Interruption of p53-MDM2 Interaction by Nutlin-3a in Human Lymphoma Cell Models Initiates a Cell-Dependent Global Effect on Transcriptome and Proteome Level

SIMPLE SUMMARY: The activation of wild-type p53 protein in human lymphoma is a promising therapeutic strategy. A precise interruption of a protein–protein interaction, such as the p53-MDM2 interaction by nutlin-3a may lead lymphoma cells to apoptotic death through the stabilization and activation of p53. Despite this well-characterized scientific fact, there are lymphoma types that prevent or delay apoptosis by still unknown or purely understood mechanisms. Even lymphoma types that were initially affected by this interruption, finally managed to avoid death. An in vitro integrative comparative multi-omics analysis of different lymphoma types, before and after, wild-type p53 activation is a powerful way to shed light on such molecular mechanisms. Our findings provide deep holistic qualitative and quantitative molecular screening that highlights the putative role of specific proteins and pathways in lymphoma pathogenesis and shed light on the global effect of nutlin-3a. This information is the basis for a targeted and detailed study on specific proteins and pathways involved in lymphoma progression and resistance. ABSTRACT: In most lymphomas, p53 signaling pathway is inactivated by various mechanisms independent to p53 gene mutations or deletions. In many cases, p53 function is largely regulated by alterations in the protein abundance levels by the action of E3 ubiquitin-protein ligase MDM2, targeting p53 to proteasome-mediated degradation. In the present study, an integrating transcriptomics and proteomics analysis was employed to investigate the effect of p53 activation by a small-molecule MDM2-antagonist, nutlin-3a, on three lymphoma cell models following p53 activation. Our analysis revealed a system-wide nutlin-3a-associated effect in all examined lymphoma types, identifying in total of 4037 differentially affected proteins involved in a plethora of pathways, with significant heterogeneity among lymphomas. Our findings include known p53-targets and novel p53 activation effects, involving transcription, translation, or degradation of protein components of pathways, such as a decrease in key members of PI3K/mTOR pathway, heat-shock response, and glycolysis, and an increase in key members of oxidative phoshosphorylation, autophagy and mitochondrial translation. Combined inhibition of HSP90 or PI3K/mTOR pathway with nutlin-3a-mediated p53-activation enhanced the apoptotic effects suggesting a promising strategy against human lymphomas. Integrated omic profiling after p53 activation offered novel insights on the regulatory role specific proteins and pathways may have in lymphomagenesis.