Search bioRxiv⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/425777

Master regulators of signaling pathways coordinate key processes of embryonic development in breast cancer

Hernandez-Lemus, E.·Tapia-Carrillo, D.·Tovar, H.·Velazquez-Caldelas, T. E.
View original source ↗Export metadata ↓

Abstract

Signal transduction pathways allow cells to respond to environmental cues and can induce intracellular changes. In some contexts, like embryonic development, signal transduction plays crucial roles in cell fate determination and differentiation, while in developed organisms some of this processes contribute in the maintenance of the structural integrity of tissues.\n\nTumor cells are recognized as having deregulated signaling which leads to a series of abnormal behaviors known as the hallmarks of cancer. Although gene regulation is often viewed as the last step in signal transduction, transcriptional regulation of the components of a pathway may impact in the long term deregulation observed in tumors. The study of gene regulatory networks centered around genes of the signal transduction pathways allows the identification of transcriptional regulators with the greatest influence over the signal transduction gene signature, also denominated Master Regulators.\n\nIn this work we identify, the master regulators that regulate the expression of genes of 25 relevant pathways grouped in KEGG within the category of signal transduction in a breast cancer dataset. For this purpose we implemented a modified MARINa algorithm that identifies, from a network of regulons, those that possess more differentially expressed genes related to the process to be studied. We identified CLOCK, TSHZ2, HOXA2, MEIS2, HOXA3, HAND2, HOXA5, TBX18, PEG3 and GLI2 as the top 10 master regulators of signaling pathways in breast cancer. Nine of them are recognized for taking part in embryonic development associated processes.\n\nIndividual enrichment GO biological function for each TMR regulons showed to be significantly enriched in embryonic development related processes. Hedgehog signaling pathway was shown as enriched and also highly deregulated. The genes of the HOXA family are shared among most of the TMRs. Overall, this suggests the importance of the aberrant reprogramming of mechanisms present during embryonic development, being coopted in favor of tumor development.

Explore related subjects

systems biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Hernandez-Lemus, E., Tapia-Carrillo, D., Tovar, H., Velazquez-Caldelas, T. E.. 2018-09-24. Master regulators of signaling pathways coordinate key processes of embryonic development in breast cancer. https://doi.org/10.1101/425777

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

Uncovering disease progression trajectories across multiple timescales with hybrid ODE-mixture models

Biological systems are capable of evolving across multiple timescales, yet most modeling approaches capture either short-term physiological responses or long-term disease progression. Additionally, methods that combine these time scales either struggle with inter-individual variation, or require large volumes of data to work. We present Latent Class Parameter Trajectory Analysis (LCPTA), a hybrid framework that combines mechanistic ordinary differential equation (ODE) modeling of short-term dynamics with latent class trajectory modeling of long-term parameter evolution. To support this approach, we developed TemporalMixtureModels.jl, a Julia package for univariate and multivariate temporal mixture modeling. We evaluated LCPTA in two synthetic longitudinal studies, covering a simulation of a heterogeneous population developing hypertension, as well as a synthetic longitudinal study of 75 virtual individuals followed over 30 years, representing muscle insulin resistance, liver insulin resistance, and healthy trajectories. We compared LCPTA with a conditional neural ODE and a conditional neural network for reconstruction of long-term parameter trajectories and subgroup separation. In both studies LCPTA recovered relevant subgroup structure and trajectory patterns. In the cardiovascular study, the neural approaches were able to distinguish inter-individual differences, but in the insulin sensitivity study, neural approaches failed to represent parameter trajectories faithfully, primarily separating individuals along a single dominant parameter and showing weaker multivariate trajectory reconstruction. In additional experiments with sparse and irregularly sampled unseen individuals, LCPTA maintained strong classification performance. We show that LCPTA is an efficient and interpretable strategy for multiscale modeling of heterogeneous metabolic disease progression, with potential utility for data-efficient digital twin applications.

systems biology↗
bioRxiv2026

The Global Phosphorylation Landscape of Acute Heat Stress in Reef-Building Corals

Warming oceans disrupt the coral-algal symbiosis that sustains reefs, yet the signaling mechanisms initiating bleaching remain poorly understood. Integrating global phosphoproteomics across three reef-building corals with protein structure modeling revealed conservation between coral and human kinases, enabling inference of coral kinase activities and uncovering a shared signaling program induced by acute heat stress. Heat rapidly activated ERK, JNK, and p38 MAP kinases, suppressed cell cycle signaling, and remodeled pathways controlling chromatin, RNA processing, and metabolism. Most strikingly, thermal stress rewired immune receptor signaling networks associated with non-self recognition, suggesting that heat shifts the coral host from tolerance to immune recognition of its algal symbionts. These findings define conserved signaling mechanisms that precede bleaching, revealing actionable molecular targets for enhancing coral resilience.

systems biology↗
bioRxiv2026

Estimating glioblastoma migration-to-proliferation ratio from single time-point MRI data via radial density distribution

Glioblastoma (GBM) tumors with a high migration-to-proliferation ratio (D/k) are associated with treatment resistance, motivating the estimation of D/k from routine pre-treatment magnetic resonance imaging (MRI) data and the investigation of mechanisms underlying its heterogeneity across patients. Unlike previous approaches based on nested spherical approximations of enhancing and non-enhancing tumor volumes, we incorporate the spatial arrangement of the enhancing and non-enhancing tumor regions by deriving a 1D tumor density distribution from their segmentations and fitting a 1D reaction-diffusion model to estimate D/k. We achieved an error of under 5% when comparing our method to synthetic density distributions and found excellent correlation with synthetic tumor segmentations (Pearson correlation coefficient (PCC) = 0.996). We then evaluated associations between patient-specific D/k values and their clinical, transcriptomic, and radiomic features. When applied to 102 pre-treatment MRI scans from the Brain Tumor Segmentation (BraTS) 2017 dataset, elevated D/k significantly correlated with reduced overall survival (log-rank p = 0.01), older age (p = 0.04), and a trend toward lower Karnofsky Performance Status (p = 0.059). In a subset of 91 patients with available microarray data, mesenchymal-like phenotypes consistently exhibited elevated D/k across three established molecular subtype classifications (p = 0.013, p = 0.055, and p = 0.127). Elastic Net regularization followed by overrepresentation analysis revealed an enrichment of glycosylation-related pathways among genes associated with D/k variability (p = 0.0123 and p = 0.0368). Furthermore, Multi-Omic Factor Analysis identified a radiomic factor correlated with D/k (r = 0.57, p = 4x10-9), with the highest-weighted features corresponding to smoothness of the non-enhancing tumor region on T2 and FLAIR.

systems biology↗