'Barcode' profiling enables analysis of hundreds of tumor marker proteins at once

A new technology allows simultaneous analysis of hundreds of cancer-related protein markers from miniscule patient samples gathered through minimally invasive methods. This new technology uses antibodies linked to unique DNA 'barcodes' to detect a wide range of target proteins and is both powerful and exquisitely sensitive.

The technology was developed at the Massachusetts General Hospital (MGH) Center for Systems Biology (CSB) in Boston. This research was reported in Science Translational Medicine (2014;6[219]:219ra9).

Minimally invasive techniques—such as fine-needle aspiration or circulating tumor cell analysis—are increasingly employed to track treatment response over time in clinical trials. Such tests can be simple and cheap to perform. Fine-needle aspirates are also much less invasive than core biopsies or surgical biopsies, because very small needles are used. The challenge has been to comprehensively analyze the very few cells that are obtained via this method.

"What this study sought to achieve was to vastly expand the information that we can obtain from just a few cells," explained coauthor Cesar Castro, MD, of the MGH. "Instead of trying to procure more tissue to study, we shrank the analysis process so that it could now be performed on a few cells."

Up until now, pathologists have been able to examine only a handful of protein markers at a time for tumor analyses. But with this new technology, researchers can look at hundreds of markers simultaneously down to the single-cell level.

"We are no longer limited by the scant cell quantities procured through minimally invasive procedures," said Castro. "Rather, the bottleneck will now be our own understanding of the various pathways involved in disease progression and drug target modulation."

The novel method centers on an approach known as DNA-barcoded antibody sensing, in which unique DNA sequences are attached to antibodies against known cancer marker proteins. The DNA 'barcodes' are linked to antibodies with a special type of ‘glue' that breaks apart when exposed to light. When mixed with a tumor sample, the antibodies seek out and bind to their targets; then a light pulse releases the unique DNA barcodes of bound antibodies that are subsequently tagged with fluorescently labeled complementary barcodes. The tagged barcodes can be detected and quantified via imaging, revealing which markers are present in the sample.

After initially demonstrating and validating the technique's feasibility in cell lines and single cells, the team went on to test it on samples from patients with lung cancer. The technology was able to reflect the great heterogeneity—differences in features such as cell-surface protein expression—of cells within a single tumor and to reveal significant differences in protein expression between tumors that appeared identical under the microscope. Examination of cells taken at various time points from participants in a clinical trial of a targeted therapy drug revealed marker patterns that distinguished those who did and did not respond to treatment.

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