Identification of Novel Somatic TP53 Mutations in Patients with High-Grade Serous Ovarian Cancer (HGSOC) Using Next-Generation Sequencing (NGS)
Abstract
:1. Introduction
2. Results
2.1. Patient Characteristics
2.2. Identification of Novel TP53 Somatic Mutations by NGS
2.3. Validation of De Novo TP53 Somatic Mutations in HGSOC
2.4. Immunohistochemical Evaluation of p53 Expression in Tumor Samples
2.5. In Silico Prediction and Structural Analysis
3. Discussion
4. Materials and Methods
4.1. Patients and Human Ethics
4.2. Case History
4.2.1. Case ID 305
4.2.2. Case ID 519
4.2.3. Case ID 627
4.2.4. Case ID 738
4.2.5. Case ID 751
4.2.6. Case ID 761
4.3. Next Generation Sequencing Analysis
4.4. Sanger Sequencing and Pyrosequencing to Validate Novel Somatic Mutations
4.5. p53 Immunohistochemistry
4.6. In Silico Analysis
Supplementary Materials
Author Contributions
Acknowledgments
Conflicts of Interest
References
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Case ID | Age a | TNM | FIGO | Histology | Grade | R | CT Setting | First Line Treatment | PFI | PFS | OS | Actual Status |
---|---|---|---|---|---|---|---|---|---|---|---|---|
(year) | (G) | (cm) | (m) | (m) | (m) | |||||||
305 | 58 | pT3cN1M0 | IIIC | Serous | G3 | 0 | I line | Carbotaxol | 38 | 43 | 43 | Dead |
519 | 52 | pT3cN1M1 | IV | Serous | G3 | 0 | I line | Carbotaxol | 80 | 85 | 98 | Alive |
627 | 68 | ypT2aN0M0 | IIA | Serous | G3 | 0 | Neo-adj | Carbotaxol | 64 | 71 | 77 | Alive |
738 | 79 | pT2cNxM0 | IIC | Serous | G3 | >1 | NA | NA | NA | NA | 9 | Dead |
751 | 71 | pT2cN0 | IIC | Serous | G3 | 0 | I line | Carbotaxol | 29 | 34 | 60 | Alive |
761 | 56 | pT3cNxM0 | IIIC | Serous | G3 | 0 | I line | Carbotaxol | 14 | 20 | 58 | Alive |
Case ID | Exon | Genomic Coordinate | Alt | Ref Read Depth | Alt Read Depth | cDNA Nucleotide Change | AA Change | Mutation Type |
---|---|---|---|---|---|---|---|---|
(%) a | ||||||||
305 | 7 | 17:7,577,541 | 58.43 | 15,734 | 9194 | c.728_739delTGGGCGGCATGA | p.Met243_Met247del | In-frame |
INDEL | ||||||||
519 | 8 | 17:7,577,128 | 47.84 | 6377 | 3051 | c.795_809delGGGACGGAACAGCTT | p.Gly266_Phe270del | In-frame |
INDEL | ||||||||
627 | 8 | 17:7,577,111 | 22.34 | 4692 | 1048 | c.826_827GC>AT | p.Ala276Ile | Missense |
738 | 10 | 17:7,574,004 | 53.41 | 4606 | 2460 | c.1022insT | p.Arg342Profs*5 | Frameshift |
INDEL | ||||||||
751 | 11 | 17:7,572,928 | 8.32 | 2994 | 249 | c.1180delT | p.Ter394Aspfs*28 | Frameshift |
INDEL | ||||||||
761 | 6 | 17:7,578,275 | 73.38 | 7205 | 5287 | c.573insT | p.Gln192Serfs*17 | Frameshift |
INDEL |
Case ID | Novel Mutp53 | p53 Domain | p53 IHC a | Predicted Damaging Effect b | Phylogenetic Conservation c | Predicted Splicing Effect | Structural Consequence | Loss of CpG Site d | Platinum Status | OS | Classification of Novel Mutp53 |
---|---|---|---|---|---|---|---|---|---|---|---|
305 | p.Met243_Met247del | DBD | ~100% (+++) | Yes | Met243 100% | Yes | Probable strong rearrangement in DNA minor groove binding surface | Yes | Sensitive | 3 ≤ years < 4 † | Uncl |
Gly244 100% | |||||||||||
Gly245 100% | |||||||||||
Met246 100% | |||||||||||
519 | p.Gly266_Phe270del | DBD | ~80% (++) | Yes | Gly266 100% | Yes | Probable change in affinity of p53 for target sequence | Yes | Sensitive | >5 years | Uncl |
Arg267 100% | |||||||||||
Asn268 60% | |||||||||||
Ser269 90% | |||||||||||
Phe270 100% | |||||||||||
627 | p.Ala276Ile | DBD | ~80% | Yes | Ala276 100% | No | Probable perturbation in proximity of DNA major groove binding surface | No | Sensitive | >5 years | Uncl |
738 | p.Arg342Profs*5 | OD | <5% (−/+) | Yes | Arg342 80% * | Yes | Partial loss of OD | No | NA | <1 year † | LOF |
Loss of C’-terminal | |||||||||||
751 | p.Ter394Aspfs*28 | C′-terminal ** | ~60% (30% +; 30% ++) | No | ** | No | Abnormal protein elongation | No | Sensitive | ≥5 years | Uncl |
761 | p.Gln192Serfs*17 | DBD | - | Yes | Gln192 90% * | Yes | Probable strong rearrangement in DNA minor groove binding surface | No | Sensitive | 4 ≤ years < 5 | LOF |
Massive loss of DBD. | |||||||||||
Loss of OD and C′-terminal. |
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Garziera, M.; Cecchin, E.; Canzonieri, V.; Sorio, R.; Giorda, G.; Scalone, S.; De Mattia, E.; Roncato, R.; Gagno, S.; Poletto, E.; et al. Identification of Novel Somatic TP53 Mutations in Patients with High-Grade Serous Ovarian Cancer (HGSOC) Using Next-Generation Sequencing (NGS). Int. J. Mol. Sci. 2018, 19, 1510. https://doi.org/10.3390/ijms19051510
Garziera M, Cecchin E, Canzonieri V, Sorio R, Giorda G, Scalone S, De Mattia E, Roncato R, Gagno S, Poletto E, et al. Identification of Novel Somatic TP53 Mutations in Patients with High-Grade Serous Ovarian Cancer (HGSOC) Using Next-Generation Sequencing (NGS). International Journal of Molecular Sciences. 2018; 19(5):1510. https://doi.org/10.3390/ijms19051510
Chicago/Turabian StyleGarziera, Marica, Erika Cecchin, Vincenzo Canzonieri, Roberto Sorio, Giorgio Giorda, Simona Scalone, Elena De Mattia, Rossana Roncato, Sara Gagno, Elena Poletto, and et al. 2018. "Identification of Novel Somatic TP53 Mutations in Patients with High-Grade Serous Ovarian Cancer (HGSOC) Using Next-Generation Sequencing (NGS)" International Journal of Molecular Sciences 19, no. 5: 1510. https://doi.org/10.3390/ijms19051510