Genetic Engineering & Biotechnology News

NOV1 2018

Genetic Engineering & Biotechnology News (GEN) is the world's most widely read biotech publication. It provides the R&D community with critical information on the tools, technologies, and trends that drive the biotech industry.

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10 | NOVEMBER 1, 2018 | Genetic Engineering & Biotechnology News | Unravelling the Secrets Inside Single Cells Continued from page 1 understand how mRNA travels from the nucleus to the cytoplasm within a cell. Visualizing Cell Activity Dr. Vertes estimates that 95% of people within the single-cell analysis field are ana- lyzing RNA. "Single-cell RNA sequencing technology is very advanced," he says. "The corresponding instrumentation and proto- cols are well developed." "They enable, for the first time, [research- ers] to look at the expression levels of mRNA in individual cells," he adds. "This opens lots of new doors to see, for example, how embry- onic development happens on a cellular scale and how treatments of cells influence their ex- pression levels." One such study is by Diether Lambrechts, Ph.D., a professor and engineering in oncol- ogy genetics at VIB-KU Leuven. He will pres- ent a study to map the microenvironment of lung tumors, with the aim of creating an at- las of cell types that—in the future—could help clinicians improve their classification of lung tumors. "In the future, we could use the atlas to classify a person's lung tumor to determine if it's aggressive and which treat- ments it responds too," he explains. Dr. Lambrechts and his colleagues took tissue samples from five patients with lung cancer. The samples came, not just from the tumor, but also the surrounding area. The tis- sue was dissociated into single cells and then processed using what's now a mainstream single-cell RNA sequencing technique. This involves passing the cells through a micro- fluidic device that encapsulates them into gel beads, along with barcoded oligonucleotides and reverse transcription reagents. When the cells are lysed and the gel beads dissolved, the barcoded RNA is released into solution ready for sequencing. Since each cell has a different barcode, the RNA could be associated with a particular cell. According to Dr. Lambrechts, his team's study was special because it looked at every cell in the tumor—rather than preselect- ing specific cell types. It was able to classify the types of cell in the tumor according to the RNAs that were expressed, and it could create complex images showing the marker genes associated with both malignant and nonmalignant cells. "Another new thing about our study is that no one has ever profiled such a large number of cells from a single cancer—we did almost 100,000, so it's the size that's impor- tant," he explains. "By looking at individual cells, we've been able to see a lot of hetero- geneity in a tumor compared to what you'd see from technology two to four years ago." As well as categorizing tumor types, the the technology will be used, Dr. Lambrechts hopes, to monitor how tumors respond to treatment. "We can see what has changed at a single-cell level," he asserts. Mapping Rare Pathologies Mickaël Ménager, Ph.D., lab director at Institut Imagine (ATIP-Avenir Inserm, Necker Hospital, Paris), will describe how he is using gene expression as a way to vi- sualize disease activity within single cells. "When I joined the Imagine Institute last year, I tried to identify the best technology to look at cells in depth," he says. "I discov- ered that microfluidics allows you to per- form one experiment per droplet, to obtain the expression of the top [percentage of] genes in each cell." His research focuses on children suffer- ing from rare genetic diseases. "We're trying to use single-cell analyses as a new way to stratify patients because sometimes you have people diagnosed with the same clinical syn- drome but with a different molecular trig- ger," he explains. "If you're doing a clinical trial on a group of patients who look to be suffering the same symptoms, but who have different molecular defects, you might think the drug is not working." Dr. Ménager used a method similar to Dr. Lambrechts' for analyzing gene expres- sion. However, instead of mapping RNA ex- pressed by tumor cells, he compared the gene expression of cells from patients with the gene expression of cells from controls. His aim was to identify clusters of cells that differ and might shed light on underlying disease mechanisms. Drug Discovery BRING A WIDE RANGE OF NUCLEIC ACIDS INTO FOCUS. Get high quality downstream QC analysis for your genomics workflow with the Fragment Analyzer ™ from Advanced Analytical - A part of Agilent. Its extraordinary sizing accuracy and wide dynamic range can quickly verify the concentration and size of your DNA and RNA samples— so you can focus on discovery. Find out how QC with the Fragment Analyzer can focus your research. Fragment Analyzer ™ Automated CE System

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