Advertisement

Breast Cancer Research and Treatment

, Volume 155, Issue 1, pp 139–149 | Cite as

Cell-free DNA as a molecular tool for monitoring disease progression and response to therapy in breast cancer patients

  • Diana H. Liang
  • Joe E. Ensor
  • Zhe-bin Liu
  • Asmita Patel
  • Tejal A. Patel
  • Jenny C. Chang
  • Angel A. Rodriguez
Epidemiology

Abstract

Due to the spatial and temporal genomic heterogeneity of breast cancer, genomic sequencing obtained from a single biopsy may not capture the complete genomic profile of tumors. Thus, we propose that cell-free DNA (cfDNA) in plasma may be an alternate source of genomic information to provide comprehensive data throughout a patient’s clinical course. We performed a retrospective chart review of 100 patients with stage 4 or high-risk stage 3 breast cancer. The degree of agreement between genomic alterations found in tumor DNA (tDNA) and cfDNA was determined by Cohen’s Kappa. Clinical disease progression was compared to mutant allele frequency using a two-sided Fisher’s exact test. The presence of mutations and mutant allele frequency was correlated with progression-free survival (PFS) using a Cox proportional hazards model and a log-rank test. The most commonly found genomic alterations were mutations in TP53 and PIK3CA, and amplification of EGFR and ERBB2. PIK3CA mutation and ERBB2 amplification demonstrated robust agreement between tDNA and cfDNA (Cohen’s kappa = 0.64 and 0.77, respectively). TP53 mutation and EGFR amplification demonstrated poor agreement between tDNA and cfDNA (Cohen’s kappa = 0.18 and 0.33, respectively). The directional changes of TP53 and PIK3CA mutant allele frequency were closely associated with response to therapy (p = 0.002). The presence of TP53 mutation (p = 0.0004) and PIK3CA mutant allele frequency [p = 0.01, HR 1.074 (95 % CI 1.018–1.134)] was excellent predictors of PFS. Identification of selected cancer-specific genomic alterations from cfDNA may be a noninvasive way to monitor disease progression, predict PFS, and offer targeted therapy.

Keywords

Cell-free DNA Breast cancer Clinical markers 

Notes

Acknowledgments

This project was supported by the Houston Methodist Cancer Center.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Ethical approval

Approval for the study was obtained from the institutional review board of the Houston Methodist Hospital. For this retrospective study, formal consent is not required.

