- Bachelor of Arts, Lawrence University, 1996
- Doctor of Philosophy, Stanford University, 2003
Research Interests: bioanalytical chemistry, aptamers, biosensors, capillary electrophoresis
Research in the Whelan lab is motivated by the need to detect and treat ovarian cancer in its early stages, when therapeutic intervention is most effective. We approach the problem of ovarian cancer detection with a diverse tool kit drawn from bioanalytical chemistry, molecular biology, bioinformatics, and nanoscience. We have an abiding interest in fundamental analytical method development as well as biomedical and clinical application. Four major projects are currently supported by the National Cancer Institute of the National Institutes of Health.
Analytical Chem, General Chem
Project 1: Identifying and Validating DNA Aptamers for Ovarian Cancer Biomarker CA125
Aptamers are single stranded oligonucleotides—DNA or RNA—that are selected out of a large, random pool on the basis of a particular function. Often aptamers function as high-affinity binders to biological molecules. The process of selecting aptamers relies on repeated cycles of selection and amplification until a small number of oligos with the desired binding property dominate the pool. Recently in the Whelan lab, significant progress was made on selecting an aptamer for cells that express high levels of the ovarian cancer biomarker CA125 (MUC16). We are currently evaluating the binding properties of selected CA125 aptamers using competitive ELISA immunoassay. In addition, high-throughput sequencing data is being analyzed using bioinformatic methods to find other potential aptamers, and identify structural trends over each round of selection.
Project 2: Optimization of Non-standard Aptamer Selection Methods
DNA aptamers are oligonucleotides that recognize and bind targets of interest. An ongoing focus of the Whelan lab is the selection of aptamers for ovarian cancer biomarkers, with intended applications in novel diagnostic and therapeutic strategies. The aim of this project is to select an aptamer for CA125, an important biomarker, widely used in the diagnosis and monitoring of ovarian cancer. We are using combination of “One-Pot” based (One-Pot SELEX) and capillary electrophoresis-based systematic evolution of ligands by exponential enrichment (CE-SELEX) to identify DNA oligos with affinity for CA125. Both One-Pot SELEX and CE-SELEX separate certain DNA sequences that bind to CA125 from many possible DNA sequences. After several rounds of SELEX, DNA aptamers with the highest affinity to CA125 are left. This approach has been shown by others to increase the speed and efficiency of the selection process.
Project 3: Aptamer-based Colorimetric Detection of CA125 Using Gold Nanoparticles
CA125 is an important biomarker for ovarian cancer in certain populations of women, such as those with a family history of the disease, those who are in remission, and those who are undergoing treatment. For these groups, frequent screening for CA125 is highly important. Currently, CA125 is assayed with an antibody-based test that is costly in terms of time, materials, and instrumentation. We aim to develop an alternative assay using gold nanoparticles (AuNPs) and DNA aptamers for detecting CA125, wherein aptamer-CA125 binding allows AuNPs, which would otherwise be stabilized by the aptamers, to aggregate in the presence of high salt concentrations. Owing to their extremely high molar absorptivity, the color change from unaggregated (red) to aggregated (blue) AuNPs is clearly visible to the naked eye. In this way, detection of CA125 could potentially be achieved in an assay that is fast, inexpensive, and instrument-free.
Project 4: Synthesis of Biologically Functionalized Iron Oxide Nanoparticles
A novel and promising strategy for cancer treatment is focused hyperthermia, in which tumor cells are transiently exposed to high temperatures, promoting their destruction. Localized heating can be achieved by attaching magnetic nanoparticles to molecules that are specific for a target protein. Interaction of the affinity molecules with their target (in our case MUC16, a protein that is over-expressed on the surface of ovarian cancer cells) adheres the nanoparticle to a cancer cell. Application of an oscillating magnetic field increases the temperature of the nanoparticle by as much as 40C, “melting” the cell membrane. Under mild conditions, this melting reversibly perforates the cell, enabling the introduction of drugs or material for gene therapy. With more vigorous heating, cells can be killed outright. DNA aptamers are only beginning to be used in applications of this sort, and they have yet to be examined in the treatment of ovarian cancer. Our work will demonstrate the use of aptamer-based targeting of ovarian cancer cells by coated magnetic nanoparticles for focused heating and destruction.
- Berman, Z.T., Moore, L.J., Knudson, K.E., and Whelan, R.J. “Synthesis and Structural Characterization of the Peptide Epitope of the Ovarian Cancer Biomarker CA125 (MUC16),” Tumor Biol. 2010, 31, 495-502.
- Shaw, C.L., Rutter, J.E., Austin, A.L., Garvin, M.C., and Whelan, R.J. "Volatile and Semivolatile Compounds in Gray Catbird Uropygial Secretions Vary with Age and Between Breeding and Wintering Grounds," J. Chem. Ecol. 2011, 37, 329-339.
- Liu, Y., Whelan, R.J., Pattnaik, B.R., Ludwig, K., Subudhi, E., Rowland, H., Claussen, N., Zucker, N., Uppal, S., Kushner, D.M., Felder, M., Patankar, M.S., and Kapur, A. “Terpenoids from Zingiber officinale (Ginger) Induce Apoptosis in Endometrial Cancer Cells through the Activation of p53,” PLoS ONE 2012, 7 (12): e53178.
- Felder, M., Kapur, A., Gonzalez-Bosquet, J., Horibata, S., Heintz, J., Albrecht, R., Fass, L., Kaur, J., Hu, K., Shojaei, H., Whelan, R.J., and Patankar, M.S. “MUC16 (CA125): Tumor Marker to Cancer Therapy, a Work in Progress,” Molecular Cancer 2014, 13, 129.
- Eaton, Rachel M., Shallcross, Jamie A., Mael, Liora E., Mears, Kepler S., Minkoff, Lisa, Scoville, Delia J., Whelan, Rebecca J. "Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing" Anal Bioanal Chem 2015, 407:6965–6973.
Rebecca Whelan Presents Ongoing ResearchApril 23, 2015
Associate Professor of Chemistry and Biochemistry Rebecca Whelan presented ongoing research at the 2015 Pittcon Conference & Expo on analytical chemistry and applied spectroscopy held in New Orleans. The title of her presentation was "Selection of aptamers for ovarian cancer biomarkers informed by next-generation sequencing and bioinformatics."
In addition, Whelan and members of her research group have co-authored a publication that will appear in the journal Analytical and Bioanalytical Chemistry. The title of the paper is "Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing." The other co-authors—Rachel Eaton, Jamie Shallcross, Liora Mael, Kepler Mears, Lisa Minkoff, and Delia Scoville—are all current or recently graduated Oberlin College students.