Single-cell analysis for the study of breast cancer metastasis

2020 Fiscal Year Annual Research Report

• Project/Area Number: 20F20112
• Research Institution: Tokyo Medical University
• Principal Investigator: 落谷 孝広 東京医科大学, 医学部, 教授 (60192530)
• Co-Investigator(Kenkyū-buntansha): PRIETO-VILA MARTA 東京医科大学, 医学部, 外国人特別研究員
• Project Period (FY): 2020-04-24 – 2022-03-31
• Keywords: RNA single-cell sequence / breast cancer / metastasis

Outline of Annual Research Achievements

During the fiscal year 2020 we started the project “Single-cell analysis for the study of breast cancer metastasis”. We received 4 paired samples of primary and metastatic sites of breast cancer tumor without any prior anticancer treatment. The four samples collected were sequenced at single-cell level with the chromium 10x machine.
The data of over 40.000 cells in total were analyzed. By the use of bioinformatic analysis, the cell type was inferred. We observed several differences in the cell-type composition of tumors between primary and metastatic sites. For instance, lymphocytes B cells were the predominant cell type in metastatic tumors, but it was almost not present in primary tumors. Then we analyzed only cancer cells in detail. It was observed that again, metastatic cells and primary cells clustered separately, indicating a difference. However, a small group of primary cells clustered together with metastatic cells, revealing that their gene expression pattern is similar to metastatic cancer cells. A preliminary conclusion we can interpret that there is already a small subpopulation of cancer cells within primary tumors with the ability to metastasize. These results are similar to our previous ones in drug resistance analysis.
Using the genetic information, we found a group of genes that are commonly co-expressed in metastatic cells. We named this group of genes as “metastatic gene expression pattern”. We are currently analyzing these genes collectively.

Current Status of Research Progress

3: Progress in research has been slightly delayed.

Reason

Due to the covid-19 situation, the start of this project was delayed since we could not receive clinical samples (it was forbidden that people from outside the hospital to access them). For that reason, we still have to collect and analyze one more sample.
Due to this delay, we started the mRNA RNA expression analysis with only 4 out of 5 samples. However, so far, we found no significant differences among patient samples. For that reason, we believe that once we add the remaining sample, the current gene expression pattern will not vary significantly. And thus, continuous smoothly with the project.

Strategy for Future Research Activity

As mentioned, first of all, this year we plan to complete the sampling step. Moreover, we will further study the subpopulation of primary cells with metastatic abilities by analyzing the gene expression profile. The gene expression profile will be corroborated both at mRNA and protein. Furthermore, we plan to identify the approximate location of those cells within the primary tumor using the fixed tumor samples and the metastatic gene expression pattern. Since the tumor microenvironment is known to be very important, we will confirm which types of cells are nearby the cells with metastatic gene expression profile.
In addition, we will analyze their importance in biological functions by the use of animal experiments.