Background:
PI3K/AKT signaling pathway is activated in breast cancer and associated with cell survival. We explored the prevalence of PI3K pathway alterations and co-expression with other markers in breast cancer subtypes.
Methods:
Samples of non-matched primary and metastatic breast cancer submitted to a CLIA-certified genomics laboratory were molecularly profiled to identify pathogenic or presumed pathogenic mutations in the
PIK3CA-AKT1-PTEN
pathway using next generation sequencing. Cases with loss of PTEN by IHC were also included. The frequency of co-alterations was examined, including DNA damage response pathways and markers of response to immuno-oncology agents.
Results:
Of 4,895 tumors profiled, 3,558 (72.7%) had at least one alteration in the
PIK3CA-AKT1-PTEN
pathway: 1,472 (30.1%) harbored a
PIK3CA
mutation, 174 (3.6%) an
AKT1
mutation, 2,682 (54.8%) had PTEN alterations (
PTEN
mutation in 7.0% and/or PTEN loss by IHC in 51.4% of cases), 81 (1.7%) harbored a
PIK3R1
mutation, and 4 (0.08%) a
PIK3R2
mutation. Most of the cohort consisted of metastatic sites (
n
= 2974, 60.8%), with
PIK3CA
mutation frequency increased in metastatic (32.1%) compared to primary sites (26.9%),
p
< 0.001. Other
PIK3CA
mutations were identified in 388 (7.9%) specimens, classified as “off-label,” as they were not included in the FDA-approved companion test for
PIK3CA
mutations. Notable co-alterations included increased PD-L1 expression and high tumor mutational burden in
PIK3CA-AKT1-PTEN
mutated cohorts. Novel concurrent mutations were identified including
CDH1
mutations.
Conclusions:
Findings from this cohort support further exploration of the clinical benefit of PI3K inhibitors for “off-label”
PIK3CA
mutations and combination strategies with potential clinical benefit for patients with breast cancer.