Biomarker Discovery

The current standard of care for locally advanced cervical cancer is radiation therapy with the concurrent administration of cisplatin chemotherapy. State of the art, advanced technologies including intensity modulated radiation therapy (IMRT) and brachytherapy are used to deliver high doses of irradiation directly to cervical tumors. Despite these efforts, up to one third of patients will experience treatment failure. Recently, large scale collaborative efforts have been used to catalogue biologic differences in cervical tumors. These differences include changes in DNA, RNA, protein, and metabolites. Through these efforts, we have identified candidate biomarkers that may be used in the future to improve treatment outcome. However, in order to determine whether any of these biologic differences are predictive for treatment outcome, these candidate biomarkers need to be prospectively evaluated in the context of uniform treatment.

GSEA enrichment plot of KEGG endometrial cancer pathway genes in PET+ vs. PET– tumors. Genes in the PI3K/AKT signaling pathway demonstrated significant enrichment in PET+ versus PET- tumors (FDR q-value = 0.006). The upper portion of the figure plots the enrichment scores for each gene, while the bottom portion of the plot shows the value of the ranking metric moving down the list of ranked genes. The table enumerates the genes in the pathway for which a majority of probe sets were significantly enriched and upregulated in PET-positive versus PET-negative tumors. (source)

Immunohistochemical staining of the TMA from human cervical cancers. Top, example of p-AKT437 staining from different cases: negative (case number: 1,15,618), weak (1,15,621), medium (1,15,630), and strong (1,15,584). Bottom, hematoxylin and eosin (H&E) staining. (source)

In the laboratory, we use specimens from a prospectively collected tumor banking study to test candidate predictive biomarkers for radiotherapy outcome. All of these samples are directly linked to a well-annotated clinical database that includes imaging, treatment planning and clinical outcome data. Our biologic samples include tumor biopsies and blood collected before and during uniform treatment with definitive radiation therapy. We are currently using these samples to 1) test the influence of HPV genotype on radiotherapy outcome; 2) characterize the biology of HPV negative cervical tumors; 3) identify novel mutations associated with local recurrence and distant metastasis after definitive radiation; 4) directly test the influence of PI3K pathway mutation on tumor glucose metabolism and the response to radiation; and 5) compare the influence of individual gene mutations in the context of various patient sub-populations.

Fiona Ruiz with her poster at the 2017 AACR Meeting in Washington DC.

Biomarker identification, characterization and validation is critically important in the clinic. The ultimate goal is to perform the mechanistic studies needed to explain why the biomarker is important. Using in vitro and in vivo preclinical models, we have developed a pipeline for mechanistic studies that are used to characterize the biologic function of each biomarker. In vitro, this approach includes siRNA and Crisper mediated knockdown, cell viability, proliferation, metabolism, migration and radiation sensitivity assays. In vivo, we take advantage of our mouse model to directly test the contribution of individual genes or gene mutations to tumor phenotypes including traditional endpoints like local growth and invasion, distant metastasis, and survival and exploratory endpoints including imaging changes on MR and PET using both standard (i.e., FDG) and investigational imaging tracers.