Work

Integrating gene expression, genomic, and phosphoproteomic data to infer transcription factor activity in lung cancer

Year: 2025

Type: article

Abstract: Transcription factors (TFs) are key regulators of cellular gene expression programs in health and disease. Here we set out to integrate genomic, transcriptomic, and phosphoproteomic data to characterize TF activity in lung adenocarcinoma patients. Using expression data from patient samples and genomic information on TF binding to super-enhancers, starting from a list of 1667 human TFs we calculated a patient-specific activity score and identified 34 with perturbed activity in the cancer samples, as evidenced by the expression of their direct targets. We then leveraged phosphoproteomic data on the same samples to identify phosphorylation events that modulate TF activity. This novel data integration approach to TF characterization led to the identification of ERG as a key regulator in lung adenocarcinoma whose activity strongly correlates with patient survival.

Source: NAR Genomics and Bioinformatics

DOI: 10.1093/nargab/lqaf068

Authors: Chiara Carrino, Gerardo Pepe, Luca Parca, Manuela Helmer-Citterich, Pier Federico Gherardini

Institutions: University of Rome Tor Vergata, Agenzia Spaziale Italiana

Language: English

Topic: Genomics and Chromatin Dynamics

Subfield: Molecular Biology

Field: Biochemistry, Genetics and Molecular Biology

Domain: Life Sciences

SDG: Good health and well-being

Open Access status: gold

Estimated APC paid: $2,766