Functional DNA Repair Signature of Cancer Cell Lines Exposed to a Set of Cytotoxic Anticancer Drugs Using a Multiplexed Enzymatic Repair Assay on Biochip

Abstract

The development of resistances to conventional anticancer drugs compromises the efficacy of cancer treatments. In the case of DNA-targeting chemotherapeutic agents, cancer cells may display tolerance to the drug-induced DNA lesions and/or enhanced DNA repair. However, the role of DNA damage response (DDR) and DNA repair in this chemoresistance has yet to be defined. To provide insights in this challenging area, we analyzed the DNA repair signature of 7 cancer cell lines treated by 5 cytotoxic drugs using a recently developed multiplexed functional DNA repair assay. This comprehensive approach considered the complexity and redundancy of the different DNA repair pathways. Data was analyzed using clustering methods and statistical tests. This DNA repair profiling method defined relevant groups based on similarities between different drugs, thus providing information relating to their dominant mechanism of action at the DNA level. Similarly, similarities between different cell lines presumably identified identical functional DDR despite a high level of genetic heterogeneity between cell lines. Our strategy has shed new light on the contribution of specific repair sub-pathways to drug-induced cytotoxicity. Although further molecular characterisations are needed to fully unravel the mechanisms underlying our findings, our approach proved to be very promising to interrogate the complexity of the DNA repair response. Indeed, it could be used to predict the efficacy of a given drug and the chemosensitivity of individual patients, and thus to choose the right treatment for individualised cancer care.

A microfluidic platform for drug screening in a 3D cancer microenvironment

“…Drug sensitivity data obtained from 2D-based cell culture systems are often ambiguous due to the variations observed in the morphology, growth pattern, and gene expression of tumour cells in a 3D matrix. In addition, compared to the planar cell culture, 3D cell culture has been shown to more accurately influence cell morphology, gene/protein expression, signal transduction, proliferation, migration, and drug tolerance (Asphahani et al, 2011; Arias et al, 2010; Gurski et al, 2010; Nyga et al, 2011; Hong et al, 2012; Ning et al, 2011; Ling et al, 2012; Forestier et al, 2012). Different drug sensitivities were observed for cells grown in 3D culture configurations compared with a 2D monolayer model (Serebriiskii et al, 2008; Doillon et al, 2004).…”

The Effect of Primary Cancer Cell Culture Models on the Results of Drug Chemosensitivity Assays: The Application of Perfusion Microbioreactor System as Cell Culture Vessel

“…2D, 3D, and spheroid cell culture models are widely used in various cancer cell-related studies [ 11 – 13 , 18 , 19 , 23 , 24 ]. In cell-based assays, however, one cannot merely extrapolate the data obtained from one cell culture model to another because the biochemical or biophysical microenvironments in the two situations could not be identical.…”

“…For the most drug chemosensitivity assays [ 11 – 13 ], moreover, two-dimensional (2D) monolayer cell cultures are commonly used, where the cancer cells attach, spread, and grow on a surface. Such a cell culture model has been widely adopted in life science-related research for more than a hundred years.…”

DNA repair-based classification of melanoma cell lines reveals an effect of mutations in BRAF and NRAS driver genes on DNA repair capacity

“…Given the important role that DNA repair plays in the etiology of cancer, including of the skin, we determined the DNA repair activities of several relevant cell lines using a precise tool that measures in parallel several excision/synthesis repair mechanisms, including defenses against oxidative DNA damage and DNA photoproducts. This tool has already been described in detail [25] and used to demonstrate that (i) chronic sun exposure impacts specifically the repair of DNA photoproducts [24] and (ii) DNA-damaging agents trigger specific DNA damage responses according to their mechanisms of action [29]. Our analysis herein shows that mutations in the BRAF or NRAS gene, major genetic drivers of melanoma, can affect the functional DNA Repair profiles of melanoma cells, with the excision/synthesis repair mechanisms of both BER and NER being influenced.…”