Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples

Olga S Kolovskaya; Alena V Zyuzyukina; Justin P Dassie; Galina S Zamay; Tatiana N Zamay; Nina V Boyakova; Vladimir A Khorzhevskii; Daria A Kirichenko; Ivan N Lapin; Irina A Shchugoreva; Polina V Artyushenko; Felix N Tomilin; Dmitry V Veprintsev; Yury E Glazyrin; Zoran Minic; Vladimir K Bozhenko; Elena A Kudinova; Yana Y Kiseleva; Alexey V Krat; Eugene V Slepov; Anton S Bukatin; Ruslan A Zukov; Pavel A Shesternya; Maxim V Berezovski; Paloma H Giangrande; Anna S Kichkailo

doi:10.3389/fmolb.2023.1184285

Monitoring of breast cancer progression via aptamer-based detection of circulating tumor cells in clinical blood samples

Front Mol Biosci. 2023 Jun 8:10:1184285. doi: 10.3389/fmolb.2023.1184285. eCollection 2023.

Authors

Olga S Kolovskaya^{1

2}, Alena V Zyuzyukina^{3

4}, Justin P Dassie⁵, Galina S Zamay^{1

2}, Tatiana N Zamay^{1

2}, Nina V Boyakova^{4

6}, Vladimir A Khorzhevskii^{7

8}, Daria A Kirichenko¹, Ivan N Lapin⁹, Irina A Shchugoreva^{1

2}, Polina V Artyushenko^{1

2

10}, Felix N Tomilin^{10

11}, Dmitry V Veprintsev², Yury E Glazyrin^{1

2}, Zoran Minic¹², Vladimir K Bozhenko¹³, Elena A Kudinova¹³, Yana Y Kiseleva¹³, Alexey V Krat^{3

4}, Eugene V Slepov^{1

4}, Anton S Bukatin^{14

15}, Ruslan A Zukov^{3

4}, Pavel A Shesternya¹, Maxim V Berezovski¹², Paloma H Giangrande^{5

16}, Anna S Kichkailo^{1

2}

Affiliations

¹ Laboratory for Biomolecular and Medical Technologies, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia.
² Laboratory for Digital Controlled Drugs and Theranostics, Federal Research Center "Krasnoyarsk Science Center of the Siberian Branch of the Russian Academy of Science", Krasnoyarsk, Russia.
³ Department of Oncology and Radiation Therapy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia.
⁴ Krasnoyarsk Regional Clinical Cancer Center Named After A.I. Kryzhanovsky, Krasnoyarsk, Russia.
⁵ Department of Internal Medicine, University of Iowa, Iowa, IA, United States.
⁶ Department of General Surgery, Named After Prof. M.I. Gulman, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia.
⁷ Department of Pathological Anatomy, Faculty of Medicine, Prof. V.F. Voino-Yasenetsky Krasnoyarsk State Medical University, Krasnoyarsk, Russia.
⁸ Krasnoyarsk Regional Pathology-Anatomic Bureau, Krasnoyarsk, Russia.
⁹ Laboratory of Advanced Materials and Technology, Siberian Physical Technical Institute, Tomsk State University, Tomsk, Russia.
¹⁰ School of Non-Ferrous Metals and Materials Science, Siberian Federal University, Krasnoyarsk, Russia.
¹¹ Laboratory of Physics of Magnetic Phenomena, Kirensky Institute of Physics, Krasnoyarsk, Russia.
¹² Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, ON, Canada.
¹³ Russian Scientific Center of Roentgenoradiology, Moscow, Russia.
¹⁴ Alferov Federal State Budgetary Institution of Higher Education and Science, Saint Petersburg National Research Academic University of the Russian Academy of Sciences, Saint Petersburg, Russia.
¹⁵ Institute for Analytical Instrumentation of the Russian Academy of Sciences, Saint Petersburg, Russia.
¹⁶ Platform Discovery Sciences, Biology, Wave Life Sciences, Cambridge, MA, United States.

Abstract

Introduction: Breast cancer (BC) diagnostics lack noninvasive methods and procedures for screening and monitoring disease dynamics. Admitted CellSearch^® is used for fluid biopsy and capture of circulating tumor cells of only epithelial origin. Here we describe an RNA aptamer (MDA231) for detecting BC cells in clinical samples, including blood. The MDA231 aptamer was originally selected against triple-negative breast cancer cell line MDA-MB-231 using cell-SELEX. Methods: The aptamer structure in solution was predicted using mFold program and molecular dynamic simulations. The affinity and specificity of the evolved aptamers were evaluated by flow cytometry and laser scanning microscopy on clinical tissues from breast cancer patients. CTCs were isolated form the patients' blood using the developed method of aptamer-based magnetic separation. Breast cancer origin of CTCs was confirmed by cytological, RT-qPCR and Immunocytochemical analyses. Results: MDA231 can specifically recognize breast cancer cells in surgically resected tissues from patients with different molecular subtypes: triple-negative, Luminal A, and Luminal B, but not in benign tumors, lung cancer, glial tumor and healthy epithelial from lungs and breast. This RNA aptamer can identify cancer cells in complex cellular environments, including tumor biopsies (e.g., tumor tissues vs. margins) and clinical blood samples (e.g., circulating tumor cells). Breast cancer origin of the aptamer-based magnetically separated CTCs has been proved by immunocytochemistry and mammaglobin mRNA expression. Discussion: We suggest a simple, minimally-invasive breast cancer diagnostic method based on non-epithelial MDA231 aptamer-specific magnetic isolation of circulating tumor cells. Isolated cells are intact and can be utilized for molecular diagnostics purposes.

Keywords: MDA-MB-231; RNA-aptamer; breast cancer; circulating tumor cells; mammaglobin; molecular subtypes.

Copyright © 2023 Kolovskaya, Zyuzyukina, Dassie, Zamay, Zamay, Boyakova, Khorzhevskii, Kirichenko, Lapin, Shchugoreva, Artyushenko, Tomilin, Veprintsev, Glazyrin, Minic, Bozhenko, Kudinova, Kiseleva, Krat, Slepov, Bukatin, Zukov, Shesternya, Berezovski, Giangrande and Kichkailo.

Grants and funding

CTCs isolation method development and clinical sample analyses were supported by the Ministry of Healthcare of Russian Federation project REYC-2023-0012. The Ministry of Science and Higher Education of the Russian Federation project FWES-2022-0005 supported aptamer characterization, molecular modeling. MDA-231/LUC cells were from R. Domann (Jenkin et al. Breast Cancer Research, 2005). Technical and instrumental support was provided by the Shared Core Facilities of Molecular and Cell Technologies at Krasnoyarsk State Medical University and Krasnoyarsk Regional Centre for Collective Use at the Federal Research Centre “KSC SB RAS.” The confocal fluorescence microscopy research was carried out with the equipment of the Tomsk Regional Core Shared Research Facilities Center of the National Research Tomsk State University. The Center was supported by the Ministry of Science and Higher Education of the Russian Federation, grant no. 075-15-2021-693 (No. 13.RFC.21.0012).