Polymorphisms associated with everolimus pharmacokinetics, toxicity and survival in metastatic breast cancer

<div><p>Purpose</p><p>Metastatic breast cancer (MBC) progressing after endocrine therapy frequently activates PI3K/AKT/mTOR pathway. The BOLERO-2 trial showed that everolimus-exemestane achieves increased progression free survival (PFS) compared with exemestane. However, there is great inter-patient variability in toxicity and response to exemestane-everolimus treatment. The objective of this study was to perform an exploratory study analyzing the implication of single nucleotide polymorphisms (SNPs) on outcomes from this treatment through a pharmacogenetic analysis.</p><p>Patients and methods</p><p>Blood was collected from 90 postmenopausal women with hormone receptor-positive, HER2-negative MBC treated with exemestane-everolimus following progression after prior treatment with a non-steroidal aromatase inhibitor. Everolimus pharmacokinetics was measured in 37 patients. Twelve SNPs in genes involved in everolimus pharmacokinetics and pharmacodynamics were genotyped and associations assessed with drug plasma levels, clinically relevant toxicities (non-infectious pneumonitis, mucositis, hyperglycemia and hematological toxicities), dose reductions or treatment suspensions due to toxicity, progression free survival (PFS) and overall survival.</p><p>Results</p><p>We found that <i>CYP3A4</i> rs35599367 variant (<i>CYP3A4*22</i> allele) carriers had higher everolimus blood concentration compared to wild type patients (P = 0.019). <i>ABCB1</i> rs1045642 was associated with risk of mucositis (P = 0.031), while <i>PIK3R1</i> rs10515074 and <i>RAPTOR</i> rs9906827 were associated with hyperglycemia and non-infectious pneumonitis (P = 0.016 and 0.024, respectively). Furthermore, <i>RAPTOR</i> rs9906827 was associated with PFS (P = 0.006).</p><p>Conclusions</p><p><i>CYP3A4*22</i> allele influenced plasma concentration of everolimus and several SNPs in PI3K/AKT/mTOR pathway genes were associated with treatment toxicities and prognosis. These results require replication, but suggest that germline variation could influence everolimus outcomes in MBC.</p></div

Box plot representing everolimus blood concentration by <i>CYP3A4</i> rs35599367 (<i>CYP3A4*22</i>) genotype.

<p>“C/C” corresponds to <i>CYP3A4*22</i> wild type patients (n = 33), and “C/G” to <i>CYP3A4*22</i> heterozygous carriers (n = 4). Comparison between groups was performed using the Mann-Whitney-U test.</p

Analysis of Paired Primary-Metastatic Hormone-Receptor Positive Breast Tumors (HRPBC) Uncovers Potential Novel Drivers of Hormonal Resistance

<div><p>We sought to identify genetic variants associated with disease relapse and failure to hormonal treatment in hormone-receptor positive breast cancer (HRPBC). We analyzed a series of HRPBC with distant relapse, by sequencing pairs (n = 11) of tumors (primary and metastases) at >800X. Comparative genomic hybridization was performed as well. Top hits, based on the frequency of alteration and severity of the changes, were tested in the TCGA series. Genes determining the most parsimonious prognostic signature were studied for their functional role <i>in vitro</i>, by performing cell growth assays in hormonal-deprivation conditions, a setting that mimics treatment with aromatase inhibitors. Severe alterations were recurrently found in 18 genes in the pairs. However, only <i>MYC</i>, <i>DNAH5</i>, <i>CSFR1</i>, <i>EPHA7</i>, <i>ARID1B</i>, and <i>KMT2C</i> preserved an independent prognosis impact and/or showed a significantly different incidence of alterations between relapsed and non-relapsed cases in the TCGA series. The signature composed of <i>MYC</i>, <i>KMT2C</i>, and <i>EPHA7</i> best discriminated the clinical course, (overall survival 90,7 vs. 144,5 months; p = 0.0001). Having an alteration in any of the genes of the signature implied a hazard ratio of death of 3.25 (p<0.0001), and early relapse during the adjuvant hormonal treatment. The presence of the D348N mutation in <i>KMT2C</i> and/or the T666I mutation in the kinase domain of <i>EPHA7</i> conferred hormonal resistance <i>in vitro</i>. Novel inactivating mutations in <i>KMT2C</i> and <i>EPHA7</i>, which confer hormonal resistance, are linked to adverse clinical course in HRPBC.</p></div

Baseline demographic and clinical characteristics.

<p>Baseline demographic and clinical characteristics.</p

External testing—Cases valid for analysis from the TCGA series.

<p>Male or nonreported patients were excluded; patients negative for both hormone receptors and/or HER-2–positive, equivocal, unavailable, and/or falling in the HER-2–enriched cluster were excluded as well. We excluded from the relapse analysis patients without a follow-up status data; in addition, 17 additional patients were excluded from the survival analysis due to death by a non–tumor-related cause (non-relapsed).</p

SNPs associated with toxicity.

<p>SNPs associated with toxicity.</p

SNPs included in the study and their genotype frequencies.

<p>SNPs included in the study and their genotype frequencies.</p

Kaplan-Meier curve for progression free survival by RAPTOR rs9906827 genotype.

<p>P-value corresponds to Cox regression analysis under a dominant genetic model including the number of previous chemotherapy lines as covariate. HR, hazard ratio; CI, confidence interval.</p

Variant call heat map.

<p>Each of the 1071 unique variants identified are depicted in the heatmap as "present" (numbered cell) or "absent" (empty) in each primary or metastatic tumor. With the exception of pair M, each tumor was more similar to its pair than to any other case, regardless of being primary (pink-colored cases) or metastatic (yellow-colored cases), or metastatizing into the same organs or not (green: bone; red: lung; blue: peritoneum).</p

Allelic Expansion of Variants Causing Severe Functional Protein Alterations from the Primary to the Metastatic Lesions.

<p>Allelic Expansion of Variants Causing Severe Functional Protein Alterations from the Primary to the Metastatic Lesions.</p