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(Reference retrieved automatically from Web of Science through information on FAPESP grant and its corresponding number as mentioned in the publication by the authors.)

In silico selection approach to develop DNA aptamers for a stem-like cell subpopulation of non-small lung cancer adenocarcinoma cell line A549

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Author(s):
Vidic, Mateja [1, 2, 3] ; Smuc, Tina [4, 5] ; Janez, Nika [4] ; Blank, Michael [6] ; Accetto, Tomaz [7] ; Mavri, Jan [4, 5] ; Nascimento, Isis C. [8] ; Nery, Arthur A. [8] ; Ulrich, Henning [8] ; Lah, Tamara T. [1, 9]
Total Authors: 10
Affiliation:
[1] Natl Inst Biol, Dept Genet Toxicol & Canc Biol, Ljubljana - Slovenia
[2] Jozef Stefan Int Postgrad Sch, Ljubljana - Slovenia
[3] Aptamer Grp, York YO10 5NY, N Yorkshire - England
[4] Ctr Biotechnol, Ctr Excellence Biosensors Instrumentat & Proc Con, Ajdovscina - Slovenia
[5] Lek Sandoz Co, Ljubljana - Slovenia
[6] AptaIT GmbH, Munich - Germany
[7] Univ Ljubljana, Biotech Fac, Dept Anim Sci, Ljubljana - Slovenia
[8] Univ Sao Paulo, Inst Chem, Dept Biochem, Av Prof Lineu Prestes 748, BR-05508000 Sao Paulo - Brazil
[9] Univ Ljubljana, Fac Chem & Chem Technol, Dept Biochem, Ljubljana - Slovenia
Total Affiliations: 9
Document type: Journal article
Source: RADIOLOGY AND ONCOLOGY; v. 52, n. 2, p. 152-159, JUN 2018.
Web of Science Citations: 1
Abstract

Background. Detection of circulating lung cancer cells with cancer-stem like characteristics would represent an improved tool for disease prognosis. However, current antibodies based methods have some disadvantages and therefore cell SELEX (Systematic Evolution of Ligands by Exponential Enrichment) was used to develop DNA aptamers, recognizing cell surface markers of non-small lung carcinoma (NSLC) cells. Materials and methods. The human adenocarcinoma cell line A549 was used for selection in seven cell SELEX cycles. We used human blood leukocytes for negative selection, and lung stem cell protein marker CD90 antibody binding A549 cells for positive selection. Results. The obtained oligonucleotide sequences after the seventh SELEX cycle were subjected to in silico selection analysis based on three independent types of bioinformatics approaches, selecting two closely related aptamer candidates in terms of consensus sequences, structural motifs, binding affinity (Kd) and stability (Delta G). We selected and identified the aptamer A155\_18 with very good binding characteristics to A459 cells, selected CD90 antibody binding. The calculated phylogenetic tree showed that aptamers A155\_18 and the known A549 cell aptamer S6 have a close structural relationship. MEME sequence analysis showed that they share two unique motifs, not present in other sequences. Conclusions. The novel aptamer A155\_18 has strong binding affinity for A549 lung carcinoma cell line subpopulation that is expressing stem cell marker CD90, indicating a possible stemness, characteristic for the A459 line, or a subpopulation present within this cell line. This aptamer can be applied as diagnostic tool, identifying NSLC circulating cells. (AU)

FAPESP's process: 15/18730-0 - Lung cancer stem cells by DNA aptamers identification / purification and kallikrein-kinin system study on tumor progression
Grantee:Isis Cristina Corrêa Do Nascimento
Support type: Scholarships in Brazil - Post-Doctorate
FAPESP's process: 12/50880-4 - Stem cells: from basic studies of kinin and purinergic receptor roles towards therapeutical applications
Grantee:Alexander Henning Ulrich
Support type: Research Projects - Thematic Grants