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Molecular Diagnostics

Sensitive and robust liquid biopsy-based detection of PIK3CA mutations in hormone-receptor-positive metastatic breast cancer patients

Abstract

Background

The benefit of alpelisib in hormone-receptor-positive (HR+) metastatic breast cancer patients provided clinical evidence for the increasing importance of PIK3CA testing. We performed a comparison of liquid biopsy and tissue-based detection of PIK3CA mutations.

Materials and methods

PIK3CA hotspot mutation analysis using a high-resolution SiMSen-Seq assay was performed in plasma from 93/99 eligible patients with HR+/HER2− breast cancer. Additionally, mFAST-SeqS was used to estimate the tumour fractions in plasma samples. In 72/93 patients, matched tissue was available and analysed using a customised Ion Torrent panel.

Results

PIK3CA mutations were detected in 48.6% of tissue samples and 47.3% of plasma samples, with identical PIK3CA mutation detected in 24/72 (33.3%) patients both in tissue and plasma. In 10 (13.9%) patients, mutations were only found in plasma, and in 6 (8.3%) patients, PIK3CA mutations found in tissue were not detectable in ctDNA. In 49/93 plasma samples without detectable PIK3CA mutations, 22 (44.9%) samples had elevated tumour fractions, implying true negative results.

Conclusion

SiMSen-Seq-based detection of PIK3CA mutations in plasma shows advantageous concordance with the tissue analyses. A combination with an untargeted approach for detecting ctDNA fractions may confirm a negative PIK3CA result and enhance the performance of the SiMSen-Seq test.

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Fig. 1: CONSORT diagram for the study.
Fig. 2: Concordance of PIK3CA mutation status between ctDNA and tissue samples in our study and in the SOLAR-1 study.

Data availability

Data are available at request from authors and were partially (SiMSen-Seq and mFAST-SeqS) deposited at the European Genome-phenome Archive (EGA; http://www.ebi.ac.uk/ega/) under study accession number EGAS00001004940 as following dataset: PIK3CA SiMSen-Seq data of plasma samples.

References

  1. Torre LA, Bray F, Siegel RL, Ferlay J, Lortet-Tieulent J, Jemal A. Global cancer statistics, 2012. CA Cancer J Clin. 2015;65:87–108.

    Article  Google Scholar 

  2. Gennari A, Conte P, Rosso R, Orlandini C, Bruzzi P. Survival of metastatic breast carcinoma patients over a 20-year period: a retrospective analysis based on individual patient data from six consecutive studies. Cancer. 2005;104:1742–50.

    Article  Google Scholar 

  3. Ribnikar D, Volovat SR, Cardoso F. Targeting CDK4/6 pathways and beyond in breast cancer. Breast. 2019;43:8–17.

    Article  Google Scholar 

  4. Karakas B, Bachman KE, Park BH. Mutation of the PIK3CA oncogene in human cancers. Br J Cancer. 2006;94:455–9.

    Article  CAS  Google Scholar 

  5. Fruman DA, Chiu H, Hopkins BD, Bagrodia S, Cantley LC, Abraham RT. The PI3K pathway in human disease. Cell. 2017;170:605–35.

    Article  CAS  Google Scholar 

  6. Koboldt DC, Fulton RS, McLellan MD, Schmidt H, Kalicki-Veizer J, McMichael JF, et al. Comprehensive molecular portraits of human breast tumours. Nature. 2012;490:61–70.

    Article  CAS  Google Scholar 

  7. Saal LH, Holm K, Maurer M, Memeo L, Su T, Wang X, et al. PIK3CA mutations correlate with hormone receptors, node metastasis, and ERBB2, and are mutually exclusive with PTEN loss in human breast carcinoma. Cancer Res. 2005;65:2554–9.

    Article  CAS  Google Scholar 

  8. Di Leo A, Johnston S, Lee KS, Ciruelos E, Lonning PE, Janni W, et al. Buparlisib plus fulvestrant in postmenopausal women with hormone-receptor-positive, HER2-negative, advanced breast cancer progressing on or after mTOR inhibition (BELLE-3): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 2018;19:87–100.

    Article  Google Scholar 

  9. Mosele F, Stefanovska B, Lusque A, Tran Dien A, Garberis I, Droin N, et al. Outcome and molecular landscape of patients with PIK3CA-mutated metastatic breast cancer. Ann Oncol. 2020;31:377–86.

    Article  CAS  Google Scholar 

  10. Moynahan ME, Chen D, He W, Sung P, Samoila A, You D, et al. Correlation between PIK3CA mutations in cell-free DNA and everolimus efficacy in HR(+), HER2(−) advanced breast cancer: results from BOLERO-2. Br J Cancer. 2017;116:726–30.

    Article  CAS  Google Scholar 

  11. Andre F, Ciruelos E, Rubovszky G, Campone M, Loibl S, Rugo HS, et al. Alpelisib for PIK3CA-mutated, hormone receptor-positive advanced breast cancer. N Engl J Med. 2019;380:1929–40.

