Double PIK3CA mutations in cis enhance PI3Kα oncogene activation and sensitivity to PI3Kα inhibitors in breast cancer
Authors: N. Vasan, P. Razavi, J.L. Johnson, H. Shao, E. Reznik, M.L. Smith, R. Sebra, L.C. Cantley, M. Scaltriti, J. Baselga
Journal: Annals of Oncology (2019)

Background: Activating mutations in PIK3CA, the gene coding for the catalytic subunit (p110α) of phosphoinositide-3-kinase (PI3K), are the most frequent oncogenic alterations in oestrogen receptor-positive (ER+) breast cancer and are also prevalent in other tumour types. PI3Kα inhibitors have recently been shown to be clinically active in ER+ breast cancers harbouring PIK3CA mutations. In early clinical trials we had observed that there was also a population of patients that displayed deep and prolonged clinical benefit. In one such patient, whose tumour we had fully genomically characterized, we detected the presence of double PIK3CA mutations in all metastatic sites and at different times over tumour evolution (Juric, Castel, and Scaltriti Nature 2015). Methods: This finding, together with our anecdotal observations of recurrent double PIK3CA mutations in a number of breast cancer genomes, prompted us to undertake a comprehensive analysis of the prevalence of these mutations and to investigate their potential biological relevance and correlation with sensitivity to PI3Kα inhibitors. Results: We observed the presence of double PIK3CA mutations in 12-15% of breast cancer and other tumour types. These double PIK3CA mutations are clonal, located in cis on the same allele, and are composed of a single hotspot mutation combined with a recurrent second-site mutation. Double PIK3CA mutations in cis result in increased PI3K activity and downstream signalling together with enhanced cell proliferation and tumour growth compared to single hotspot mutations. The biochemical mechanisms underlying this increased oncogenicity include increased disruption of p110α binding to the inhibitory subunit p85α, which relieves its catalytic inhibition, and increased membrane lipid binding. Finally, these double PIK3CA mutations predict for increased sensitivity to PI3Kα inhibitors compared to single hotspot mutations in experimental models and in patients with breast cancer. Conclusions: These findings implicate double PIK3CA mutations in cis as a hypermorphic oncogene relative to single hotspot mutations, providing a rationale to develop PI3Kα inhibitors for the therapy of double PIK3CA mutant breast cancer and other cancers. Legal entity responsible for the study: Memorial Sloan Kettering Cancer Center. Funding: Grants from the NIH, including awards P30 CA008748, R01 CA190642 (M.S. and J.B.), R21 CA223789 (M.S.), and R35 CA197588 (L.C.C.). Grants from Stand Up to Cancer (Cancer Drug Combination Convergence Team), the V Foundation and the National Science Foundation (G.X., R.R., and M.S.). N.V. is supported by the Conquer Cancer Foundation of ASCO/Breast Cancer Research Foundation YIA and by a grant from the Society of MSK. N.V. and E.R. are supported by the Fund for Innovation in Cancer Informatics. N.V., E.T., G.X., and M.S. are supported by a kind gift from Mrs. Barbara Smith and her husband. Disclosure: N. Vasan: Advisory board activities: Novartis. P. Razavi: Advisory board activities: Novartis; Research support: Illumina, Grail. R. Sebra: Vice president of Sema4, a Mount Sinai Venture. L.C. Cantley: Founder and member of the board of directors and scientific advisory board: Agios Pharmaceuticals; Co-founder, member of the scientific advisory board, shareholder, laboratory funding: Petra Pharmaceuticals. M. Scaltriti: Research funds: Puma Biotechnology, Daiichi-Sankio, Immunomedics, Menarini Ricerche; Co-founder: Medendi Medical Travel. J. Baselga: Employee: AstraZeneca; Board of directors: Foghorn; Past board member: Varian Medical Systems, Bristol‐Myers Squibb, Grail, Aura Biosciences, Infinity Pharmaceuticals; Consulting and/or advisory work: Grail, PMV Pharma, ApoGen, Juno, Lilly, Seragon, Novartis, Northern Biologics; Stock or other ownership interests: PMV Pharma, Grail, Juno, Varian, Foghorn, Aura, Infinity Pharmaceuticals, ApoGen, Tango, Venthera, for which is a co‐founder; Honoraria or travel expenses: Roche, Novartis, Eli Lilly. All other authors have declared no conflicts of interest.