Differential SELEX in human glioma cell lines
Authors: Laura Cerchia
Andreas H Jacobs
Vittorio de Franciscis
Bertrand Tavitian
Carla Lucia Esposito
Journal: PloS one (2009)
Discipline: Multidisciplinary
Keywords: therapeutic interventions; tumor types; responsiveness; therapeutic plan; tumor specific signatures
Affiliations: Istituto per l'Endocrinologia e l'Oncologia Sperimentale del CNR G Salvatore, Naples, Italy.

Abstract:  The hope of success of therapeutic interventions largely relies on the possibility to distinguish between even close tumor types with high accuracy. Indeed, in the last ten years a major challenge to predict the responsiveness to a given therapeutic plan has been the identification of tumor specific signatures, with the aim to reduce the frequency of unwanted side effects on oncologic patients not responding to therapy. Here, we developed an in vitro evolution-based approach, named differential whole cell SELEX, to generate a panel of high affinity nucleic acid ligands for cell surface epitopes. The ligands, named aptamers, were obtained through the iterative evolution of a random pool of sequences using as target human U87MG glioma cells. The selection was designed so as to distinguish U87MG from the less malignant cell line T98G. We isolated molecules that generate unique binding patterns sufficient to unequivocally identify any of the tested human glioma cell lines analyzed and to distinguish high from low or non-tumorigenic cell lines. Five of such aptamers act as inhibitors of specific intracellular pathways thus indicating that the putative target might be important surface signaling molecules. Differential whole cell SELEX reveals an exciting strategy widely applicable to cancer cells that permits generation of highly specific ligands for cancer biomarkers. 

Retracted: Yes

PubPeer comments:
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 2020 retraction https: journals.plos.org plosone article?id=10.1371 journal.pone.0228838 Following the publication of this article [1], concerns have been raised regarding Figure 5: In Figure 5A, the upper left pcyclin D1 panel, the band in lane 5 appears similar to the band in lane 6, if stretched horizontally. In Figure 5A, the upper left cyclin D1 panel, the band in lane 5 appears similar to the band in lane 6, if stretched horizontally. In Figure 5A, the lower left pcyclin D1 panel, the bands in lane 1, 2, 3, 5, and 6 appear similar. In Figure 5A, the lower left cyclin D1 panel, the band in lane 1 appears similar to the band in lane 6 when horizontally flipped. In Figure 5A, the upper right pcyclin D1 panel, the bands in lane 1, 2, 4, and 5 appear similar. In Figure 5B, the upper left ERK panel appears similar to the lower left ERK panel if the lower panel is stretched horizontally. In Figure 5B, the lower left pERK panel, the bands in lane 1, 2, 5, and 6 appear similar. In Figure 5B, the upper right pERK panel, the bands in lane 1, 2, 4, and 5 appear similar. In Figure 5B, the upper right ERK panel, the bands in lane 1, 2, and 4 appear similar. Multiple vertical discontinuities in the background of the blots have been detected in the following panels: Figure 5A, pcyclin D1 upper left, lower left, and upper right panels. Figure 5A, cyclin D1 upper left, lower left, and upper right panels. Figure 5B, pERK upper left, lower left, and upper right panels. Figure 5B ERK upper right panel. Original data for the western blots presented in the paper are no longer available. Replication data have been provided in support of results in Figure 5A, pcyclin D1 cyclin D1 u03b1tubulin upper left, lower left, and upper right panels as well as Figure 5B pERK ERK upper right and lower left panels. However, these data did not resolve the concerns about western blot data reporting in the original figure. In light of the unresolved concern about Figure 5 that calls into question the integrity of the reported results, the PLOS ONE Editors retract this article. AHA, BT did not respond. LC, CLE, and VdF disagree with retraction and maintain that all the findings of the work reported in this article are still reliable. Reference 1.Cerchia L, Esposito CL, Jacobs AH, Tavitian B, de Franciscis V (2009) Differential SELEX in Human Glioma Cell Lines. PLoS ONE 4(11): e7971. https: doi.org 10.1371 journal.pone.0007971 ,