A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma

PLOS ONE, Dec 2019

Trabectedin, a new antitumor compound originally derived from a marine tunicate, is clinically effective in soft tissue sarcoma. The drug has shown a high selectivity for myxoid liposarcoma, characterized by the translocation t(12;16)(q13; p11) leading to the expression of FUS-CHOP fusion gene. Trabectedin appears to act interfering with mechanisms of transcription regulation. In particular, the transactivating activity of FUS-CHOP was found to be impaired by trabectedin treatment. Even after prolonged response resistance occurs and thus it is important to elucidate the mechanisms of resistance to trabectedin. To this end we developed and characterized a myxoid liposarcoma cell line resistant to trabectedin (402-91/ET), obtained by exposing the parental 402-91 cell line to stepwise increases in drug concentration. The aim of this study was to compare mRNAs, miRNAs and proteins profiles of 402-91 and 402-91/ET cells through a systems biology approach. We identified 3,083 genes, 47 miRNAs and 336 proteins differentially expressed between 402-91 and 402-91/ET cell lines. Interestingly three miRNAs among those differentially expressed, miR-130a, miR-21 and miR-7, harbored CHOP binding sites in their promoter region. We used computational approaches to integrate the three regulatory layers and to generate a molecular map describing the altered circuits in sensitive and resistant cell lines. By combining transcriptomic and proteomic data, we reconstructed two different networks, i.e. apoptosis and cell cycle regulation, that could play a key role in modulating trabectedin resistance. This approach highlights the central role of genes such as CCDN1, RB1, E2F4, TNF, CDKN1C and ABL1 in both pre- and post-transcriptional regulatory network. The validation of these results in in vivo models might be clinically relevant to stratify myxoid liposarcoma patients with different sensitivity to trabectedin treatment.

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A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma

et al. (2012) A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma. PLoS ONE 7(4): e35423. doi:10.1371/journal.pone.0035423 A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma Sarah Uboldi 0 Enrica Calura 0 Luca Beltrame 0 Ilaria Fuso Nerini 0 Sergio Marchini 0 Duccio Cavalieri 0 Eugenio Erba 0 Giovanna Chiorino 0 Paola Ostano 0 Daniela D'Angelo 0 Maurizio D'Incalci 0 Chiara Romualdi 0 Paolo Provero, University of Turin, Italy 0 1 Department of Oncology, Mario Negri Institute for Pharmacological Research , Milan , Italy , 2 Department of Biology, University of Padova , Padova , Italy , 3 Department of Computational Biology, Research and Innovation Centre , San Michele all'Adige, Trento , Italy , 4 Fondazione Edo ed Elvo Tempia Valenta, Cancer Genomics Laboratory , Biella, Italy, 5 Experimental Endocrinology and Oncology, CNR, Naples , Italy Trabectedin, a new antitumor compound originally derived from a marine tunicate, is clinically effective in soft tissue sarcoma. The drug has shown a high selectivity for myxoid liposarcoma, characterized by the translocation t(12;16)(q13; p11) leading to the expression of FUS-CHOP fusion gene. Trabectedin appears to act interfering with mechanisms of transcription regulation. In particular, the transactivating activity of FUS-CHOP was found to be impaired by trabectedin treatment. Even after prolonged response resistance occurs and thus it is important to elucidate the mechanisms of resistance to trabectedin. To this end we developed and characterized a myxoid liposarcoma cell line resistant to trabectedin (402-91/ET), obtained by exposing the parental 402-91 cell line to stepwise increases in drug concentration. The aim of this study was to compare mRNAs, miRNAs and proteins profiles of 402-91 and 402-91/ET cells through a systems biology approach. We identified 3,083 genes, 47 miRNAs and 336 proteins differentially expressed between 402-91 and 40291/ET cell lines. Interestingly three miRNAs among those differentially expressed, miR-130a, miR-21 and miR-7, harbored CHOP binding sites in their promoter region. We used computational approaches to integrate the three regulatory layers and to generate a molecular map describing the altered circuits in sensitive and resistant cell lines. By combining transcriptomic and proteomic data, we reconstructed two different networks, i.e. apoptosis and cell cycle regulation, that could play a key role in modulating trabectedin resistance. This approach highlights the central role of genes such as CCDN1, RB1, E2F4, TNF, CDKN1C and ABL1 in both pre- and post-transcriptional regulatory network. The validation of these results in in vivo models might be clinically relevant to stratify myxoid liposarcoma patients with different sensitivity to trabectedin treatment. - Funding: This work was supported by University of Padova (CPDR075919 to CR). Furthermore, the authors want to acknowledge the CINECA Award N. HP10BDJ9X8, 2010 for the availability of high performance computing resources and support. The authors acknowledge the generous contribution of the Italian Association for Cancer Research (AIRC). IFN is recipient of a fellowship from ACTO foundation. PO and GC are supported by Compagnia di San Paolo, Torino, Italy. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Trabectedin (YondelisH) is a tetrahydroisoquinoline molecule originally derived from the Caribbean marine tunicate, Ecteinascidia turbinata, with peculiar in vitro and in vivo cytotoxic activity in a wide range of tumor type: it has been approved by EMEA for the second line therapy of soft tissue sarcomas and ovarian cancer [1 7]. From a mechanistic point of view, trabectedin binds to the minor groove of DNA, differently from the conventional alkylating agents, forming DNA adducts on N2 position of guanine, and bends DNA towards the major groove; two of the three fused rings of this molecule are involved in the minor groove binding while the third (ring C) plays an important role in the process of interaction with different DNA-binding proteins [8,9]. It is now widely accepted that trabectedin-DNA interaction affects transcription regulation although the level of selectivity is not completely elucidated [8,10,11]. Although trabectedin has shown activity against several types of sarcomas, its higher activity has been observed in patients with myxoid liposarcoma (MLS). The high sensitivity displayed by MLS tumors is probably correlated to the ability of trabectedin to block the aberrant transcription activity of FUS-CHOP, the chimeric protein hallmark of MLS, generated by the chromosomal translocation t(12;16)(q13;p11) [12,13]. Desp (...truncated)


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Sarah Uboldi, Enrica Calura, Luca Beltrame, Ilaria Fuso Nerini, Sergio Marchini, Duccio Cavalieri, Eugenio Erba, Giovanna Chiorino, Paola Ostano, Daniela D'Angelo, Maurizio D'Incalci, Chiara Romualdi. A Systems Biology Approach to Characterize the Regulatory Networks Leading to Trabectedin Resistance in an In Vitro Model of Myxoid Liposarcoma, PLOS ONE, 2012, 4, DOI: 10.1371/journal.pone.0035423