A novel RNA aptamer identifies plasma membrane ATP synthase beta subunit as an early marker and therapeutic target in aggressive cancer

Abstract

Purpose Primary breast and prostate cancers can be cured, but metastatic disease cannot. Identifying cell factors that predict metastatic potential could guide both prognosis and treatment. Methods We used Cell-SELEX to screen an RNA aptamer library for differential binding to prostate cancer cell lines with high vs. low metastatic potential. Mass spectroscopy, immunoblot, and immunohistochemistry were used to identify and validate aptamer targets. Aptamer properties were tested in vitro, in xenograft models, and in clinical biopsies. Gene expression datasets were queried for target associations in cancer. Results We identified a novel aptamer (Apt63) that binds to the beta subunit of F 1 F o ATP synthase (ATP5B), present on the plasma membrane of certain normal and cancer cells. Apt63 bound to plasma membranes of multiple aggressive breast and prostate cell lines, but not to normal breast and prostate epithelial cells, and weakly or not at all to non-metastasizing cancer cells; binding led to rapid cell death. A single intravenous injection of Apt63 induced rapid, tumor cell-selective binding and cytotoxicity in MDA-MB-231 xenograft tumors, associated with endonuclease G nuclear translocation and DNA fragmentation. Apt63 was not toxic to non-transformed epithelial cells in vitro or adjacent normal tissue in vivo. In breast cancer tissue arrays, plasma membrane staining with Apt63 correlated with tumor stage ( p < 0.0001, n = 416) and was independent of other cancer markers. Across multiple datasets, ATP5B expression was significantly increased relative to normal tissue, and negatively correlated with metastasis-free ( p = 0.0063, 0.00039, respectively) and overall ( p = 0.050, 0.0198) survival. Conclusion Ecto-ATP5B binding by Apt63 may disrupt an essential survival mechanism in a subset of tumors with high metastatic potential, and defines a novel category of cancers with potential vulnerability to ATP5B-targeted therapy. Apt63 is a unique tool for elucidating the function of surface ATP synthase, and potentially for predicting and treating metastatic breast and prostate cancer. Electronic supplementary material The online version of this article (10.1007/s10549-019-05174-3) contains supplementary material, which is available to authorized users.

Mitochondrial ATP Synthase Trafficking along Microtubules to Cell Surface Depends on KIF5B and DRP1

“…Numerous studies have revealed the roles of PM-located ATP synthase (eATP synthase) in cancers (Li et al, 2017;Lu et al, 2009;Speransky et al, 2019). In this work, we aimed to establish the mechanism responsible for the transport of eATP synthase.…”

“…Moreover, in association with KIF5B, DRP1 carries these fragmented mitochondria containing ATP synthase along the microtubules toward the cell surface. Some evidence points to a positive correlation between eATP synthase and the migratory capability of tumors (Li et al, 2017;Speransky et al, 2019). Identification of these ATP synthase trafficking-related regulators may thus provide useful information for the development of potential therapies against metastatic cancer.…”

Advances in Screening and Development of Therapeutic Aptamers Against Cancer Cells

“…Therapeutic Aptamers Against Prostate Cancer Cells Speransky et al (2019) designed an RNA aptamer (Apt63) to distinguish prostate cancer cell lines with high metastatic potential from low metastatic potential. Apt63 was not bound to non-metastatic cancer cells but stuck to the beta subunit of F1Fo ATP synthase (ATP5B), which existed in the plasma membrane of cancer cells.…”

“…Apt63 was not bound to non-metastatic cancer cells but stuck to the beta subunit of F1Fo ATP synthase (ATP5B), which existed in the plasma membrane of cancer cells. The binding of Apt63 and plasma membrane-located ATP synthase (Ecto-ATP5B) could destroy the basic survival mechanism of tumors with high metastatic potential and lead to rapid cell death ( Speransky et al, 2019 ). Prostate-specific membrane antigen (PSMA) is a glycosylated type II membrane protein.…”

Cellular Mechanisms of Circulating Tumor Cells During Breast Cancer Metastasis

“…The application of angiostatin, an inhibitor of cell migration and the proliferation, binds to the α-subunit of the ecto F 1 Fo ATP synthase and inhibits angiogenesis [ 128 ]. The expression of the β-subunit of the ecto F 1 Fo ATP synthase is also higher in breast cancer cells than normal cells [ 129 ], and application of an aptamer or an antibody targeting the β-subunit induced cytotoxicity in various epithelial cells including breast cancer cells [ 129 , 130 ]. Inhibition of the β-subunit increased apoptosis and blocked phosphorylation of ERK and Akt, thus the ecto β-subunit may regulate survival genes that are under the control of the ERK and Akt pathways [ 130 ].…”