IGERT student profile: Jacob Koskimaki

Picture of Jacob Koskimaki
Jacob Koskimaki. Credit: Mary Spiro/JHU

Blood flow gives life to both normal and cancerous tissues. Cutting off cancer cells from their blood supply through drugs that prevent blood vessel growth can control tumor growth. Jacob Koskimaki is a third year biomedical engineering graduate student with the NanoBio IGERT* at Johns Hopkins Institute for NanoBioTechnology (INBT). He uses bioinformatics techniques to search for proteins that are antiangiogenic—meaning that they inhibit blood vessel growth. Koskimaki works in the systems biology lab of Aleksander Popel, biomedical engineering professor at the School of Medicine and an INBT affiliated faculty member.

“These proteins have several therapeutic advantages in that they are naturally occurring in the body, so they have low toxicity and can be reproduced synthetically,“ Koskimaki says. He uses a systematic searching technique to data mine the human genome maintained by the National Center for Biotechnology Information called BLAST (Basic Local Alignment Search Tool). BLAST can compare the sequences of proteins known to halt the growth of blood vessels to the protein sequences of domains that are not yet known to be antiangiogenic. This method has helped discover new protein fragments with antiangiogenic properties. The resulting fragments are then experimentally applied to several disease models as novel treatments for lung and breast cancer. (This is a continuation of the research by a former PhD student in the Popel lab Emmanouil Karagiannis, now a postdoc at MIT).

“There has been a lot of interest in finding antiangiogenic compounds,“ Koskimaki says, “and a lot of money has been invested leading to several promising treatments.“ For example, he adds, the drug Avastin was the first FDA approved anti-angiogenic drug. When used in conjunction with chemotherapy, Avastin can extend a patient’s life by blocking angiogenic growth factors and halting tumor progression.

Koskimaki also collaborates with Zaver Bhujwalla, radiology professor at the Johns Hopkins School of Medicine. Bhujwalla develops noninvasive imaging techniques to understand cancer. She also directs the In Vivo Cellular and Molecular Imaging Center (ICMIC). Using functional magnetic resonance imaging (fMRI) they can understand important characteristics of peptide-treated tumors such as blood vessel permeability and volume.

Koskimaki traveled many academic paths before setting his sights on science. He began college as a piano performance major at the University of Utah, but was drawn to the technical aspects of biomedical engineering. In addition, he double majored in economics seeking to obtain a broad perspective. Koskimaki explains, “science funding and research are inherently linked to the larger economic landscape, and knowledge of economics is a great asset to any research career.“ During his biomedical engineering studies, he researched the mechanical properties of the glycocalyx, the outer coating of the cell membrane. His positive experiences, along with his interest in developing novel therapeutics lead him to pursue a Ph.D. in the field.

Always interested in trends and politics, Koskimaki could see himself pursuing careers in industry, academia, or writing. He recently began working as a science writing intern for the Institute for Nanobiotechnology and is looking for other opportunities to write. He also enjoys traveling and spent two weeks in India this fall.

*IGERT, which stands for Integrative Graduate Education and Research Traineeship, is a program funded by the National Science Foundation.

For more information on the INBT IGERT program, go to http://inbt.jhu.edu/igert.php

To learn more about the research of the Popel Lab, go to http://inbt.jhu.edu/facultyexpertise.php?id=personalresult&usr=179

For more information on ICMIC and Dr. Bhujwalla, go to http://icmic.rad.jhmi.edu/index.cfm?section=home

Story by Mary Spiro

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