Limits...
Heterogeneous Mechanisms of Secondary Resistance and Clonal Selection in Sarcoma during Treatment with Nutlin.

Laroche A, Tran-Cong K, Chaire V, Lagarde P, Hostein I, Coindre JM, Chibon F, Neuville A, Lesluyes T, Lucchesi C, Italiano A - PLoS ONE (2015)

Bottom Line: Further, secondary resistance to nutlin was associated with deregulation of apoptosis-related genes and marked productive autophagy, the inhibition of which resulted in significant restoration of nutlin-induced cell death.Collectively, our findings argue that secondary resistance to nutlin in STS involved heterogeneous mechanisms resulting from clonal evolution and several biological pathways.Alternative dosing regimens and combination with other targeted agents are needed to achieve successful development of nutlin in the clinical setting.

View Article: PubMed Central - PubMed

Affiliation: INSERM U916, Institut Bergonié, Bordeaux, France; Sarcoma Unit, Institut Bergonié, Bordeaux, France.

ABSTRACT
Nutlin inhibits TP53-MDM2 interaction and is under investigation in soft-tissue sarcomas (STS) and other malignancies. Molecular mechanisms of secondary resistance to nutlin in STS are unknown. We performed whole-transcriptome sequencing (RNA-seq) on three pretreatment and secondary resistant STS cell lines selected based on their high primary sensitivity to nutlin. Our data identified a subset of cancer gene mutations and ploidy variations that were positively selected following treatment, including TP53 mutations in 2 out of 3 resistant cell lines. Further, secondary resistance to nutlin was associated with deregulation of apoptosis-related genes and marked productive autophagy, the inhibition of which resulted in significant restoration of nutlin-induced cell death. Collectively, our findings argue that secondary resistance to nutlin in STS involved heterogeneous mechanisms resulting from clonal evolution and several biological pathways. Alternative dosing regimens and combination with other targeted agents are needed to achieve successful development of nutlin in the clinical setting.

No MeSH data available.


Related in: MedlinePlus

Variants in sensitive and secondary resistant STS cells.From top to bottom rows, plots of IB111, IB115 and IB128 variants. A. AAR scatters parental (X axis) and resistant (Y axis), red points: AAR higher in resistant, blue points: AAR lower in resistant, gray points: AAR unchanged (parental variants), dotted lines: AAR difference isomers (lines of same AAR difference). B. Parental variants, on Y axis the AAR in parental and resistant samples. C. variants whose AAR increases in resistant samples (15 in IB111, 5 in IB115, 9 in IB128) D. variants whose AAR decreases in resistant samples.
© Copyright Policy
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4591276&req=5

pone.0137794.g004: Variants in sensitive and secondary resistant STS cells.From top to bottom rows, plots of IB111, IB115 and IB128 variants. A. AAR scatters parental (X axis) and resistant (Y axis), red points: AAR higher in resistant, blue points: AAR lower in resistant, gray points: AAR unchanged (parental variants), dotted lines: AAR difference isomers (lines of same AAR difference). B. Parental variants, on Y axis the AAR in parental and resistant samples. C. variants whose AAR increases in resistant samples (15 in IB111, 5 in IB115, 9 in IB128) D. variants whose AAR decreases in resistant samples.

Mentions: To identify changes in the mutation profiles of secondary resistant cells, we compared the abundance of somatic mutations found in the parental and secondary resistant cell lines. For each cell line, we examined a conservative list of mutations and used Fisher’s exact test to identify those specifically associated with secondary resistance (see material and methods). In all cell lines the majority of variants were common to the parental and resistant cells (Fig 4). The number of non-synonymous mutations with significant changes in normalized abundance between parental and resistant cell lines ranged from 10 to 23 for each case. These include mutations in well-known cancer genes, genes linked to drug resistance and drug metabolism, and genes not previously associated with carcinogenesis or therapy resistance (Table 2). The TP53 gene was the only recurrent gene we identified as having mutations with significant changes in abundance between the secondary resistant and the parental cell lines. Indeed, we identified one TP53 mutation in the IB115 cell line (C275S) and three different TP53 mutations in the IB128 cell line (R248P, G199E, T125R). These mutations have all been previously reported in human tumor samples (http://cancer.sanger.ac.uk/wgs/gene/analysis?ln=TP53#dist) and are located in the highly- conserved DNA binding domain of TP53. All these positions have been validated with ultra-deep DNA resequencing of the TP53 coding region (data not shown). No TP53 mutations were identified in the IB111 cell line.


