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Intra-tumor heterogeneity in TP53 High Grade Serous Ovarian Carcinoma progression.

Mota A, Triviño JC, Rojo-Sebastian A, Martínez-Ramírez Á, Chiva L, González-Martín A, Garcia JF, Garcia-Sanz P, Moreno-Bueno G - BMC Cancer (2015)

Bottom Line: Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples.Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1.Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain. amota@iib.uam.es.

ABSTRACT

Background: High grade serous ovarian cancer is characterised by high initial response to chemotherapy but poor outcome in the long term due to acquired resistance. One of the main genetic features of this disease is TP53 mutation. The majority of TP53 mutated tumors harbor missense mutations in this gene, correlated with p53 accumulation. TP53 tumors constitute a specific subgroup characterised by nonsense, frameshift or splice-site mutations associated to complete absence of p53 expression. Different studies show that this kind of tumors may have a worse prognosis than other TP53 mutated HGSC.

Methods: In this study, we sought to characterise the intra-tumor heterogeneity of a TP53 HGSC consisting of six primary tumor samples, two intra-pelvic and four extra-pelvic recurrences using exome sequencing and comparative genome hybridisation.

Results: Significant heterogeneity was found among the different tumor samples, both at the mutational and copy number levels. Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples. Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1. Using functional annotation and network analysis, we identified those biological functions most significantly altered in this tumor. Remarkably, unexpected functions such as microtubule-based movement and lipid metabolism emerged as important for tumor development and progression, suggesting its potential interest as therapeutic targets.

Conclusions: Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies.

No MeSH data available.


Related in: MedlinePlus

Intra-tumoral mutational pattern and hierarchical clustering to establish a clonal evolution in a TP53  HGSC. a Selected variants detected by whole-exome sequencing were reanalysed in 12 tumoral samples (P: Primary tumor, IR: intrapelvic recurrence, ER: extrapelvic recurrence) and normal tissue (N) by Sanger sequencing. b Hierarchical clustering of the analysed samples on the basis of the similarities in mutation pattern
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Fig4: Intra-tumoral mutational pattern and hierarchical clustering to establish a clonal evolution in a TP53 HGSC. a Selected variants detected by whole-exome sequencing were reanalysed in 12 tumoral samples (P: Primary tumor, IR: intrapelvic recurrence, ER: extrapelvic recurrence) and normal tissue (N) by Sanger sequencing. b Hierarchical clustering of the analysed samples on the basis of the similarities in mutation pattern

Mentions: To further investigate intra-tumor heterogeneity, a subset of 20 of the variants detected by exome sequencing was validated by Sanger sequencing in the four original samples (N, P1, IR1, ER1) and in nine additional FFPE samples of tumor implants representing different regions of the primary tumor and recurrences (P2-P6, IR2, ER2-ER4) (Fig. 4a). For the location of the different tumor regions, see Fig. 1a. Variants analysed were selected to represent the different distributions identified in whole-exome sequencing: nine ubiquitous (TP53, CSMD3, CTC1, FAP, KIF21B, LAMA2, SMG7, UBR3 and ZFAT), one shared by P1 and IR1 (FRMPD1), four shared by IR1 and ER1 (HEPHL1, KIF21A, OR56B1 and ZNF664), three P1 specific (CNOT1, PLXNA1 and TRERF1), two IR1 specific (ROBO2 and TFDP1) and one ER1 specific (GPNMB). All these variants were potentially damaging, nonsense, frameshift or splice site variants (Additional file 1: Table S1).Fig. 4


Intra-tumor heterogeneity in TP53 High Grade Serous Ovarian Carcinoma progression.

