Difficulties in accessing intracranial tissue samples have hampered development of systemic treatments that could have an effect in the treatment of patients with BMs. To our knowledge, this is one of the largest cohorts of genetically characterized BC BM, consisting of 52 analyzed cases, most notably including 37 cases with matched PT, all from one region in Sweden. Despite this, the relatively small number of patients in each BC subgroup is a limitation of the present study, reflecting the difficulty to obtain matched PT/BM tissue. Sequencing results by NGS were successfully obtained in 90% of the BMs. At least one mutation, among 50 cancer driver genes, was present in 62% of the analyzed samples similar to previously published data [16–21]. Concordant with these studies TP53 and PIK3CA are the most commonly mutated driver genes, both in the BMs and PTs. Of these two mutations, PIK3CA are considered targetable, whilst TP53 mutations can be indirectly attacked through restoration of the transcriptional activity resulting in a functional wild-type TP53 protein 
The drug alpelisib, is a PI3Kα-specific inhibitor available for patients with recurrent PIK3CA mutated Luminal/HER2 negative BC . Previous published data show that approximately 40% of ER + PT harbor a PIK3CA mutation . Two studies that compared PIK3CA mutations in PTs and BC metastases reported mutations in 33% of PTs and 30% of metastases and 45% of PTs and 53% in metastases respectively [18, 25]. There were few or no patients with BMs in the above mentioned studies. We report lower figures with PIK3CA mutations in breast cancer among patients with BMs with a mutation frequency of 20% in PTs and 23% in the BMs. Interestingly, a recently published systematic review investigated 164 BMs with its matched PT in 126 patients extracted from 13 studies, found PIK3CA mutations in 22% of the patients with BMs . These similarities raise the hypothesis that PIK3CA mutations is lower in BMs compared to other metastatic sites, however, additional studies are required to adequately answer this question. As expected, we found the highest proportion of PIK3CA mutations in Luminal BC. Of note, in our material two out of eight pathogenic PIK3CA mutations and five TP53 mutations were found in the BMs only and not in the PT underlining the need for re-evaluation of metastatic tissue or possibly by analysis of cell free DNA (cfDNA).
We found PIK3CA mutations as the second most common mutation after TP53 in matched pairs of TNBC with 18% PIK3CA mutations all concordant in PTs and BMs. This is in line with previous published data in which PIK3CA mutations was the second most common mutation after TP53, especially in basal-like and luminal androgen receptor subtypes of TNBC [27–29]. The combined treatment of alpelisib and nab-paclitaxel is currently under investigation in pre-treated TNBC with either loss of PTEN expression or a PIK3CA mutation (NCT04251533).
The prognostic role of PIK3CA mutations in HER2 + BC has been extensively investigated with less effect of HER2 blocking therapy, both in the neo-adjuvant setting, and for recurrent BC in terms of lower pCR rates and shorter survival respectively [30, 31]. We found PIK3CA mutations in only 10% of the HER2 + cases. This is lower than previously reported of 20–40%. . The limited number of HER2 + patients in our cohort may be the cause of this discrepancy. The effect of alpelisib in HER2 + breast cancer is under investigation in one ongoing and one completed clinical trial (NCT02038010; NCT04208178).
Almost 50% of the PTs in the present study population with a high proportion of TNBC harbored a TP53 mutation, in contrast to the 20–35% mutation prevalence reported in unselected primary BC . The Cancer Genome Atlas reveals an enrichment of TP53 mutations in basal-like and HER2 enriched BC . Interestingly, previous data reveal that a high proportion of patients with a TP53 mutation in the primary BC developed BM [33, 34]. We lack data on the molecular subtypes in our material, but find an increased number of TP53 mutations in TNBC and HER2/ER- BC. Enrichment of TP53 mutations in BMs was not seen in the HER2 amplified subgroup, a finding that must be interpreted with caution due to the very small sample size of the HER2 group.
Roughly 25% of the matched pairs changed IHC based BC subtype in the BMs. The most common change was from Luminal A in PT to other subtypes, in most cases Luminal B in BMs. This is in accordance with previous results in which 219 patients showed a 36% overall discordance with the most common change in form of loss of PgR . In a review pooling a total of 3384 matched pairs of BC and metastases from all organs, BM showed a discordant median rate of 22% compared to 45% in liver metastases and 16% in lymph node metastasis . TNBC was the most stable group with less than 10% showing a gain in ER (one case) and HER2 (one case). Other detected mutations in our series, CDH1, EGFR, HRAS, RB1, CDKN2A and PTEN were rare, in general found in single or both samples from one patient.
A limitation of our current study is that genetic profiling was performed using a relatively small NGS panel of 50 genes. Even though the panel gives broad coverage of important cancer driver genes, more comprehensive sequencing might have provided further details in the landscape of mutation discordancy between PTs and BMs. Still, we believe that the relatively large number of matched PT and BM may increase knowledge about the biology of BMs, how the metastatic process affects actionable genes, ultimately helping patients suffering from BM.