Breast cancer: The diversity of metastases

Metastatic breast cancer (MBC) is the most common cause of cancer-related death in women worldwide. Despite considerable progress in cancer therapy and modern targeted treatment approaches, many metastatic tumors are still incurable. One reason for this is the complex heterogeneity of tumors, which has so far only been studied to a limited extent due to methodological challenges. An international team led by LMU biomedical scientist Johanna Klughammer together with Daniel Abravanel, Aviv Regev and Nikhil Wagle, researchers at the Dana-Farber Cancer Institute and Broad Institute of MIT and Harvard University, has now used various methods in a comprehensive study to analyze the diversity of metastatic cells and their interaction with the environment. The results are a valuable basis for future studies and provide new insights into the biology of metastatic breast cancer.

As part of the Human Tumor Atlas Network (HTAN), the researchers analyzed the entirety of all RNA molecules from a total of 67 biopsies from 60 patients with breast cancer metastases. These so-called transcriptomes show which genes are active at a certain point in time. The scientists used two different approaches: Either the entire transcriptome of the cells is measured or only that of the cell nucleus. However, with these methods, information about the spatial arrangement of the cells is lost. In order to capture this information as well, the researchers also created spatial expression profiles for 15 samples and analyzed serial tissue sections using up to four different spatially resolved methods.

Extensive data set

"With this extensive data set, we were able to compare the various methods and identify similarities and differences. Our results can help researchers in the future to select the most suitable method for their research question," says Klughammer, who was responsible for the data analysis. The metastases studied originated from nine different locations in the body - including the brain, liver and bone - and comprised different clinically relevant subtypes. "The broad approach somewhat limits the statistical significance of individual variables, but we still found interesting clues about the biology of the metastatic cells," says Klughammer. This includes information about which cell types occur in the metastases, how certain genes are activated in these cells and how the cells are spatially arranged in the metastases.

One surprising finding for the researchers was that the malignant cells in the body of one patient showed very stable expression profiles. "We examined more than one biopsy from some patients and found very similar expression profiles, even if the metastases came from different parts of the body or there were up to 200 days between sampling," says Klughammer. However, the researchers found major differences between the patients.

Various cell profiles characterized

The researchers were also able to link some clinical characteristics to different malignant expression phenotypes: Most malignant cells showed typical characteristics of epithelial cells. In some samples, however, the researchers also observed the expression of genes associated with stem cells, neurons or cartilage tissue. The sample with stem cell-like behavior came from a patient who, despite early diagnosis and correct treatment, had the shortest survival time in the group. The sample with "cartilaginous" behavior was the only one with histology typical of a rare and often difficult-to-treat form of breast cancer.

Metastases usually consist of cancer cells, the natural cells of the affected tissue and migrated immune cells that can potentially fight cancer cells. "An exciting finding was that the expression profile of the malignant cells differed depending on whether they had certain immune cells (so-called T cells or NK cells) in their vicinity or not," says Klughammer. For example, the researchers found that malignant cells that had no T/NK cells in their vicinity expressed more of the SOX4 gene. This suggests that immune escape mechanisms may have a very localized effect and not just at the level of the entire metastasis.

"Overall, our study offers new insights into the biology of metastatic breast cancer and shows the potential of spatially resolved analyses," explains Klughammer. "In the long term, our results could help to classify patients in a more nuanced way and develop more targeted therapeutic approaches."

J. Klughammer et al.: A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features. Nature Medicine 2024