Kuijjer Lab

New publication

July 31, 2023

We recently published our latest work, led by Tatiana, in NAR Cancer. Tatiana developed a computational approach, called PORCUPINE, to map heterogeneity in individual patient gene regulatory networks and applied it to study leiomyosarcoma, an aggressive cancer that can develop in smooth muscle tissue.

    PORCUPINE combines PCA with permutations to identify pathways contributing to regulatory heterogeneity in a patient population. Importantly, instead of identifying discrete subtypes, it can map subtle gradients of heterogeneity not detected by standard subtyping methods. Applying the method to two leiomyosarcoma data sets, we identified 37 heterogeneously regulated pathways, incl. targetable pathways such as E2F signaling. These findings were independent of mutations and could thus be a new way of stratifying patients for personalized medicine. Finally, we found that heterogeneous regulation is generally associated with open chromatin—indicating that genes located in open chromatin are more likely to be regulated by different sets of TFs—and that differential accessibility may explain subtle differences in regulation.
    In summary, we uncovered patterns of inter-patient heterogeneity at the level of transcriptional regulation, and identified genes and pathways that may represent therapeutic entry points in leiomyosarcoma.
Graphical abstract of the work. PORCUPINE can be applied to networks modeled for individual patients, such as single-sample gene regulatory networks modeled with PANDA and LIONESS. The method applies PCA to network edges connected to biological pathways and extracts the variance explained by the first principle component. It repeats this approach randomly generated gene sets of the same size as the selected pathway, and estimates the effect size and significance that the selected pathway explains a higher proportion of regulatory heterogeneity than expected by chance. After doing this for all pathways, it corrects p-values for multiple testing and returns those pathways that are significantly heterogeneously regulated in a patient population. As such, PORCUPINE can facilitate the identification of new molecular subtypes.