Biology subjects

de Anda-Jauregui, G.

Publications and source records attributed to de Anda-Jauregui, G..

4 recordsLinked to original sources

bioRxiv2025

Network Pharmacognosy of Galphimia glauca: Mapping the Molecular Landscape of a Traditional Mexican Medicinal Plant

This study explores the pharmacological landscape of Galphimia glauca, a traditional Mexican medicinal plant known for its sedative and anti-inflammatory effects. Using network pharmacognosy, we analyzed the interactions of G. glaucas bioactive compounds, Galphimines A-I, with human protein targets. SwissTargetPrediction identified 214 unique protein targets across the galphimines, revealing a core-periphery structure in a bipartite network where 41 targets are shared among all compounds. Further interaction analysis using STRING-DB generated a dense protein-protein interaction network comprising 1,386 connections. Centrality analysis highlighted proteins such as SRC, MTOR, and MAPK3 as key nodes involved in cell growth, proliferation, and immune regulation pathways, suggesting these as pivotal mediators of G. glaucas pharmacological effects. Community detection with the Walktrap algorithm further segmented the network into functionally relevant modules linked to cell survival, immune response, and inflammation, reflecting the therapeutic effects historically attributed to G. glauca. Our findings underscore the plants multi-target therapeutic potential and highlight the value of network-based approaches in understanding traditional medicine. This work lays the groundwork for further studies aimed at refining therapeutic strategies based on G. glaucas bioactive compounds and suggests network pharmacognosy as a promising tool for assessing other traditional medicinal plants.

systems biology↗

bioRxiv2019

Highly-connected, non-redundant microRNAs functional control in breast cancer molecular subtypes

Transcriptional patterns are altered in breast cancer. These alterations capture the heterogeneity of breast cancer, leading to the emergence of molecular subtypes. Network biology approaches to study gene co-expression are able to capture the differences between breast cancer subtypes.\n\nNetwork biology approaches may be extended to include other co-expression patterns, like those found between genes and non-coding RNA: such as mi-croRNAs (miRs). Commodore miRs are microRNAs that, based on their connectivity and redundancy in co-expression networks, have been proposed as potential control elements of biological functions.\n\nIn this work, we reconstructed miR-gene co-expression networks for each breast cancer molecular subtype. We identified Commodore miRs in three out of four molecular subtypes. We found that in each subtype, each cdre-miR had a different set of associated genes, as well as a different set of associated biological functions. We used a systematic literature validation strategy, and identified that the associated biological functions to these cdre-miRs are hallmarks of cancer.

genomics↗

bioRxiv2018

Loss of Trans Regulation in Breast Cancer Molecular Subtypes

Breast carcinomas are characterized by anomalous gene regulatory programs. As is well known, gene expression programs are able to shape phenotypes. Hence, the understanding of gene co-expression may shed light on the underlying mechanisms behind the transcriptional regulatory programs affecting tumor development and evolution. For instance, in breast cancer, there is a clear loss of inter-chromosomal (trans-) co-expression, compared with healthy tissue. At the same time cis- (intra-chromosomal) interactions are favored in breast tumors. In order to have a deeper understanding of regulatory phenomena in cancer, here, we constructed Gene Co-expression Networks by using 848 RNA-seq whole-genome samples corresponding to the four breast cancer molecular subtypes, as well as healthy tissue. We quantify the cis-/trans- co-expression imbalance in all phenotypes. Additionally, we measured the association between co-expression and physical distance between genes, and characterized the proportion of intra/inter-cytoband interactions per phenotype. We confirmed loss of trans- co-expression in all molecular subtypes. We also observed that gene cisco-expression decays abruptly with distance in all tumors in contrast with healthy tissue. We observed co-expressed gene hotspots, that tend to be connected at cytoband regions, and coincide accurately with already known copy number altered regions, such as Chr17q12, or Chr8q24.3 for all subtypes. Our methodology recovered different alterations already reported for specific breast cancer subtypes, showing how co-expression network approaches might help to capture distinct events that modify the cell regulatory program.

systems biology↗

bioRxiv2018

Identification of Casiopeina II-gly secondary targets through a systems pharmacology approach

Casiopeinas are a group of copper-based compounds designed to be used as less toxic, more efficient chemotherapeutic agents. In this study, we analyzed the in vitro effects of Casiopeina Il-gly on the expression of canonical biological pathways. Using microarray data from HeLa cell lines treated with Casiopeina II-gly, we identified biological pathways that are perturbed after treatment. We present a novel approach integrating pathway analysis and network theory: The Pathway Crosstalk Network. We constructed a network with deregulated pathways, featuring links between those pathways that crosstalk with each other. We identified modules grouping deregulated pathways that are functionally related. Through this approach, we were able to identify three features of Casiopeina treatment: a) Perturbation of signaling pathways, related to induction of apoptosis; b) perturbation of metabolic pathways, and c) activation of immune responses. These findings can be useful to drive new experimental exploration on their role in adverse effects and efficacy of Casiopeinas.

systems biology↗