Delineating developmental programs driving tumorigenesis in triple-negative breast cancer

PROJECT SUMMARY Triple-negative breast cancer (TNBC) is the deadliest and 2nd most common subtype of breast cancer in the United States.

Although promising new drugs based on PARP inhibition and immunotherapy can extend survival in selected patients, 1 in 3 patients die from TNBC.

Increasing evidence suggests that human breast tumors harbor immature cancer cells which are a distinct subset of tumorigenic cancer cells, are less-differentiated, capable of replenishing cancer cell populations indefinitely, and strongly implicated in drug resistance. Unfortunately, existing marker genes for studying these cells are not specific, precluding rational drug development.

We hypothesize that precise identification of immature cancer cells could present new therapeutic opportunities to revolutionize TNBC treatment.

We recently showed that the number of expressed genes per cell is a powerful surrogate of cellular differentiation status independently of known marker genes.

We leveraged this finding to develop CytoTRACE, a new framework for predicting cellular differentiation status from single-cell RNA sequencing (scRNA-seq) data.

Our published data show that immature cancer cells predicted by CytoTRACE preferentially express genes essential for tumorigenicity in TNBC.

In pilot data, we identified 10 putative cancer cell populations, including at least 3 immature ones, from scRNA-seq data of 19 primary breast tumors.

Here, we propose to study over 800 TNBC patients to determine whether immature cancer cells represent at least 3 distinct populations (Aim 1); differ by key clinical covariates (Aim 2); and are clonogenic and produce specific progeny populations predicted in silico (Aim 3).

To accomplish these aims, we will leverage new analytical methods, including a deconvolution approach for integrating scRNA-seq with bulk tumor transcriptomic data in order to characterize cellular heterogeneity at scale.

Successful completion of the proposed project will validate and refine our pilot data toward advancing our understanding of cancer cell populations, especially immature cells, in TNBC.

As such, we expect this study to facilitate new opportunities for the development of targeted drugs to improve TNBC outcomes.