Blasco, T. (Telmo)
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- BN-BacArena: Bayesian network extension of BacArena for the dynamic simulation of microbial communities(Oxford University Press, 2024) Balzerani, F. (Francesco); Valcárcel-García, L.V. (Luis Vitores); Blasco, T. (Telmo); Larrañaga, P. (Pedro); Rufián-Henares, J.Á. (Ángel José); Francino, M.P. (M. Pilar); Planes-Pedreño, F.J. (Francisco Javier); Bielza, C. (Concha); Pérez-Burillo, S. (Sergio)Motivation: Simulating gut microbial dynamics is extremely challenging. Several computational tools, notably the widely used BacArena, enable modeling of dynamic changes in the microbial environment. These methods, however, do not comprehensively account for microbe–microbe stimulant or inhibitory effects or for nutrient–microbe inhibitory effects, typically observed in different compounds present in the daily diet. Results: Here, we present BN-BacArena, an extension of BacArena consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe–microbe and nutrient–microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient–bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria–bacteria significant relationships. With test data, BN-BacArena demonstrates a statistically significant improvement over BacArena to predict the time-dependent relative abundance of bacterial species involved in the gut microbiota upon different nutritional interventions. As a result, BN-BacArena opens new avenues for the dynamic modeling and simulation of the human gut microbiota metabolism.
- Whole-transcriptome analysis in peripheral blood mononuclear cells from patients with lipid-specific oligoclonal IgM band characterization reveals two circular RNAs and two linear RNAs as biomarkers of highly active disease(MDPI AG, 2020) Iparraguirre, L. (Leire); Sepúlveda, L. (Lucía); Otaegui, D. (David); Prada, Á. (Álvaro); Muñoz-Culla, M. (Maider); Villar, L.M. (Luisa María); Blasco, T. (Telmo); Espiño, M. (Mercedes); Costa-Frossard, L. (Lucienne); Olaverri, D. (Danel); Castillo-Triviño, T. (Tamara)The presence of anti-myelin lipid-specific oligoclonal IgM bands (LS-OCMBs) has been defined as an accurate predictor of an aggressive evolution of multiple sclerosis. However, the detection of this biomarker is performed in cerebrospinal fluid, a quite invasive liquid biopsy. In the present study we aimed at studying the expression profile of miRNA, snoRNA, circRNA and linearRNA in peripheral blood mononuclear cells (PBMCs) from patients with lipid-specific oligoclonal IgM band characterization. We included a total of 89 MS patients, 47 with negative LS-OCMB status and 42 with positive status. Microarray (miRNA and snoRNA) and RNA-seq (circular and linear RNAs) were used to perform the profiling study in the discovery cohort and candidates were validated by RT-qPCR in the whole cohort. The biomarker potential of the candidates was evaluated by ROC curve analysis. RNA-seq and RT-qPCR validation revealed that two circular (hsa_circ_0000478 and hsa_circ_0116639) and two linear RNAs (IRF5 and MTRNR2L8) are downregulated in PBMCs from patients with positive LS-OCMBs. Finally, those RNAs show a performance of a 70% accuracy in some of the combinations. The expression of hsa_circ_0000478, hsa_circ_0116639, IRF5 and MTRNR2L8 might serve as minimally invasive biomarkers of highly active disease.