Cordero Varela, J. A. | bioRxiv Science

bioRxiv2024

Rho GTPases signaling mediates aggressiveness and differentiation in neuroblastoma tumors

BackgroundNeuroblastoma (NB) is a pediatric cancer with highly variable outcomes, necessitating improved understanding of the molecular pathways driving its progression. Intratumor cellular heterogeneity related to neural differentiation has emerged as a defining characteristic that can explain its aggressive behavior. Although recurrent driver mutations are not typically observed in these tumors, Rho GTPases signaling genes have been identified as one of the most frequently mutated in aggressive NB cases. Rho GTPases are key regulators of cell morphology, migration, and differentiation, yet their role in NB remains underexplored. This study aims to comprehensively evaluate the expression and clinical significance of Rho GTPase signaling networks in NB tumors. MethodsWe analyzed the expression profiles of Rho GTPases, their regulators, and effectors, across multiple NB patient cohorts. Gene expression correlations with clinical parameters were assessed, and bioinformatics analyses were employed to identify gene expression patterns and interactions in tumors. Functional studies were performed in NB cell lines and in vivo models to validate the role of key Rho GTPases, including Cdc42, in NB progression and differentiation. ResultsOur analysis revealed widespread dysregulation of Rho GTPase signaling in NB tumors. Specific GTPases, such as RHOA or RHOV, were upregulated in advanced disease stages, while others, including RHOB, RHOU and CDC42, were downregulated and associated with poor prognosis. A minimal Rho-related gene signature was identified as a strong predictor of NB patient survival. Functional validation highlighted Cdc42 as a key regulator of NB differentiation, where its downregulation was necessary for maintaining the malignant, undifferentiated phenotype of NB cells. We also identified ARHGAP31/CdGAP as a critical regulator of Cdc42 in NB progenitor cells, suggesting a mechanism for Cdc42 suppression in aggressive NB. ConclusionsAn important role for Rho GTPase signaling in NB progression is revealed, providing a foundation for further exploration of Rho GTPase-targeted therapies in NB. In particular, Cdc42 signaling intervene in the balance between differentiation and stemness in NB cells, suggesting specific signaling events controlling the identity and plasticity of NB cells.

cancer biology↗

bioRxiv2017

Phenotype prediction in an Escherichia coli strain panel

Understanding how genetic variation contributes to phenotypic differences is a fundamental question in biology. Here, we set to predict fitness defects of an individual using mechanistic models of the impact of genetic variants combined with prior knowledge of gene function. We assembled a diverse panel of 696 Escherichia coli strains for which we obtained genomes and measured growth phenotypes in 214 conditions. We integrated variant effect predictors to derive gene-level probabilities of loss of function for every gene across strains. We combined these probabilities with information on conditional gene essentiality in the reference K-12 strain to predict the strains growth defects, providing significant predictions for up to 38% of tested conditions. The putative causal variants were validated in complementation assays highlighting commonly perturbed pathways in evolution for the emergence of growth phenotypes. Altogether, our work illustrates the power of integrating high-throughput gene function assays to predict the phenotypes of individuals.\n\nHighlightsO_LIAssembled a reference panel of E. coli strains\nC_LIO_LIGenotyped and high-throughput phenotyped the E. coli reference strain panel\nC_LIO_LIReliably predicted the impact of genetic variants in up to 38% of tested conditions\nC_LIO_LIHighlighted common genetic pathways for the emergence of deleterious phenotypes\nC_LI

systems biology↗