Rebecca J. Whelan

Achieving improved clinical outcomes for cancer patients will require discovery of new biological markers and improved understanding of biomarkers already in use. To this end, the Whelan lab employs diverse analytical methods including proteomics, microscale separations, bioinformatics, and affinity reagent development. Areas of ongoing research focus include:

Characterization of ovarian cancer biomarker CA125 using bioanalytical methods. CA125 is the gold standard biomarker for managing ovarian cancer. Despite its clinical importance, little is known about its structure and function. We are interested in identifying the binding site(s) of CA125-specific antibodies as part of a long-term effort to intelligently develop alternative affinity recognition approaches. This effort uses solid-phase peptide synthesis or bacterial protein expression to prepare individual subdomains of CA125. We then characterize the interactions between these subdomains and CA125-specific antibodies using Western blotting, enzyme-linked immunoassay, surface plasmon resonance spectroscopy, and affinity-probe capillary electrophoresis. In parallel efforts, CA125 is isolated from patient-derived samples, enzymatically digested into peptides, and analyzed using nano-liquid chromatography/tandem mass spectrometry. Novel analytical methods—including preparative capillary electrophoresis fractionation and solid-phase supported deglycosylation—have been developed in our lab to improve peptide and protein identification of CA125 and other targets. These proteomics-based studies are complemented by ongoing efforts to determine the cDNA sequence of CA125 in cell lines and patient samples using nanopore sequencing. Such sequence data may reveal differences in the composition of this important biomarker across individuals and during cancer treatment.

Development and application of nucleic-acid affinity reagents. Ovarian cancer is most often diagnosed as advanced, metastatic disease. Analytical methods to reliably detect biomarkers of ovarian cancer at earlier stage would improve long-term survival. Motivated by the idea that a biomarker is only as good as the tools available to detect it, we have developed aptamers: single-stranded oligonucleotides that function as “artificial antibodies” and could be the basis of new affinity-based detection methods that complement the existing immunoassay. We selected aptamers for CA-125 using a novel “one-pot” method, and for a complementary cancer marker (HE4) using capillary electrophoresis. We were early adopters of high-throughput DNA sequencing as the penultimate step in aptamer selection, an approach that yields orders of magnitude more data than conventional DNA cloning and sequencing. Exploiting this rich sequence data requires developing and adapting aptamer-specific bioinformatics tools. Ongoing aptamer selection efforts go beyond isolated protein biomarker targets to focus on whole-cell targets. Once cancer-specific aptamers are developed, they will be used as payload-directing agents for targeted therapies, and as the basis of instrument-free detection devices, in a platform similar to a home pregnancy test.