Pathologists at Dana-Farber analyze tumor samples from tissues collected from patients as part of research studies. Their goal is to learn as much as possible about the sample so that they determine the best way to diagnose the disease precisely and guide treatment decisions.
As research advances, more and more factors are influencing diagnoses and treatments. For example, the presence of specific gene mutations in a tumor might indicate that a certain treatment is appropriate. A lack of immune activity might indicate that immunotherapy is not appropriate.
At Dana-Farber, pathologists are using innovative microscopy technologies to look at tumor samples both more holistically and more precisely, an approach called spatial biology. The pathology team is using this and other technologies to support cancer research and enable discoveries that improve treatments for patients.
“Cancers are complex systems, like cities,” says Dana-Farber research scientist Namrata Singh, PhD, in the Department of Pathology at Dana-Farber. “We want to take a census of all these features, see where they are and how they relate to each other and to know what the system looks like when treatments are working and when they are not working.”

Tried and true tech
The most fundamental form of microscopy used to analyze tissue samples is traditional H&E (Haemotoxylin and Eosin) stains. These pink and purple shaded stains help pathologists see cell structures, such as the nuclei, cytoplasm, and cell membranes.
In cancer diagnostics, a trained pathologist can glean many features of cancer from a simple H&E stained slide. Researchers are also investigating methods that use AI to analyze the slides and extract even more detail from them.
Detecting specific biomarkers under the microscope
As researchers learn more about cancer, they are discovering that some cancers have specific features, called biomarkers, that can be targeted by precision medicines.
For example, precision medicines that target the EGFR (epidermal growth factor receptor) receptor in lung and other cancers and the HER2 (human epidermal growth factor receptor 2) in breast and other cancers have revolutionized the way these cancers are diagnosed and treated.
Pathologists analyze tissue samples to identify these biomarkers during diagnosis. One traditional method is immunohistochemistry (IHC). With this method, cells on a slide are stained to provide a view of the cellular structure. Then additional stains, either chemicals or antibodies, are layered on. The added stains reveal the presence of biomarkers of interest.
In breast cancer, for example, IHC is performed to diagnose HER2-positive, HER2-negative, and HER2-low breast cancer, ER-positive breast cancer, triple-negative breast cancer.
There are many biomarkers in cancer, however, and traditional IHC is limited to analyzing two or three biomarkers per sample. To identify more markers, pathologists also rely on next-generation sequencing (NGS) of the genes in the cells of a tumor sample to identify all the genetic alterations in the sample.
The challenge with NGS, though, is that diagnostic methods mix all the cells together before analyzing the genes. As a result, pathologists can no longer see where key markers are in relation to the tumor or the tissue around it. New technologies, however, that enable an approach called spatial biology are helping to solve this challenge.
Getting the whole picture with novel microscopy

An instrument called the phenocycler-fusion is making it possible for pathologists to see up to 100 molecular biomarkers across every cell in a tumor sample without disturbing the cells on the slide. This is, for the first time, providing both a holistic and precise view of a tumor sample.
To use the system, Singh uses the system’s microfluidic system to apply a cocktail of up to 40 antibodies to a slide containing a tissue sample:
- The system flows the antibodies in for staining and imaging, and then removes them in preparation for another cocktail.
- During staining, each antibody binds to a biomarker of interest and carries a fluorescent reporter that glows a distinct color to signal the presence of a particular biomarker.
- During imaging, the slide will light up with fluorescent colors indicating the presence and location of the biomarkers.
Singh can switch signals on and off, for instance, to focus on immune biomarkers or to examine biomarkers that indicate a specific type, stage, or feature of the cancer.
At Dana-Farber, this technology is not yet used for diagnostics for patients visiting the clinic, but it is being used in research to learn more about how tumors behave after treatment and how the immune system behaves in relation to the cancer and in response to immunotherapy. It is also being used to discover new potentially important biomarkers and find new ways to predict how a tumor will respond to therapy.
“This technology allows us to capture wonderfully detailed maps and to enumerate every nest of cancer cells, every blood vessel, every immune cell,” says Singh. “The images are simply beautiful, and the results make each study rewarding.”
Feel free to reach out to our team for more information or to schedule a demo. We’re excited to see the transformative impact this technology will have on your research!
Thanks @ElizabethDougherty and @PeggyKaszas