    Article  CAS  Google Scholar 

  12. Rugo HS, Lerebours F, Ciruelos E, Drullinsky P, Ruiz-Borrego M, Neven P, et al. Alpelisib plus fulvestrant in PIK3CA-mutated, hormone receptor-positive advanced breast cancer after a CDK4/6 inhibitor (BYLieve): one cohort of a phase 2, multicentre, open-label, non-comparative study. Lancet Oncol. 2021;22:489–98.

    Article  CAS  Google Scholar 

  13. Aftimos PG, Antunes De Melo e Oliveira AM, Hilbers F, Venet D, Vingiani A, Nili Gal Yam E, et al. First report of AURORA, the breast international group (BIG) molecular screening initiative for metastatic breast cancer (MBC) patients (pts). Ann Oncol. 2019;30:iii48.

  14. Aftimos P, Oliveira M, Irrthum A, Fumagalli D, Sotiriou C, Nili Gal-Yam E, et al. Genomic and transcriptomic analyses of breast cancer primaries and matched metastases in AURORA, the Breast International Group (BIG) molecular screening initiative. Cancer Discov. 2021; 11:2796-2811.

    Article  CAS  Google Scholar 

  15. Heitzer E, Ulz P, Belic J, Gutschi S, Quehenberger F, Fischereder K, et al. Tumor-associated copy number changes in the circulation of patients with prostate cancer identified through whole-genome sequencing. Genome Med. 2013;5:30.

    Article  CAS  Google Scholar 

  16. Stahlberg A, Krzyzanowski PM, Egyud M, Filges S, Stein L, Godfrey TE. Simple multiplexed PCR-based barcoding of DNA for ultrasensitive mutation detection by next-generation sequencing. Nat Protoc. 2017;12:664–82.

    Article  Google Scholar 

  17. Belic J, Koch M, Ulz P, Auer M, Gerhalter T, Mohan S, et al. Rapid identification of plasma DNA samples with increased ctDNA levels by a modified FAST-SeqS approach. Clin Chem. 2015;61:838–49.

    Article  CAS  Google Scholar 

  18. Belic J, Graf R, Bauernhofer T, Cherkas Y, Ulz P, Waldispuehl-Geigl J, et al. Genomic alterations in plasma DNA from patients with metastasized prostate cancer receiving abiraterone or enzalutamide. Int J Cancer. 2018;143:1236–48.

    Article  CAS  Google Scholar 

  19. Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.

    Article  Google Scholar 

  20. Cingolani P, Platts A, Wang le L, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly (Austin). 2012;6:80–92.

    Article  CAS  Google Scholar 

  21. Vasan N, Razavi P, Johnson JL, Shao H, Shah H, Antoine A, et al. Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kalpha inhibitors. Science. 2019;366:714–23.

    Article  CAS  Google Scholar 

  22. Suppan C, Brcic I, Tiran V, Mueller HD, Posch F, Auer M, et al. Untargeted assessment of tumor fractions in plasma for monitoring and prognostication from metastatic breast cancer patients undergoing systemic treatment. Cancers (Basel). 2019;11:1171.

    Article  CAS  Google Scholar 

  23. Baselga J, Im SA, Iwata H, Cortes J, De Laurentiis M, Jiang Z, et al. Buparlisib plus fulvestrant versus placebo plus fulvestrant in postmenopausal, hormone receptor-positive, HER2-negative, advanced breast cancer (BELLE-2): a randomised, double-blind, placebo-controlled, phase 3 trial. Lancet Oncol. 2017;18:904–16.

    Article  CAS  Google Scholar 

  24. Baselga J, Dent SF, Cortés J, Im Y-H, Diéras V, Harbeck N, et al. Phase III study of taselisib (GDC-0032) + fulvestrant (FULV) v FULV in patients (pts) with estrogen receptor (ER)-positive, PIK3CA-mutant (MUT), locally advanced or metastatic breast cancer (MBC): primary analysis from SANDPIPER. J Clin Oncol. 2018;36:LBA1006–LBA1006.

    Article  Google Scholar 

  25. Baselga J, Sellami D, El-Hashimy M, Dharan B, Wang A, Scheuer N, et al. Abstract A050: PIK3CA mutation status in tumor tissue and ctDNA as a biomarker for PFS in patients with HR+, HER2- ABC treated with buparlisib or placebo plus fulvestrant: results from the BELLE-2 and BELLE-3 randomized studies. Mol Cancer Ther. 2018;17:A050–A050.

    Google Scholar 

  26. Martinez-Saez O, Chic N, Pascual T, Adamo B, Vidal M, Gonzalez-Farre B, et al. Frequency and spectrum of PIK3CA somatic mutations in breast cancer. Breast Cancer Res. 2020;22:45.

    Article  CAS  Google Scholar 

  27. Juric D, Ciruelos E, Rubovszky G, Campone M, Loibl S, Rugo H, et al. Abstract GS3-08: Alpelisib + fulvestrant for advanced breast cancer: subgroup analyses from the phase III SOLAR-1 trial. Cancer Res. 2019;79:GS3-08-GS3.

