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

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 F1Fo 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.

Abstract P6-01-05: Novel cytotoxic RNA aptamers that distinguish between metastasis-prone and indolent breast and prostate cancers

Background: Prostate and breast cancers are, respectively, the most common malignancies diagnosed in men and women worldwide. These cancers develop in different organs but have significant biological similarities: both are typically hormone-dependent, and both require early detection and treatment, as metastatic disease is incurable. At the same time, early stage tumors are often over-treated. Better markers for tumor aggressiveness would help to optimize treatment strategies in both breast and prostate cancer.

Objective: Develop high affinity nucleic acid oligomers (aptamers) that can distinguish between indolent tumors that will remain organ-confined and those with heightened potential to metastasize.

Methods: We performed subtractive RNA Cell-SELEX to select for surface ligands specific to aggressive tumors, using as a positive selector the highly metastasis-competent LN3 subclone of prostate cancer cell line LNCaP, and as negative selectors parental LNCaP and a non-metastasizing subclone, Pro5. . The RNA aptamer pool was PCR amplified from a 40-mer random nucleotide cDNA library with appropriate flanking sequences, and transcribed in vitro. After 11 SELEX cycles, aptamer pools from cycles 0, 4, 9, and 11 were subjected to high-throughput sequencing. Eight aptamers, representing 4 sequence families, were chosen for further study. Representative relevant and irrelevant aptamers were labeled with Cy3 and used to stain LNCaP-LN3 and LNCaP-Pro5 in culture and as xenografts in NOD-SCID-gamma mice. Additional cell and tumor lines from both breast and prostate cancer were used for validation.

Results: Two aptamers bound avidly to the surface of the aggressive LNCaP-LN3 subclone, both in culture and in fixed xenograft tumors, but not to the indolent Pro5 subclone. Aptamer binding led to rapid and specific cytotoxicity in vitro but had no effect on other cell lines to which the aptamer did not bind. The same aptamers showed similar high specificity for multiple other metastasis-competent cancer cells, including the prostate adenocarcinoma PC-3 and PC-3ML subclones, breast cancer cell lines MDA-MB436 and MDA-MB231, and the primary dissociated breast tumor DT28 , while exhibiting no detectable binding to the non-metastasizing MCF-7 breast cancer cell line and DT22 primary dissociated breast tumor cells, and the non-tumorigenic prostate epithelial cell line RPWE-1.

Conclusion: We identified RNA aptamers that specifically bind to metastasis-prone prostate cancer and breast cancer cell surface targets, and exert cell-specific toxicity dependent upon aptamer binding. While the target(s) remain to be identified, we propose that these aptamers may discriminate between progressive and indolent breast and prostate cancers, and may have substantial promise as anticancer agents either alone or suitably liganded to toxic moieties.

Citation Format: Bishopric NH, Speransky S, Serafini P, De la Fuente AC, Bicciato S, El-Ashry D, Lippman ME. Novel cytotoxic RNA aptamers that distinguish between metastasis-prone and indolent breast and prostate cancers [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P6-01-05.

Abstract P4-03-18: A hierarchy of cancer associated fibroblasts in situ and in circulation promote breast cancer metastasis

Background: Metastasis is the primary cause of breast cancer mortality. Interactions between cancer cells and non-cancer cells of the tumor microenvironment (TME) are pivotal in governing tumor initiation, progression and metastasis, and cancer associated fibroblasts (CAFs) are critical orchestrators of these interactions. We recently identified circulating CAFs (cCAFs) as a novel circulating biomarker associated with metastatic breast cancer. We established CAF cell lines from dissociated luminal A, ER- Her-2 amplified, and triple-negative/basal-like (TN) breast tumors. We demonstrated that “aggressive” CAFs differentially secrete miRNAs that contribute to ER-negativity, activated growth factor signaling, and induction of EMT in breast cancers compared to “indolent” CAFs. We hypothesized that a hierarchy exists within CAFs regarding their ability to facilitate tumor progression and metastasis. Here we demonstrate that CAFs derived from aggressive TN breast tumors differ from those derived from more indolent Luminal A breast tumors in secretion of cytokines and chemokines that can confer differential effects on the behavior of breast cancer cells. We also demonstrate that “aggressive” CAFs more potently facilitate tumor progression and metastasis than “indolent” CAFs. We additionally evaluated if “aggressive” and “indolent” CAFs differ in their ability to mobilize CTCs and circulating CAFs into circulation.

Methods: Conditioned media (CM) from “aggressive” and “indolent” CAFs was analyzed for chemokine/cytokine expression. Luminal A breast cancer cells (MCF-7) or primary tumor cells from an aggressive TN tumor (DT28) were injected into the mammary fat pad of 6-8 week old female NSG mice, either alone or in combination with CAF19-I or CAF23-A. Tumor progression was monitored and mice were examined for metastasis at necropsy. Tissues were harvested for histology and blood was collected by cardiac puncture. Plasma was analyzed for cytokine/chemokine expression and blood was processed for enumeration of circulating tumor cells (CTCs) and cCAFs.

Results: “Aggressive” CAF CM had significantly higher levels of a number of factors, including IL-8, SDF-1, and CXCL1, compared to “indolent” CAF CM. MCF-7 cells co-injected with “aggressive” CAFs formed tumors much faster than those co-injected with the “indolent” CAFs or without CAFs. While DT28 cells readily form tumors and metastasize in the NSG model, fewer DT28 cells do not form metastases in the timeframe that this same lower number of DT28 cells co-injected with “aggressive” CAFs demonstrated robust tumor growth and developed metastases in liver and pancreas. DT28 cells co-injected with “indolent” CAFs did not exhibit metastases.

Conclusion: The data presented here further demonstrate that there is a hierarchy within CAFs regarding their ability to facilitate tumor growth and metastasis, and that this may largely be mediated by secreted soluble factors. “Aggressive” CAFs may retain their programmed role in circulation and accelerate metastasis more than “indolent” CAFs. We suggest that targeting CAFs in situ and in circulation and disrupting their interactions with breast cancer cells could provide novel strategies to combat breast cancer and breast cancer metastasis.

Citation Format: Sharma U, Miller P, Speransky S, Medina-Saenz K, Ferrer P, Lippman M, El-Ashry D. A hierarchy of cancer associated fibroblasts in situ and in circulation promote breast cancer metastasis [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P4-03-18.