References

  1. 1.
    Meyerson M, Gabriel S, Getz G (2010) Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 11:685–696. doi: 10.1038/nrg2841 PubMedCrossRefGoogle Scholar
  2. 2.
    Sato F, Saji S, Toi M (2015) Genomic tumor evolution of breast cancer. Breast Cancer. doi: 10.1007/s12282-015-0617-8 PubMedCentralGoogle Scholar
  3. 3.
    Bourdeanu L, Luu T (2014) Targeted therapies in breast cancer: implications for advanced oncology practice. J Adv Pract Oncol 5:246–260PubMedPubMedCentralGoogle Scholar
  4. 4.
    Bettegowda C, Sausen M, Leary RJ, Kinde I, Wang Y, Agrawal N, Bartlett BR, Wang H, Luber B, Alani RM, Antonarakis ES, Azad NS, Bardelli A, Brem H, Cameron JL, Lee CC, Fecher LA, Gallia GL, Gibbs P, Le D, Giuntoli RL, Goggins M, Hogarty MD, Holdhoff M, Hong SM, Jiao Y, Juhl HH, Kim JJ, Siravegna G, Laheru DA, Lauricella C, Lim M, Lipson EJ, Marie SK, Netto GJ, Oliner KS, Olivi A, Olsson L, Riggins GJ, Sartore-Bianchi A, Schmidt K, Shih l M, Oba-Shinjo SM, Siena S, Theodorescu D, Tie J, Harkins TT, Veronese S, Wang TL, Weingart JD, Wolfgang CL, Wood LD, Xing D, Hruban RH, Wu J, Allen PJ, Schmidt CM, Choti MA, Velculescu VE, Kinzler KW, Vogelstein B, Papadopoulos N, Diaz LA, Jr. (2014) Detection of circulating tumor DNA in early- and late-stage human malignancies. Sci Transl Med 6:224ra224. doi:  10.1126/scitranslmed.3007094
  5. 5.
    Gerlinger M, Rowan AJ, Horswell S, Larkin J, Endesfelder D, Gronroos E, Martinez P, Matthews N, Stewart A, Tarpey P, Varela I, Phillimore B, Begum S, McDonald NQ, Butler A, Jones D, Raine K, Latimer C, Santos CR, Nohadani M, Eklund AC, Spencer-Dene B, Clark G, Pickering L, Stamp G, Gore M, Szallasi Z, Downward J, Futreal PA, Swanton C (2012) Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N Engl J Med 366:883–892. doi: 10.1056/NEJMoa1113205 PubMedCrossRefGoogle Scholar
  6. 6.
    Wang Y, Waters J, Leung ML, Unruh A, Roh W, Shi X, Chen K, Scheet P, Vattathil S, Liang H, Multani A, Zhang H, Zhao R, Michor F, Meric-Bernstam F, Navin NE (2014) Clonal evolution in breast cancer revealed by single nucleus genome sequencing. Nature 512:155–160. doi: 10.1038/nature13600 PubMedPubMedCentralCrossRefGoogle Scholar
  7. 7.
    Navin N, Kendall J, Troge J, Andrews P, Rodgers L, McIndoo J, Cook K, Stepansky A, Levy D, Esposito D, Muthuswamy L, Krasnitz A, McCombie WR, Hicks J, Wigler M (2011) Tumour evolution inferred by single-cell sequencing. Nature 472:90–94. doi: 10.1038/nature09807 PubMedPubMedCentralCrossRefGoogle Scholar
  8. 8.
    Zardavas D, Irrthum A, Swanton C, Piccart M (2015) Clinical management of breast cancer heterogeneity. Nat Rev Clin Oncol 12:381–394. doi: 10.1038/nrclinonc.2015.73 PubMedCrossRefGoogle Scholar
  9. 9.
    Bedard PL, Hansen AR, Ratain MJ, Siu LL (2013) Tumour heterogeneity in the clinic. Nature 501:355–364. doi: 10.1038/nature12627 PubMedCrossRefGoogle Scholar
  10. 10.
    Diaz LA Jr, Williams RT, Wu J, Kinde I, Hecht JR, Berlin J, Allen B, Bozic I, Reiter JG, Nowak MA, Kinzler KW, Oliner KS, Vogelstein B (2012) The molecular evolution of acquired resistance to targeted EGFR blockade in colorectal cancers. Nature 486:537–540. doi: 10.1038/nature11219 PubMedPubMedCentralGoogle Scholar
  11. 11.
    Ma QC, Ennis CA, Aparicio S (2012) Opening Pandora’s Box–the new biology of driver mutations and clonal evolution in cancer as revealed by next generation sequencing. Curr Opin Genet Dev 22:3–9. doi: 10.1016/j.gde.2012.01.008 PubMedCrossRefGoogle Scholar