Heterogeneous Mechanisms of Secondary Resistance and Clonal Selection in Sarcoma during Treatment with Nutlin.

Laroche A, Tran-Cong K, Chaire V, Lagarde P, Hostein I, Coindre JM, Chibon F, Neuville A, Lesluyes T, Lucchesi C, Italiano A - PLoS ONE (2015)

Variants in sensitive and secondary resistant STS cells.From top to bottom rows, plots of IB111, IB115 and IB128 variants. A. AAR scatters parental (X axis) and resistant (Y axis), red points: AAR higher in resistant, blue points: AAR lower in resistant, gray points: AAR unchanged (parental variants), dotted lines: AAR difference isomers (lines of same AAR difference). B. Parental variants, on Y axis the AAR in parental and resistant samples. C. variants whose AAR increases in resistant samples (15 in IB111, 5 in IB115, 9 in IB128) D. variants whose AAR decreases in resistant samples.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4591276&req=5

pone.0137794.g004: Variants in sensitive and secondary resistant STS cells.From top to bottom rows, plots of IB111, IB115 and IB128 variants. A. AAR scatters parental (X axis) and resistant (Y axis), red points: AAR higher in resistant, blue points: AAR lower in resistant, gray points: AAR unchanged (parental variants), dotted lines: AAR difference isomers (lines of same AAR difference). B. Parental variants, on Y axis the AAR in parental and resistant samples. C. variants whose AAR increases in resistant samples (15 in IB111, 5 in IB115, 9 in IB128) D. variants whose AAR decreases in resistant samples.
Mentions: To identify changes in the mutation profiles of secondary resistant cells, we compared the abundance of somatic mutations found in the parental and secondary resistant cell lines. For each cell line, we examined a conservative list of mutations and used Fisher’s exact test to identify those specifically associated with secondary resistance (see material and methods). In all cell lines the majority of variants were common to the parental and resistant cells (Fig 4). The number of non-synonymous mutations with significant changes in normalized abundance between parental and resistant cell lines ranged from 10 to 23 for each case. These include mutations in well-known cancer genes, genes linked to drug resistance and drug metabolism, and genes not previously associated with carcinogenesis or therapy resistance (Table 2). The TP53 gene was the only recurrent gene we identified as having mutations with significant changes in abundance between the secondary resistant and the parental cell lines. Indeed, we identified one TP53 mutation in the IB115 cell line (C275S) and three different TP53 mutations in the IB128 cell line (R248P, G199E, T125R). These mutations have all been previously reported in human tumor samples (http://cancer.sanger.ac.uk/wgs/gene/analysis?ln=TP53#dist) and are located in the highly- conserved DNA binding domain of TP53. All these positions have been validated with ultra-deep DNA resequencing of the TP53 coding region (data not shown). No TP53 mutations were identified in the IB111 cell line.

Bottom Line: Further, secondary resistance to nutlin was associated with deregulation of apoptosis-related genes and marked productive autophagy, the inhibition of which resulted in significant restoration of nutlin-induced cell death.Collectively, our findings argue that secondary resistance to nutlin in STS involved heterogeneous mechanisms resulting from clonal evolution and several biological pathways.Alternative dosing regimens and combination with other targeted agents are needed to achieve successful development of nutlin in the clinical setting.

View Article: PubMed Central - PubMed

Affiliation: INSERM U916, Institut Bergonié, Bordeaux, France; Sarcoma Unit, Institut Bergonié, Bordeaux, France.

ABSTRACT
Nutlin inhibits TP53-MDM2 interaction and is under investigation in soft-tissue sarcomas (STS) and other malignancies. Molecular mechanisms of secondary resistance to nutlin in STS are unknown. We performed whole-transcriptome sequencing (RNA-seq) on three pretreatment and secondary resistant STS cell lines selected based on their high primary sensitivity to nutlin. Our data identified a subset of cancer gene mutations and ploidy variations that were positively selected following treatment, including TP53 mutations in 2 out of 3 resistant cell lines. Further, secondary resistance to nutlin was associated with deregulation of apoptosis-related genes and marked productive autophagy, the inhibition of which resulted in significant restoration of nutlin-induced cell death. Collectively, our findings argue that secondary resistance to nutlin in STS involved heterogeneous mechanisms resulting from clonal evolution and several biological pathways. Alternative dosing regimens and combination with other targeted agents are needed to achieve successful development of nutlin in the clinical setting.

No MeSH data available.


Related in: MedlinePlus