Clinical OMICS

MAY-JUN 2017

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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22 Clinical OMICs May/June 2017 www.clinicalomics.com but contain a rare subpopulation of drug resistant cells that underlie tumor relapse. Similarly, metastasis may be driven by very few cells that have the ability to invade other tissues and adapt to those niches," explained Dr. Tirosh. Elise Courtois, Ph.D., of the Genome Institute of Singa- pore, worked with Dr. Robson on a study using single cell RNA-seq on cells from 11 colorectal tumors that was recently published in Nature Genetics. Discussing their work, Dr. Courtois said:"If we compare this to previous studies based on bulk transcriptomics, we were able to use this single cell signature to subdivide the different types of patients and identify important cell types for the survival of the patient, or a worse prognosis." Transitioning from Bench to Bedside Single-cell cancer genomics is still in the early stages of being developed and has yet to reach the clinic in a mean- ingful way. However, the consensus of researchers in the field seems to be that this goal is firmly on the horizon. Thierry Voet, Ph.D., is a founding member of the Sanger- EBI Single-Cell Genomics Centre in the U.K., as well as an associate professor at the University of Leuven. Speaking about how he thought single cell research will positively impact patients he said: "I think what technology will bring in the first instance is a better understanding of tumor biol- ogy. Based on that, if we understand the cellular hetero- geneity that arises within the tumor, we can devise better anticancer treatments." Dr. Voet highlighted the problems with cancer treatment failure caused by drug resistance. "There may be a variety of drug resistance mechanisms that can arise within a tumor," he explained. "Understanding how these are acquired (continued from previous page) A useful addition to the single-cell analysis repertoire would be the ability to image the location of specific genes. Mazhar Adli, Ph.D., and colleagues at the University of Virginia recently succeeded in fluorescent labelling of dif- ferent genomic areas using the RNA-guided CRISPR-Cas9 gene-editing tool. "What this live cell imaging allows us to do is to look at a single living cell, and see what is the position of a par- ticular gene in three dimensional nuclear space," explained Dr. Adli. "For example, we can track two separate genes or genomic regions that we know have different expressional status… when we look at the expressed ones they are in the nucleus and they are moving much faster than the non-expressed genes on the periphery of the nucleus." While other groups have used CRISPR technology to label chromosomal locations before now, these have always been at highly repetitive areas such as centromeric or telomeric regions. This is the first time this technique has successfully labelled non-repetitive regions. "With CRISPR we can target this to anywhere in the genome," Dr. Adli told Clinical Omics. "We can target expressed genes and non-expressed genes; we can target intergenic regions that don't code for anything. That gives us the opportunity to look anywhere in the genome that we want." Dr. Adli and his team are using the new technique they have developed to track the location of enhancer elements that regulate gene expression, but are not necessarily located near the gene they have influence over. Lighting up the Genome From the study, Live cell imaging of low- and non-repetitive chromosome loci using CRISPR-Cas9, shows snapshots of a 4 h long movie of a HeLa cell co-transfected with dCas9-mCherry, MCP–YFP and sgRNA 14 × -MS2 targeting locus #1. dCas9-sgRNA (yellow spots) remains stably bound to its targeted site throughout the cell cycle. dCas9 spots marked with a single arrow split into two closely spaced loci (double arrows) in different frames. UVA Health System Daniel Sone / National Cancer Institute (continued on page 24)

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