  12. 12.
    Dawson SJ, Tsui DW, Murtaza M, Biggs H, Rueda OM, Chin SF, Dunning MJ, Gale D, Forshew T, Mahler-Araujo B, Rajan S, Humphray S, Becq J, Halsall D, Wallis M, Bentley D, Caldas C, Rosenfeld N (2013) Analysis of circulating tumor DNA to monitor metastatic breast cancer. N Engl J Med 368:1199–1209. doi: 10.1056/NEJMoa1213261 PubMedCrossRefGoogle Scholar
  13. 13.
    Schwarzenbach H (2013) Circulating nucleic acids as biomarkers in breast cancer. Breast Cancer Res 15:211. doi: 10.1186/bcr3446 PubMedPubMedCentralCrossRefGoogle Scholar
  14. 14.
    Leon SA, Shapiro B, Sklaroff DM, Yaros MJ (1977) Free DNA in the serum of cancer patients and the effect of therapy. Cancer Res 37:646–650PubMedGoogle Scholar
  15. 15.
    Stroun M, Anker P, Maurice P, Lyautey J, Lederrey C, Beljanski M (1989) Neoplastic characteristics of the DNA found in the plasma of cancer patients. Oncology 46:318–322PubMedCrossRefGoogle Scholar
  16. 16.
    Kohler C, Radpour R, Barekati Z, Asadollahi R, Bitzer J, Wight E, Burki N, Diesch C, Holzgreve W, Zhong XY (2009) Levels of plasma circulating cell free nuclear and mitochondrial DNA as potential biomarkers for breast tumors. Mol Cancer 8:105. doi: 10.1186/1476-4598-8-105 PubMedPubMedCentralCrossRefGoogle Scholar
  17. 17.
    Olsson E, Winter C, George A, Chen Y, Howlin J, Tang MH, Dahlgren M, Schulz R, Grabau D, van Westen D, Ferno M, Ingvar C, Rose C, Bendahl PO, Ryden L, Borg A, Gruvberger-Saal SK, Jernstrom H, Saal LH (2015) Serial monitoring of circulating tumor DNA in patients with primary breast cancer for detection of occult metastatic disease. EMBO Mol Med 7:1034–1047. doi: 10.15252/emmm.201404913 PubMedPubMedCentralCrossRefGoogle Scholar
  18. 18.
    Lanman RB, Mortimer SA, Zill OA, Sebisanovic D, Lopez R, Blau S, Collisson EA, Divers SG, Hoon DS, Kopetz ES, Lee J, Nikolinakos PG, Baca AM, Kermani BG, Eltoukhy H, Talasaz A (2015) Analytical and clinical validation of a digital sequencing panel for quantitative, highly accurate evaluation of cell-free circulating tumor DNA. PLoS ONE 10:e0140712. doi: 10.1371/journal.pone.0140712 PubMedPubMedCentralCrossRefGoogle Scholar
  19. 19.
    Shah M, Denlinger CS (2015) Optimal post-treatment surveillance in cancer survivors: is more really better? Oncology (Williston Park) 29:230–240Google Scholar
  20. 20.
    Shaw JA, Stebbing J (2014) Circulating free DNA in the management of breast cancer. Ann Transl Med 2:3. doi: 10.3978/j.issn.2305-5839.2013.06.06 PubMedPubMedCentralGoogle Scholar
  21. 21.
    Smerage JB, Barlow WE, Hortobagyi GN, Winer EP, Leyland-Jones B, Srkalovic G, Tejwani S, Schott AF, O’Rourke MA, Lew DL, Doyle GV, Gralow JR, Livingston RB, Hayes DF (2014) Circulating tumor cells and response to chemotherapy in metastatic breast cancer: SWOG S0500. J Clin Oncol 32:3483–3489. doi: 10.1200/JCO.2014.56.2561 PubMedPubMedCentralCrossRefGoogle Scholar
  22. 22.
    Rothe F, Laes JF, Lambrechts D, Smeets D, Vincent D, Maetens M, Fumagalli D, Michiels S, Drisis S, Moerman C, Detiffe JP, Larsimont D, Awada A, Piccart M, Sotiriou C, Ignatiadis M (2014) Plasma circulating tumor DNA as an alternative to metastatic biopsies for mutational analysis in breast cancer. Ann Oncol 25:1959–1965. doi: 10.1093/annonc/mdu288 PubMedCrossRefGoogle Scholar
  23. 23.
