How it all began...
ngTMA® was driven by our motivation to study protein expression in tumor buds in colorectal cancers. Tumor buds are single cells or small tumor cell clusters found either at the invasion front or within the main tumor body of many different cancer types.
Convinced that these cells were a cause of distant metastatic spread, we wanted to characterize tumor buds on a protein and molecular level and relate the differences in expression back to patient outcome.
Although with standard tissue microarraying we could get the sample size, the standard punch diameter was too small to ensure the capture of these tiny cell clusters. Capturing high-grade budding was nearly impossible without knowing exactly where to punch.
The task was simply unachievable and it was clear that we needed a much more precise way to punch these tumor buds out.
In 2011, we were introduced to the technology that could make this happen: a slide scanner and automated tissue microarrayer by 3DHistech. A slide could be scanned, annotated and then aligned to the image of the donor block. The annotated regions were cored and transferred into a TMA block- this is what we needed for our budding! This is what everyone needed to answer their targeted biomarker research questions.
Enter ngTMA in October 2012 and the rest, as they say, is history …
Our logo and trademark
Approximately 30% of the ngTMAs that we construct are used to investigate biomarkers from the gastrointestinal tract. A large proportion of these cases are cancers from the stomach, esophagus and colorectum.
However, tissues from both adult and pediatric patients with non-cancerous entities have also been assembled for ngTMA, for example, those with inflammatory bowel disease or juvenile polyps. The group of “Other” tissues includes multi-tissue ngTMAs, or special tissue types such as the eye or heart.
Not only human!
Although most of what we construct comes from human patient samples, there are a growing number of projects performed on animal tissues. These ngTMAs are typically made using mouse tissues and are used for several purposes, including establishment of antibodies for our Comparative Pathology platform (www.compath.ch). We have constructed whole-organ ngTMAs, primary cancer xenograft ngTMAs and experimental ngTMAs that compare wild-type and knock-out mice in a side-by-side approach for evaluating protein expression.
Why cell lines?
We include cell lines into ngTMAs when they are used as immunohistochemistry controls. Moreover, screening of many cell lines side-by-side for expression of a certain number of biomarkers is increasingly demanded and more cost effective than using whole sections when a large number are investigated.
What happens after?
ngTMAs are a powerful tool to study protein, RNA and even DNA aberrations. Based on the aim and the methods planned to visualize these molecules afterward, we help design the ngTMA that will lead to the optimal result.
Our own TRU lab has a list of more than 400 antibodies against human and animal tissues (also including on occasion rat, pig and horse in addition to mouse), that are routinely used to stain ngTMAs. Double immunohistochemistry is standardly performed (below, cytokeratin and CD8).
In our lab, we love double-staining!
Even more, we have successfully established mRNA ISH probes (and miRNA ISH) as well as DNA FISH or SISH on our ngTMAs. Combinations of mRNA and protein are also done. Even if you do not want us to make the staining, we suggest we cut the blocks for you- this is a very specialized histopathological skill. You will find some of our publications using ngTMA here.
Digital image analysis
DIA has become an extremely important and highly valuable method to evaluate expression of proteins and genes, especially on ngTMAs. Since ngTMA annotations are so easy to make, a HUGE increase in the number of cores per patient has occured.
Now, we are talking about evaluating 1’000 cores instead of 100. The excellent article by Nolte and colleagues outlines guidelines for the use of ngTMA combined with DIA and relevant aspects to look out for.
The right core diameter
Although the classic 0.6 mm diameter TMA core is still preferred, there are several reasons we often recommend a larger punch size. ngTMAs with 2.0 mm cores have been produced for animal models, while those with 1.5 mm were found to capture heterogeneous regions more optimally in endometrial carcinomas than smaller sizes.
Tumor microenvironment studies are often performed with 1.0 mm cores, especially when only a few cells are the target of investigation. In general, the decision regarding size of needle, depends on the tissue type, the abundance of tissue in the block and most importantly the interfaces that need to be captured.
ngTMA® clients- who are they?
We construct ngTMAs for many different types of researchers. The first two years after our launch, there was a massive interest in ngTMA in our own Institute, so primarily our own pathologists were putting together cohorts and constructing ngTMAs. The news of ngTMA began to spread and we are now delighted to work with clinicians and researchers from all across Switzerland and abroad.
Some examples in Switzerland are the Insel Hospital, Department of Clinical Research in Bern, Institute for Biochemistry and Molecular Medicine, Ecole Polytechnique Federale de Lausanne (EPFL), Hopital Universitaire de Geneve (HUG), and University Hospital of Basel.
We have international and recurrent clients from hospitals, research centers and clinical trials organisations in Germany, the Netherlands, France and Belgium working to investigate biomarkers in cancers and rare diseases.