Mota A, Triviño JC, Rojo-Sebastian A, Martínez-Ramírez Á, Chiva L, González-Martín A, Garcia JF, Garcia-Sanz P, Moreno-Bueno G - BMC Cancer (2015)

Intra-tumoral mutational pattern and hierarchical clustering to establish a clonal evolution in a TP53  HGSC. a Selected variants detected by whole-exome sequencing were reanalysed in 12 tumoral samples (P: Primary tumor, IR: intrapelvic recurrence, ER: extrapelvic recurrence) and normal tissue (N) by Sanger sequencing. b Hierarchical clustering of the analysed samples on the basis of the similarities in mutation pattern
© Copyright Policy - OpenAccess
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4666042&req=5

Fig4: Intra-tumoral mutational pattern and hierarchical clustering to establish a clonal evolution in a TP53 HGSC. a Selected variants detected by whole-exome sequencing were reanalysed in 12 tumoral samples (P: Primary tumor, IR: intrapelvic recurrence, ER: extrapelvic recurrence) and normal tissue (N) by Sanger sequencing. b Hierarchical clustering of the analysed samples on the basis of the similarities in mutation pattern
Mentions: To further investigate intra-tumor heterogeneity, a subset of 20 of the variants detected by exome sequencing was validated by Sanger sequencing in the four original samples (N, P1, IR1, ER1) and in nine additional FFPE samples of tumor implants representing different regions of the primary tumor and recurrences (P2-P6, IR2, ER2-ER4) (Fig. 4a). For the location of the different tumor regions, see Fig. 1a. Variants analysed were selected to represent the different distributions identified in whole-exome sequencing: nine ubiquitous (TP53, CSMD3, CTC1, FAP, KIF21B, LAMA2, SMG7, UBR3 and ZFAT), one shared by P1 and IR1 (FRMPD1), four shared by IR1 and ER1 (HEPHL1, KIF21A, OR56B1 and ZNF664), three P1 specific (CNOT1, PLXNA1 and TRERF1), two IR1 specific (ROBO2 and TFDP1) and one ER1 specific (GPNMB). All these variants were potentially damaging, nonsense, frameshift or splice site variants (Additional file 1: Table S1).Fig. 4

Bottom Line: Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples.Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1.Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies.

View Article: PubMed Central - PubMed

Affiliation: Departamento de Bioquímica, Universidad Autónoma de Madrid (UAM), Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), IdiPAZ, Madrid, Spain. amota@iib.uam.es.

ABSTRACT

Background: High grade serous ovarian cancer is characterised by high initial response to chemotherapy but poor outcome in the long term due to acquired resistance. One of the main genetic features of this disease is TP53 mutation. The majority of TP53 mutated tumors harbor missense mutations in this gene, correlated with p53 accumulation. TP53 tumors constitute a specific subgroup characterised by nonsense, frameshift or splice-site mutations associated to complete absence of p53 expression. Different studies show that this kind of tumors may have a worse prognosis than other TP53 mutated HGSC.

Methods: In this study, we sought to characterise the intra-tumor heterogeneity of a TP53 HGSC consisting of six primary tumor samples, two intra-pelvic and four extra-pelvic recurrences using exome sequencing and comparative genome hybridisation.

Results: Significant heterogeneity was found among the different tumor samples, both at the mutational and copy number levels. Exome sequencing identified 102 variants, of which only 42 were common to all three samples; whereas 7 of the 18 copy number changes found by CGH analysis were presented in all samples. Sanger validation of 20 variants found by exome sequencing in additional regions of the primary tumor and the recurrence allowed us to establish a sequence of the tumor clonal evolution, identifying those populations that most likely gave rise to recurrences and genes potentially involved in this process, like GPNMB and TFDP1. Using functional annotation and network analysis, we identified those biological functions most significantly altered in this tumor. Remarkably, unexpected functions such as microtubule-based movement and lipid metabolism emerged as important for tumor development and progression, suggesting its potential interest as therapeutic targets.

Conclusions: Altogether, our results shed light on the clonal evolution of the distinct tumor regions identifying the most aggressive subpopulations and at least some of the genes that may be implicated in its progression and recurrence, and highlights the importance of considering intra-tumor heterogeneity when carrying out genetic and genomic studies, especially when these are aimed to diagnostic procedures or to uncover possible therapeutic strategies.

No MeSH data available.


Related in: MedlinePlus