    Huang ZH, Li LH, Hua D (2006) Quantitative analysis of plasma circulating DNA at diagnosis and during follow-up of breast cancer patients. Cancer Lett 243:64–70. doi: 10.1016/j.canlet.2005.11.027 PubMedCrossRefGoogle Scholar
  24. 24.
    Higgins MJ, Jelovac D, Barnathan E, Blair B, Slater S, Powers P, Zorzi J, Jeter SC, Oliver GR, Fetting J, Emens L, Riley C, Stearns V, Diehl F, Angenendt P, Huang P, Cope L, Argani P, Murphy KM, Bachman KE, Greshock J, Wolff AC, Park BH (2012) Detection of tumor PIK3CA status in metastatic breast cancer using peripheral blood. Clin Cancer Res 18:3462–3469. doi: 10.1158/1078-0432.CCR-11-2696 PubMedPubMedCentralCrossRefGoogle Scholar
  25. 25.
    Board RE, Wardley AM, Dixon JM, Armstrong AC, Howell S, Renshaw L, Donald E, Greystoke A, Ranson M, Hughes A, Dive C (2010) Detection of PIK3CA mutations in circulating free DNA in patients with breast cancer. Breast Cancer Res Treat 120:461–467. doi: 10.1007/s10549-010-0747-9 PubMedCrossRefGoogle Scholar
  26. 26.
    Leiserson MD, Blokh D, Sharan R, Raphael BJ (2013) Simultaneous identification of multiple driver pathways in cancer. PLoS Comput Biol 9:e1003054. doi: 10.1371/journal.pcbi.1003054 PubMedPubMedCentralCrossRefGoogle Scholar
  27. 27.
    Gustin JP, Cosgrove DP, Park BH (2008) The PIK3CA gene as a mutated target for cancer therapy. Curr Cancer Drug Targets 8:733–740PubMedPubMedCentralCrossRefGoogle Scholar
  28. 28.
    Ahn T, Park T (2014) Pathway-driven discovery of rare mutational impact on cancer. Biomed Res Int 2014:171892. doi: 10.1155/2014/171892 PubMedPubMedCentralGoogle Scholar
  29. 29.
    Mayer IA, Arteaga CL (2014) PIK3CA activating mutations: a discordant role in early versus advanced hormone-dependent estrogen receptor-positive breast cancer? J Clin Oncol 32:2932–2934. doi: 10.1200/JCO.2014.55.9591 PubMedCrossRefGoogle Scholar
  30. 30.
    Loi S, Haibe-Kains B, Majjaj S, Lallemand F, Durbecq V, Larsimont D, Gonzalez-Angulo AM, Pusztai L, Symmans WF, Bardelli A, Ellis P, Tutt AN, Gillett CE, Hennessy BT, Mills GB, Phillips WA, Piccart MJ, Speed TP, McArthur GA, Sotiriou C (2010) PIK3CA mutations associated with gene signature of low mTORC1 signaling and better outcomes in estrogen receptor-positive breast cancer. Proc Natl Acad Sci USA 107:10208–10213. doi: 10.1073/pnas.0907011107 PubMedPubMedCentralCrossRefGoogle Scholar
  31. 31.
    Kalinsky K, Jacks LM, Heguy A, Patil S, Drobnjak M, Bhanot UK, Hedvat CV, Traina TA, Solit D, Gerald W, Moynahan ME (2009) PIK3CA mutation associates with improved outcome in breast cancer. Clin Cancer Res 15:5049–5059. doi: 10.1158/1078-0432.CCR-09-0632 PubMedCrossRefGoogle Scholar
  32. 32.
    Kroigard AB, Larsen MJ, Laenkholm AV, Knoop AS, Jensen JD, Bak M, Mollenhauer J, Kruse TA, Thomassen M (2015) Clonal expansion and linear genome evolution through breast cancer progression from pre-invasive stages to asynchronous metastasis. Oncotarget 6:5634–5649PubMedPubMedCentralCrossRefGoogle Scholar
  33. 33.
    Pestrin M, Salvianti F, Galardi F, De Luca F, Turner N, Malorni L, Pazzagli M, Di Leo A, Pinzani P (2015) Heterogeneity of PIK3CA mutational status at the single cell level in circulating tumor cells from metastatic breast cancer patients. Mol Oncol 9:749–757. doi: 10.1016/j.molonc.2014.12.001 PubMedCrossRefGoogle Scholar
  34. 34.
