This time of year definitely feels like conference season! Our bags are barely unpacked from ASHG in Canada before it’s time to head south over the border to North Carolina for the 2016 annual meeting of the Association of Molecular Pathologists.

Molecular pathology as a discipline benefits enormously from rapid advances in our understanding of the genome. In a relatively short space of time we have gone from single molecule tests to highly sophisticated assays that can screen for just about anything, from DNA, to transcriptome, to proteins. At this year’s meeting, NanoString will be showcasing some of these advances in two workshops designed to show how this new generation of molecular assays can support and enhance the work of molecular pathologists. 

To find out more about how NanoString are advancing the world of molecular assays, we sat down with Sean Ferree, Vice President of Diagnostic Development.

FLG: We’re constantly told that our DNA is what makes us unique. This can give people a simplistic view that everything important happens at the sequence level. But what’s really important is gene expression, and is an area that NanoString really specialise in. What kind of work are your customers applying your technology to?

SF: That’s a great question. I think the response at the highest level is everything. This technology is broadly applicable and we have researchers using it for everything from developmental biology in model organisms, to research in infectious diseases, inflammation and immunology. The most common application is oncology research. There’s even agricultural research going on. You name it! The technology is very powerful.

As you mentioned, genetic information at the DNA level is very important but it’s only part of the picture. We know now, and we’ve known for decades, that DNA is just one part of the equation. That DNA needs to be transcribed into RNA and protein, and these are tightly regulated processes. You can have an identical DNA sequence, but with different epigenetics or different transcriptional control that results in very different downstream biological consequences. This is important in applications from human disease to agriculture to developmental biology, and can be widely applied in many different fields.

FLG: NanoString have carved out a great niche in translational genomics. That’s an exciting place to be as you’re directly impacting real world applications. As a company, you’re very well known for helping researchers quantify and profile RNA, DNA, and even proteins. Where do you think the biggest impact will be from having a greater understanding of how those molecules behave and interact?

SF: It really is the translational research applications of the technology that are going to have the greatest impact. One of the hallmarks of the NanoString technology is its robustness. This is the only technology out that that can directly, without any enzymology, profile mRNA in a biological sample digitally. That ability to directly look at mRNA without any enzymatic reaction, with no reverse transcription, no PCR amplification, makes the process exquisitely simple and exquisitely robust. We can work with extremely challenging sample types, like formalin fixed paraffin embedded tissue (FFPE) samples, and we can get reproducible RNA expression profiles out of these samples. We’ve worked with samples that are 40 years old! A box that had been stored in a filing cabinet somewhere for 40 years, we can pull those samples out and we can profile them using the NanoString technology. This wasn’t possible just a few years ago, and now we can do it with the nCounter.

What that means is that we can now apply these complex genetic tests in any laboratory anywhere in the world, and we can get equivalently robust and reproducible data on this platform no matter where we run it. That robustness really lends itself to translational research; those researchers who are making discoveries in their laboratories and have the aspiration to take them all the way to the bedside to help patients. To do that you really want to have a technology that’s going to stand up to that test, that’s going to be deployable in a clinical setting. You need to know that the data that you’re generating in your laboratory are going to be representative of the data that will be generated in a clinical laboratory when this gets converted into a clinical test. This is the only technology out there that has this reproducibility and robustness.

We’re already having an impact here; we have translated academic discoveries and industrial discoveries several times, and we expect to repeat that over and over again in the future.

FLG: Companion diagnostics represent the promise of precision medicine. In combination with the right drug, companion diagnostics can help you identify the right patient for a much more effective treatment. But the number of approved companion diagnostics isn’t huge. The development process is technically intensive, and it is also followed by a strenuous regulatory process. Can you give a brief explanation of what the current situation for companion diagnostics is, and what you’d like it to look like in the near future?

SF: Today there are really just a handful of different flavours of companion diagnostics. The majority of tests are three main technologies that form the basis of companion diagnostics today: immunohistochemistry (IHC), fluorescent in situ hybridisation (FISH), and looking at point mutations in the DNA to target therapeutics. That’s the state of the world today, and we had aspirations and hopes over the last few decades that there would be many different companion diagnostics using these simple technologies to direct therapeutic treatments. However it turns out that, in oncology, where essentially all of these companion diagnostics are employed, that the biology is much more complex than that, and we’ve been stymied over and over again finding good biomarkers that can predict response. As the biology is more complex, typically that means you need a more complex biomarker.