    Google Scholar 

  28. Dandachi N, Posch F, Graf R, Suppan C, Klocker EV, Müller HD, et al. Longitudinal tumor fraction trajectories predict risk of progression in metastatic HR + breast cancer patients undergoing CDK4/6 treatment. Mol Oncol. 2020;15:2390-2400.

    Article  Google Scholar 

  29. Li H, Davis AA, Liu X-R, Xie F, Gui X-Y, Chen Y-F, et al. Cell-free DNA comparative analysis of hormone receptor-positive, first-line metastatic breast cancer genomic landscape in the United States and China. J Clin Oncol. 2020;38:1059.

    Article  Google Scholar 

  30. Tzanikou E, Markou A, Politaki E, Koutsopoulos A, Psyrri A, Mavroudis D, et al. PIK3CA hotspot mutations in circulating tumor cells and paired circulating tumor DNA in breast cancer: a direct comparison study. Mol Oncol. 2019;13:2515–30.

    Article  CAS  Google Scholar 

  31. Markou A, Farkona S, Schiza C, Efstathiou T, Kounelis S, Malamos N, et al. PIK3CA mutational status in circulating tumor cells can change during disease recurrence or progression in patients with breast cancer. Clin Cancer Res. 2014;20:5823–34.

    Article  CAS  Google Scholar 

  32. Bi L, Okabe I, Bernard DJ, Wynshaw-Boris A, Nussbaum RL. Proliferative defect and embryonic lethality in mice homozygous for a deletion in the p110alpha subunit of phosphoinositide 3-kinase. J Biol Chem. 1999;274:10963–8.

    Article  CAS  Google Scholar 

  33. O’Leary B, Cutts RJ, Liu Y, Hrebien S, Huang X, Fenwick K, et al. The genetic landscape and clonal evolution of breast cancer resistance to palbociclib plus fulvestrant in the PALOMA-3 trial. Cancer Discov. 2018;8:1390–403.

    Article  Google Scholar 

  34. Turner NC, Kingston B, Kilburn LS, Kernaghan S, Wardley AM, Macpherson IR, et al. Circulating tumour DNA analysis to direct therapy in advanced breast cancer (plasmaMATCH): a multicentre, multicohort, phase 2a, platform trial. Lancet Oncol. 2020;21:1296–308.

    Article  CAS  Google Scholar 

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Acknowledgements

We thank Klara Balic for English proofreading. In addition, we want to acknowledge that part of this manuscript was published as a doctoral thesis.

Funding

This work was supported by the Christian Doppler Research Fund for Liquid Biopsies for Early Detection of Cancer led by EH supported by the Federal Ministry of Digital and Economic Affairs and by Novartis and Pfizer.

Author information

Authors and Affiliations

Authors

Contributions

CS, AT, ND and MB designed the study. RG and KK performed sequencing experiments, SJ and PR performed pathological evaluation, CS, EVK, AT, FP and MB contributed to patient care and data acquisition. ND and FP performed the statistical analysis, CS, AT, ND, MB, EH and PJJ performed interpretation of results. CS, ND, MB and FP drafted and revised the manuscript. ND, EH and MB supervised the study. All authors reviewed the manuscript and approved its final version.

Corresponding authors

Correspondence to Nadia Dandachi or Marija Balic.

Ethics declarations

Ethics approval and consent to participate

The study was approved by the ethics committee of the Medical University Graz (ethical approval number 21–227 ex 09/10), and written informed consent was obtained from all patients.

Competing interests

CS received travel expenses, consulting fees and honoraria from Amgen, Astra Zeneca, Eli Lilly, Novartis, Pfizer, Roche and Samsung, SJ received honoraria from Novartis and Roche, EVK has received travel expenses and honoraria from Astra Zeneca and Pierre- Fabre, RB had a consulting role, received honoraria, research funding and travel expenses from Astra Zeneca, Daiichi, Eisai, Eli Lilly, MSD, Novartis, Pfizer, Pierre-Fabre, Puma, Roche, AT received honoraria and research funding from Astra Zeneca, BMS, Merck and Roche. KK received honoraria and advisory from Astra Zeneca, Thermo Fischer, Novartis and BMS. PR received consulting fees, honoraria and travel expenses from Diaceutics, Novartis, and Roche, PJJ has had a consulting or advisory role, received honoraria, research funding and/or travel/accommodation expenses from Abbvie, Bayer, Boehringer, Novartis, Pfizer, Servier, Roche, BMS and Celgene, HG is a full time/part-time employee by Novartis, EH Servier, has received funding from Servier, Freenome, CA and PreAnalytiX and had an advisory role for Roche. MB has received honoraria, consulting fees research funds and/or travel expenses from Amgen, Astra Zeneca, Daichii, Eli Lilly, MSD, Novartis, Pierre- Fabre, Pfizer, Roche and Samsung.

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Suppan, C., Graf, R., Jahn, S. et al. Sensitive and robust liquid biopsy-based detection of PIK3CA mutations in hormone-receptor-positive metastatic breast cancer patients. Br J Cancer 126, 456–463 (2022). https://doi.org/10.1038/s41416-021-01601-9

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