    Deng G, Krishnakumar S, Powell AA, Zhang H, Mindrinos MN, Telli ML, Davis RW, Jeffrey SS (2014) Single cell mutational analysis of PIK3CA in circulating tumor cells and metastases in breast cancer reveals heterogeneity, discordance, and mutation persistence in cultured disseminated tumor cells from bone marrow. BMC Cancer 14:456. doi: 10.1186/1471-2407-14-456 PubMedPubMedCentralCrossRefGoogle Scholar
  35. 35.
    Maxwell KN S-ED, Carpenter EL, Troxel AB, Colameco C, Clark C, et al. (2015) Comparison of mutational spectra in metastatic tumors and cell-free DNA in breast cancer patients.. Cancer Res. 75 (15 Supp): Abstract nr618Google Scholar
  36. 36.
    Oshiro C, Kagara N, Naoi Y, Shimoda M, Shimomura A, Maruyama N, Shimazu K, Kim SJ, Noguchi S (2015) PIK3CA mutations in serum DNA are predictive of recurrence in primary breast cancer patients. Breast Cancer Res Treat 150:299–307. doi: 10.1007/s10549-015-3322-6 PubMedCrossRefGoogle Scholar
  37. 37.
    Murtaza M, Dawson SJ, Tsui DW, Gale D, Forshew T, Piskorz AM, Parkinson C, Chin SF, Kingsbury Z, Wong AS, Marass F, Humphray S, Hadfield J, Bentley D, Chin TM, Brenton JD, Caldas C, Rosenfeld N (2013) Non-invasive analysis of acquired resistance to cancer therapy by sequencing of plasma DNA. Nature 497:108–112. doi: 10.1038/nature12065 PubMedCrossRefGoogle Scholar
  38. 38.
    Sefrioui D, Perdrix A, Sarafan-Vasseur N, Dolfus C, Dujon A, Picquenot JM, Delacour J, Cornic M, Bohers E, Leheurteur M, Rigal O, Tennevet I, Thery JC, Alexandru C, Guillemet C, Moldovan C, Veyret C, Frebourg T, Di Fiore F, Clatot F (2015) Short report: monitoring ESR1 mutations by circulating tumor DNA in aromatase inhibitor resistant metastatic breast cancer. Int J Cancer 137:2513–2519. doi: 10.1002/ijc.29612 PubMedCrossRefGoogle Scholar
  39. 39.
    Guttery DS, Page K, Hills A, Woodley L, Marchese SD, Rghebi B, Hastings RK, Luo J, Pringle JH, Stebbing J, Coombes RC, Ali S, Shaw JA (2015) Noninvasive detection of activating estrogen receptor 1 (ESR1) mutations in estrogen receptor-positive metastatic breast cancer. Clin Chem 61:974–982. doi: 10.1373/clinchem.2015.238717 PubMedCrossRefGoogle Scholar
  40. 40.
    Madic J, Kiialainen A, Bidard FC, Birzele F, Ramey G, Leroy Q, Rio Frio T, Vaucher I, Raynal V, Bernard V, Lermine A, Clausen I, Giroud N, Schmucki R, Milder M, Horn C, Spleiss O, Lantz O, Stern MH, Pierga JY, Weisser M, Lebofsky R (2015) Circulating tumor DNA and circulating tumor cells in metastatic triple negative breast cancer patients. Int J Cancer 136:2158–2165. doi: 10.1002/ijc.29265 PubMedCrossRefGoogle Scholar
  41. 41.
    Van Poznak C, Somerfield MR, Bast RC, Cristofanilli M, Goetz MP, Gonzalez-Angulo AM, Hicks DG, Hill EG, Liu MC, Lucas W, Mayer IA, Mennel RG, Symmans WF, Hayes DF, Harris LN (2015) Use of Biomarkers to Guide Decisions on Systemic Therapy for Women With Metastatic Breast Cancer: American Society of Clinical Oncology Clinical Practice Guideline. J Clin Oncol 33:2695–2704. doi: 10.1200/JCO.2015.61.1459 PubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Diana H. Liang
    • 1
    • 2
  • Joe E. Ensor
    • 2
    • 3
  • Zhe-bin Liu
    • 2
    • 4
  • Asmita Patel
    • 3
  • Tejal A. Patel
    • 3
  • Jenny C. Chang
    • 3
  • Angel A. Rodriguez
    • 3
  1. 1.Department of SurgeryHouston Methodist HospitalHoustonUSA
  2. 2.Houston Methodist Research InstituteHouston Methodist HospitalHoustonUSA
  3. 3.Houston Methodist Cancer CenterHoustonUSA
  4. 4.Department of Breast SurgeryFudan University Shanghai Cancer CenterShanghaiChina

Personalised recommendations