In addition to the biology being challenging, drug development is also hugely challenging. We have to take our hats off to the incredibly smart people out there doing drug development. At the same time we need equivalent development programs for biomarkers and companion diagnostics. We need to be able to develop these complex diagnostics to really match the complexity of the disease, so that we can truly identify the patients who are going to best respond to this next generation of therapeutics.

It is our belief here at NanoString that this will not be single analyte assays; we’re going to be running multiplexed assays such as multiplexed gene expression assays. Currently we’ve got several assays in development looking at diffuse large B-cell lymphoma; looking at gene expression signatures in triple negative breast cancer to identify patients that will respond to anti-androgen receptor therapy; and then we have collaborated with Merck to develop a tumour inflammation gene expression signature that can identify the inflammation status of a solid tumour and and is being validated to understand which patients would benefit from PD-1 inhibition.

Today all these signatures are multiplexed gene expression assays, but we see a future where we don’t limit ourselves to just gene expression. We believe that there are alterations at the DNA level, at the RNA level, and the protein level that are important. We look to a future where these assays, that we call 3D Biology assays, can be taken to the clinic as well.

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FLG: As you would expect, NanoString have a strong presence at next month’s Association for Molecular Pathology Annual Meeting. If there’s a particular group of people that should be very interested in what you do, it’s very much molecular pathologists. As their field changes as genomics, and other omic technologies, develop, where do NanoString fit in for them?

SF: The workhorses of molecular biology and molecular pathology over the past decade have been FISH, other ISH technologies, and quantitative PCR for detection of single nucleotide polymorphisms. Today we’re moving more into next generation sequencing, which can give you information at the DNA level, and some abilities with RNA profiling. The NanoString platform sits in very nicely there, in many cases can complement these older technologies, and even replace them.

There have been a number of different publications using the NanoString technology for identification of expressed fusions, such as ALK fusions in lung cancer, which can be multiplexed together. So you have your five different fusions that you are interested in for targeting patient therapies, and rather than running five different FISH assays, we can multiplex those together into a single assay. FISH is quite a labour-intensive process, so in this instance we can really complement the existing technology for expressed fusions, which will be a real boon to molecular pathologists.

For quantitative PCR, just recently at ASHG 2016 we launched a new, research-use only panel for identification of single nucleotide variants in oncology, and we see that this technology can be applied at the DNA level for applications that today use qPCR. This is a multiplexed targeted assay where we can identify hundreds of variants using the NanoString technology. One of the great things about our 3D biology applications is that we can even combine this together with RNA expression profiles, or even protein profiles.

So we hope that in the near future this technology can be of enormous benefit to molecular pathologists by decreasing the amount of labour that they put into running these assays, and increase the amount of information that they get.

FLG: You’re putting a big emphasis on education for AMP 2016, with a couple of workshops on the agenda. Can you tell us a bit more about those workshops, what people are likely to learn, and why should they be there?

SF: We’ll the running two workshops this year. The first focusses on our collaboration with Merck to develop a tumour inflammation signature. Merck has been and remains a thought leader in the development of biomarkers for immuno-oncology, and they have been deploying the NanoString system in their research labs for quite a number of years. They identified an RNA expression signature that can predict response to their PD-1 inhibitor in a number of different tumour types. We’ve partnered with Merck to develop this into a clinical assay, and potentially a companion diagnostic for a number of different tumour types.  Dr Matt Marton is going to be presenting data from this collaboration in the workshop, and I think it’s going to be a really exciting presentation. You’ll learn how the assay was developed, learn about the robustness and reproducibility of this assay, and the application of this assay across a broad range of tumour types.

The second workshop is a presentation by our Senior Vice President of Research and Development here at Nanostring, who will be talking about a new method for using optical barcodes for spatial profiling of protein and RNA on FFPE samples.  This is a new technology that we have developed, and is really exciting because in immuno-oncology IHC has really been the workhorse for understanding the interplay between the immune system and the tumour. One thing that we have seen over and over again is there’s spatial heterogeneity in this interaction. IHC is a fantastic technology for evaluating that spatial heterogeneity, and for understanding that interplay, but the challenge is that it covers a single molecule at a time and is very low multiplex. What we have developed is a technology where we can multiplex together the detection of many different proteins, as well as the detection of mRNA expression in a spatially resolved manner.