A Mathematical Methodology for Determining the Temporal Order of Pathway Alterations Arising during Gliomagenesis

Human cancer is caused by the accumulation of genetic alterations in cells. Of special importance are changes that occur early during malignant transformation because they may result in oncogene addiction and thus represent promising targets for therapeutic intervention. We have previously described a computational approach, called Retracing the Evolutionary Steps in Cancer (RESIC), to determine the temporal sequence of genetic alterations during tumorigenesis from cross-sectional genomic data of tumors at their fully transformed stage. Since alterations within a set of genes belonging to a particular signaling pathway may have similar or equivalent effects, we applied a pathway-based systems biology approach to the RESIC methodology. This method was used to determine whether alterations of specific pathways develop early or late during malignant transformation. When applied to primary glioblastoma (GBM) copy number data from The Cancer Genome Atlas (TCGA) project, RESIC identified a temporal order of pathway alterations consistent with the order of events in secondary GBMs. We then further subdivided the samples into the four main GBM subtypes and determined the relative contributions of each subtype to the overall results: we found that the overall ordering applied for the proneural subtype but differed for mesenchymal samples. The temporal sequence of events could not be identified for neural and classical subtypes, possibly due to a limited number of samples. Moreover, for samples of the proneural subtype, we detected two distinct temporal sequences of events: (i) RAS pathway activation was followed by TP53 inactivation and finally PI3K2 activation, and (ii) RAS activation preceded only AKT activation. This extension of the RESIC methodology provides an evolutionary mathematical approach to identify the temporal sequence of pathway changes driving tumorigenesis and may be useful in guiding the understanding of signaling rearrangements in cancer development.
Author Summary Cancer is a deadly disease that develops through the accumulation of genetic changes over time. Many biological models do not incorporate this temporal aspect of tumor formation and progression, in part due to the difficulty of determining the sequence of events through biological experimentation for most cancer types. We previously developed a computational algorithm with which we can quickly and cost-effectively determine the order in which mutations arise in the tumor even when large numbers of mutations are considered. In this paper, we extended our method to incorporate biological knowledge of the common pathways by which cancer progresses. We applied these techniques to primary glioblastoma, the most common form of brain cancer. We found that when all samples are taken into account, a temporal sequence of pathway events emerges; however, different subtypes of glioblastoma vary in their temporal sequence of events. This algorithm can also be easily applied to other cancer types as clinical data becomes available, showing the benefit of computational and mathematical tools in cancer research. Using temporal information, cancer biologists will be able to develop more accurate animal models of tumor formation and learn more about how mutations interact in time, thus leading to better treatments for cancer.