloproteinase (MMP)-2, and lung metastasis. We also examined the effects of estradiol and Faslodex on MMP2 expression and activity in tuberin-deficient cells in vitro. Estradiol resulted in a marked reduction of Type IV collagen deposition in xenograft tumors, associated with 2-fold greater MMP2 concentrations compared with placebo-treated mice. Faslodex normalized the Type IV collagen changes in xenograft tumors, enhanced the survival of the mice, and completely blocked lung metastases. In vitro, estradiol enhanced MMP2 transcripts, protein accumulation, and activity. These estradiol-induced changes in MMP2 were blocked by Faslodex. In TSC2-deficient cells, estradiol increased MMP2 concentrations in vitro and in vivo, and induced extracellular matrix remodeling. Faslodex inhibits the estradiol-induced lung metastasis of TSC2-deficient cells. Targeting estrogen receptors with Faslodex may be of efficacy in the treatment of LAM.

Maternal history, sensitization to allergens, and current wheezing, rhinitis, and eczema among children in Costa Rica.

Little is known about the factors associated with asthma, allergic rhinitis, and eczema in Latin American countries. We investigated the relation between potential risk factors and current wheezing, allergic rhinitis, and eczema among 208 Costa Rican children aged 10-13 years participating in phase II of the International Study of Asthma and Allergies in Childhood (ISAAC). The geometric mean ( +/- SD) serum total IgE level of children with current wheezing was significantly higher than that of children without current wheezing (533.8 +/- 5.2 vs. 144.7 +/- 6.0 IU/mL, P < 0.01). In a multivariate analysis, a maternal history of asthma, skin test reactivity (STR) to house dust mites, and STR to Alternaria were significantly associated with current wheezing. Children who had a maternal history of asthma had 2.4 times higher odds of current wheezing than those without maternal history of asthma (95% CI for OR = 1.1-5.3). Sensitization to either house dust mite or Alternaria was associated with 3.3 times increased odds of current wheezing (95% CI for OR for STR to dust mite = 1.6-6.7; 95% CI for OR for STR to Alternaria = 1.1-11.0). In a multivariate analysis, STR to house dust mite and STR to cat dander were significantly associated with allergic rhinitis, and a maternal history of eczema and STR to dog dander were associated with eczema in the child. The interaction between familial factors and lifestyle changes resulting from social reforms implemented 60 years ago may explain the high prevalence of atopic diseases in Costa Rica.