Vesicle DNA, RNA and protein analysis can ID tumor vulnerabilities, guide treatment decisions and monitor response
Precision cancer treatment relies on obtaining molecular information about the tumor to guide effective treatment decisions. Because needle biopsies of brain tumors are invasive and difficult, bioengineers have developed micro technologies that capture extracellular vesicles (EVs) released by brain tumors. The vesicles carry samples of the mutated genetic material and proteins causing malignancy that researchers hope to analyze to optimize treatment.
Although they carry a wealth of information, EVs from tumors are very small particles, made of lipids, and are relatively rare. Therefore, researchers have developed microfluidic devices that can take a small sample of blood from a patient and capture the EVs and their contents for analysis. Work reported in the February issue of Nature Communications describes development of a new microfluidic device, the EVHB-Chip, that significantly increases the capture of EVs from volumes smaller than a single drop of blood.1
A major factor in isolating these rare EVs from cancer cells is that they are mixed in with billions of EVs from healthy cells that appear to be part of a communication network used to change or augment the function of surrounding cells. For example, in healthy cells, EVs contain a subset of nucleic acids that can manipulate their cellular microenvironments to promote wound healing. Conversely, cancer EVs carry molecules that promote cancer spread through angiogenesis (creation of new blood vessels), invasiveness, and metastasis.
Led by Shannon Stott, Ph.D., Assistant Professor at the Center for Engineering in Medicine at Massachusetts General Hospital, bioengineers designed a microfluidic chip with a staggered herringbone surface. The herringbone chamber is coated with antibodies known to bind to proteins found in brain tumors and that are carried on the surface of the EVs. EV yield is enhanced by turbulence created by the herringbone structure, which increases the frequency with which EVs collide with the capturing antibodies on the chamber walls.
Using the EVHB-Chip, the researchers analyzed blood samples from 13 patients with the brain tumor glioblastoma multiforme (GBM). The EVHB-Chip successfully isolated enough tumor-specific EVs from all 13 patients to analyze the cancer genes present. The analysis revealed high levels of more than 50 cancer-associated genes including the cancer-specific GBM mutation EGFRvIII.
“We are also excited about the potential of this technology with pediatric brain cancer patients, from which only very small amounts of blood can be obtained, especially repeatedly to monitor the effectiveness of therapy. Effectiveness is measured by molecular changes in the captured EVs over the course of treatment,” said Stott.
The work was supported by grants EB002503 and EB008047 from the National Institute of Biomedical Imaging and Bioengineering, the National Cancer Institute, the Wang Pediatric Brain Tumor Collaborative, and the Canadian Institute of Health Research.
1. Engineered nanointerfaces for microfluidic isolation and molecular profiling of tumor-specific extracellular vesicles. Reátegui E, van der Vos KE, Lai CP, Zeinali M, Atai NA, Aldikacti B, Floyd FP Jr., H Khankhel A, Thapar V, Hochberg FH, Sequist LV, Nahed BV, S Carter B, Toner M, Balaj L, T Ting D, Breakefield XO, Stott SL. Nat Commun. 2018 Jan