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'Barcoding' enables analysis of hundreds of tumor marker proteins at once from tiny tumor samples

'Barcoding' enables analysis of hundreds of tumor marker proteins at once from tiny tumor samples | Open Mind & Open Heart | Scoop.it
A new technology developed at the Massachusetts General Hospital Center for Systems Biology allows simultaneous analysis of hundreds of cancer-related protein markers from miniscule patient samples gathered through minimally invasive methods.

 

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, as such tests can be simple and cheap to perform. Fine needle aspirates are also much less invasive than core biopsies or surgical biopsies, since 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," explains Cesar Castro, MD, of the MGH Cancer Centerand CSB, a co-author of the Science Translational Medicine paper. "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 at CSB have demonstrated the ability to 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," says 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 the 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. 


Via Dr. Stefan Gruenwald
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Comparing Genome Editing Technologies

Comparing Genome Editing Technologies | Open Mind & Open Heart | Scoop.it
ZFN, TALEN, and CRISPR/Cas systems help scientists dissect
the vast amount of information accumulated through
the Genomic Revolution.

 

The Genomic Revolution has promised to advance medicine and biotechnology by providing scientists with enormous amounts of data that can be converted into useful information.

 

Over 10 years ago, the Human Genome Project produced the first draft of the more than 3 billion base pairs of DNA that make up the genetic code in each of our cells.

 

More recent efforts like the 1000 Genomes and HapMap Projects have since focused on identifying the differences within these billions of base pairs of DNA between individuals, while genome-wide association studies have pinpointed specific sequences that determine health and disease. The ENCODE Project and other studies have annotated chromatin states, regulatory elements, transcription factor binding sites, and other epigenetic states throughout the genome.

 

Dozens of other species have since undergone similar analyses, with the number of sequenced genomes continuously growing. Collectively, these efforts have generated an incredibly rich source of data that promises to aid our understanding of the function and evolution of any genome. However, until recently, scientists have been lacking the tools necessary to interrogate the structure and function of these elements.

 

While conventional genetic engineering methods could be used to add extra genes to cells, they cannot be easily used to modify the sequences or control the expression of genes that already exist within these genomes. These types of tools are necessary to determine not only the function of genes, but also the role of genetic variants and regulatory elements. They can also be used to overcome longstanding challenges in the field of gene therapy. Without these technologies, it has been difficult—and in some cases impossible—for scientists to capitalize on the Genomic Revolution.


Via Dr. Stefan Gruenwald
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