Melanoma is a somewhat unusual cancer that blooms before our eyes, often on sun-exposed skin, and can quickly become deadly by turning our own skin against us and spreading to other organs.
Fortunately, when caught early, melanoma can often be cured with simple surgery, and there are now better treatments for advanced cases, including immunotherapies that prime a patient’s immune system to fight the cancer. .
However, much remains unknown about melanoma, including the details of its development in the early stages and how best to identify and treat the most dangerous early cases.
Now, a Harvard Medical School team has created single-cell-level spatial maps that reveal, in unprecedented detail, how melanoma cells and neighboring cells, including immune cells, interact as they go. as a tumor grows.
The maps, described in Discovery of canceroffer insight into how interactions between cells change as melanoma progresses and how cancer cells suppress the immune system when they take over.
“The primary goal was to understand the early events of melanoma that lead to tumor development,” said lead author Ajit Nirmal, a researcher at Harvard Medical School.
The HMS team is building the maps into an atlas of melanoma that will be freely available to the scientific community as part of the National Cancer Institute’s Human Tumor Atlas Network. They hope that eventually the atlas can serve as a starting point for scientists to study how to prevent melanoma and how to treat it in its early stages before it becomes full-blown cancer. The ultimate goal of these efforts is to help doctors diagnose melanoma and help them prescribe treatment tailored to each patient’s individual tumor profile.
“This was an opportunity to study melanoma in its early stages and collect a resource of information that we can share with the community,” said Sandro Santagata, HMS associate professor of pathology at Brigham and Women’s Hospital and co-author main of the article. with Peter Sorger, HMS Otto Krayer Professor of Systems Pharmacology.
Map the unknown
In recent years, a considerable amount of melanoma research has focused on two areas: DNA sequencing of early tumor samples to understand the genetic changes that occur when this particular cancer arises, and sequencing of Single-cell RNA from the immediate environment of the tumor – the so-called tumor microenvironment – to profile the types of cells present. However, researchers have remained largely in the dark about how tumor cells and neighboring cells are physically arranged in space, and how these cells interact at the molecular level as melanoma grows.
“What we still don’t know is how the microenvironment is organized to allow a tumor to grow,” Nirmal said. “In theory, immune cells are supposed to identify tumor cells and kill them very quickly, but clearly something went wrong, and that’s one of the main reasons why we want spatial resolution. “
Such spatial resolution, as well as small-scale molecular data, has only recently become possible with the advent of more advanced single-cell imaging technologies, including cyclic immunofluorescence, or CyCIF, a multiplexed imaging technique developed by the Sorger laboratory.
In the new paper, the researchers combined CyCIF imaging data with high-resolution 3D microscopy and large-scale RNA sequencing to create maps capturing where cells are and how they interact when normal tissue transforms. in melanoma.
“We’re able to see everything from normal skin to early lesions to invasive melanoma, sometimes all in a single piece of tissue,” Santagata said. “You end up with this map of how melanoma grows right in front of you.”
The maps reveal what Santagata describes as “the battle between tumor cells and immune cells” that results in melanoma death when immune cells are victorious and melanoma progression when tumor cells win.
Specifically, the maps showed that in the early stages of melanoma, so-called precursor lesions were composed of cell types and proportions similar to normal skin, but these cells had a radically different pattern of interaction, which included signs of immunosuppression.
“This indicates that there is likely some level of restructuring in the tumor microenvironment that could potentially promote tumor development,” Nirmal said.
At the onset of melanoma, PD-L1 – a protein that suppresses the immune system and allows cancer to grow – was not expressed in tumor cells but was present in adjacent immune cells called myeloid cells. As the tumor grew, PD-L1-expressing myeloid cells increasingly interacted with primed T cells to kill the tumor cells. This interaction between immune cells, rather than between cancer cells and immune cells, may be a mechanism that cancer uses to weaken the immune system so that it can grow unchecked.
“This may mean that the immune system is suppressed, or inactivated, by itself, and not directly by the cancer,” Sorger said.
Immunotherapies that inhibit PD-L1 and its binding partner PD-1 and thus unleash the immune system against the tumor have revolutionized the treatment of advanced melanoma. However, not all melanoma patients respond, and these therapies have not been as effective in treating some other cancers. So, Sorger hopes that basic research on PD-L1 expression will provide a foundation for understanding which melanoma patients are most likely to benefit from immunotherapies and how scientists can make therapies work in more cancers. Knowledge may also inform therapeutic strategies for melanomas that remain resistant to available treatments.
In more advanced melanoma, the condition of the cancer cells differed depending on their physical location. Cells in the middle of a tumor that were surrounded by other cancer cells behaved markedly differently than cells at the outer edges of the tumor that could interact with nearby immune cells and stromal cells. This finding suggests that this cellular mixed bag — known as tumor heterogeneity — may be partly due to epigenetic changes that occur in tumor cells when they interact with other cell types, Nirmal said. Understanding tumor heterogeneity is important, he added, for understanding why and how certain parts of a tumor survive treatment while others do not, especially in the context of therapies that target specific molecular pathways. .
Taken together, the results demonstrate that “these local environments involve far more physical interactions between cells than we might have thought,” Sorger said. “Cells are actually in an incredibly dense communication network.”
“Tumor cell neighborhoods and cell-cell interactions tell us how the tumor may progress, and this is a whole new form of biomarker that hasn’t been applied before,” Santagata added. “With these new spatial maps, we have the ability to link cellular interactions to physiological behavior and, eventually, to clinical outcomes.”
With this paper, the researchers are releasing the largest image-based melanoma dataset to date – and the dataset will be freely available through Minerva, an online visualization tool developed by the lab to make complex data easier to understand and use. Now the team is working on adding more melanoma samples to the project, with the goal of better understanding what features and interactions can be considered typical.
“We want to be able to tell what’s happening in a recurring way, rather than idiosyncratically. Quantity has a quality of its own, and so scaling is a critical step,” Sorger said.
The researchers are building the maps into an open-source melanoma atlas within the Human Tumor Atlas Network that captures the full range of molecular interactions between cells at different stages of disease. They envision the atlas to have a similar impact to previous cancer genomics atlases, including the Cancer Genome Atlas. Ultimately, they hope their work will propel new insights into melanoma that will lead to precisely targeted individualized treatments based on a patient’s tumor characteristics.
“There is no precision medicine without diagnosis,” Sorger said, but 85-90% of cancers are diagnosed based on tissue samples alone. He believes the process of diagnosing and treating melanoma could be improved by incorporating multiplexed imaging techniques, like CyCIF, which provide fine-scale molecular information about the tumor ecosystem and comparing the results to an atlas of melanoma. .
The study was funded by the NIH (U2C-CA233262; K99-CA256497), the Ludwig Center at HMS, the NCI (R50-CA252138), the Finnish Medical Foundation, and the Relander Foundation.
Other authors include Zoltan Maliga, Tuulia Vallius, Alyce Chen, Connor Jacobson, Roxanne Pelletier, Clarence Yapp, Raquel Arias-Camison and Yu-An Chen of HMS; and Christine Lian, George Murphy and Brian Quattrochi of Brigham and Women’s Hospital.