Identification and Pharmacological Targeting of Treatment-Resistant, Stem-like Breast Cancer Cells for Combination Therapy

Abstract

Tumors frequently harbor isogenic yet epigenetically distinct subpopulations of multi-potent cells with high tumor-initiating potential-often called Cancer Stem-Like Cells (CSLCs). These can display preferential resistance to standard-of-care chemotherapy. Single-cell analyses can help elucidate Master Regulator (MR) proteins responsible for governing the transcriptional state of these cells, thus revealing complementary dependencies that may be leveraged via combination therapy. Interrogation of single-cell RNA sequencing profiles from seven metastatic breast cancer patients, using perturbational profiles of clinically relevant drugs, identified drugs predicted to invert the activity of MR proteins governing the transcriptional state of chemoresistant CSLCs, which were then validated by CROP-seq assays. The top drug, the anthelmintic albendazole, depleted this subpopulation in vivo without noticeable cytotoxicity. Moreover, sequential cycles of albendazole and paclitaxel-a commonly used chemotherapeutic-displayed significant synergy in a patient-derived xenograft (PDX) from a TNBC patient, suggesting that network-based approaches can help develop mechanism-based combinatorial therapies targeting complementary subpopulations.

Competing Interest Statement

P.A.S. receives patent royalties from Guardant Health. A.C. is founder, equity holder, and consultant of DarwinHealth Inc., a company that has licensed some of the algorithms used in this manuscript from Columbia University. Columbia University is also an equity holder in DarwinHealth Inc. P.D. received stock and/or royalties from Oncomed Pharmaceuticals, Quanticel Pharmaceuticals and Forty Seven Inc., as a result of his acknowledgment as a co-inventor on patents licensed from the University of Michigan (US-07723112) and Stanford University (US-09329170, US-09850483, US-10344094, US-11130813), and related to: 1) the discovery of surface markers for the differential purification of cancer stem cell populations from human malignancies; 2) the use of single-cell genomics technologies for the identification of pharmacological targets expressed in cancer stem cell populations; 3) the combination of anti-CD47 and anti-EGFR monoclonal antibodies for the treatment of human colon cancer. P.D. recently owned stock of Eli Lilly and Company. P.Ds spouse is employed by Regeneron Pharmaceuticals Inc., and owns (or recently owned) stock of the following pharmaceutical companies: AbbVie, Amgen, AstraZeneca, Eli Lilly and Company, Gilead Sciences Inc., GlaxoSmithKline (GSK), Johnson & Johnson, Merck & Co., Novartis, Organon & Co., Pfizer, Teva Pharmaceutical Industries Ltd. and Viatris. A.L.K. is on the Scientific Advisory Board of Emendo Biotherapeutics, Karyopharm Therapeutics, Imago BioSciences, and DarwinHealth; is co-Founder and on the Scientific Advisory Board of Isabl; has equity interest in Imago BioSciences, Emendo Biotherapeutics and Isabl; and receives royalty income from Labcorp.

Footnotes

* removal of GEO accession number. There are no changes to the data or analysis in this manuscript.