Skip to main content
Premium Trial:

Request an Annual Quote

Spatial Molecular Microscopy Enables Mapping of Breast Cancer Clones

NEW YORK — With a molecular microscopy approach, an international team of researchers has mapped the different clones making up breast tumors from two patients. The results provide new insights into how tumors develop and interact with their environment.

The workflow used in the study draws on the base-specific in situ sequencing (BaSISS) method and enables the generation of quantitative maps of the genetic makeup of tumor clones and their spatial organization.

The team applied this approach to map eight tissues from two patients with multifocal breast cancers, including samples from differing stages of cancer development. As they reported in Nature on Wednesday, the researchers found that the samples showed a spatial organization of clones, with specific gene expression patterns as well as microenvironments and microanatomical niches.

"This innovative technique allowed us to accurately reconstruct the spread of these clones," co-senior author Mats Nilsson from the Science for Life Laboratory at Stockholm University said in a statement. "An important insight from our research is that it may not be the genetic changes alone that are the reason that the cancer cells survive and spread; it could also be where they are. This adds an additional layer of complexity as well as new potential ways to target the disease."

For BaSISS, fresh-frozen tissue blocks undergo serial cryo-sectioning to allow for spatial clone mapping and phenotyping. After using bulk sequencing to uncover de novo mutations and tumor subclones, specific fluorescent molecular probes are designed to detect where in the section the transcripts are expressed. Clone maps can then be generated using computational techniques.

Nilsson and his colleagues applied this approach to eight tissue blocks from two patients, one who had two ER-positive but HER-negative primary invasive breast cancers and one who had two triple-negative primary invasive breast cancers. The tissue samples covered the early histological stages of cancer progression, from ductal carcinoma in situ to invasive cancer and lymph node metastases.

The analysis uncovered complex patterns of subclonal growth. For instance, the researchers found that subclones tended to form spatial patterns that were generally related to their histological progression state. However, each breast cancer sample also harbored a subclone with hundreds of private mutations, found within both carcinoma in situ and invasive histology states. This suggested that there are also disconnects between histological and genetic disease progression.

The researchers also noted ties between the phenotypic or histological state and the genetic state of cells. Clones harboring PTEN mutations had denser Ki-67 IHC nuclear staining than their ancestral wild-type PTEN clones, for example. At the same time, though, for any clone, the Ki-67 score was similar no matter whether it was in a DCIS or invasive state, suggesting that while the upregulation of Ki-67 occurs at a similar time as a PTEN mutation, it occurs before the tumor becomes invasive.

Still, the expression of genes like CLDN4 or ACTB differed based on whether the clones were located in DCIS or invasive compartments, suggesting the changes were linked to the histological transition.

"[T]he exciting thing about this technology is that for the first time, we can see how the environment shapes cancer evolution," co-senior author Moritz Gerstung of the German Cancer Research Center said in a statement. "We were able to see which cancer clones progress to become more aggressive, and which don't, and this will enable us to get a much better understanding of what the key steps are in tumor growth, and how we can lessen or prevent disease."