Pareto task inference analysis reveals cellular trade-offs in diffuse large B-Cell lymphoma transcriptomic data

One of the main challenges in cancer treatment is the selection of treatment resistant clones which leads to the emergence of resistance to previously efficacious therapies. Identifying vulnerabilities in the form of cellular trade-offs constraining the phenotypic possibility space could allow to avoid the emergence of resistance by simultaneously targeting cellular processes that are involved in different alternative phenotypic strategies linked by trade-offs. The Pareto optimality theory has been proposed as a framework allowing to identify such trade-offs in biological data from its prediction that it would lead to the presence of specific geometrical patterns (polytopes) in, e.g., gene expression space, with vertices representing specialized phenotypes. We tested this approach in diffuse large B-cell lymphoma (DLCBL) transcriptomic data. As predicted, there was highly statistically significant evidence for the data forming a tetrahedron in gene expression space, defining four specialized phenotypes (archetypes). These archetypes were significantly enriched in certain biological functions, and contained genes that formed a pattern of shared and unique elements among archetypes, as expected if trade-offs between essential functions underlie the observed structure. The results can be interpreted as reflecting trade-offs between aerobic energy production and protein synthesis, and between immunotolerant and immune escape strategies. Targeting genes on both sides of these trade-offs simultaneously represent potential promising avenues for therapeutic applications.