PIK3CA Mutations In Breast Cancer Research Articles

Abstract PO4-01-02: High throughput analysis in HER2 positive locally advanced breast cancer: pCR and mutational status

Abstract Background Pathologic complete response (pCR) after neoadjuvant treatment (NAD) is a strong prognostic biomarker associated with improved survival in breast cancer patients, especially with HER2-positive and Triple negative subtypes. PIK3CA is mutated in up to 20% of HER2 positive breast cancers, contributes to anti-HER-2 resistance and may be predictive of the lack of response to anti HER2 NAD. PIK3CA mutations in breast cancer occur primarily at hotspots E545K at exon 9 and H1047R at exon 20. Next generation sequencing has improved our knowledge regarding the biology of the mechanisms behind treatment resistance. The aim of this study is to evaluate the genomic landscape of tissue samples obtained from locally advanced breast cancer patients treated in an neoadjuvant setting, in order to correlate the genomic analysis to response and clinical outcome. Methods DNA extracted from the archival 84 formalin-fixed paraffin-embedded (FFPE) samples from core needle biopsies was subjected to deep sequencing using the TruSight Oncology (TSO) 500 panel (Illumina, San Diego, USA; 523 genes, size: 1.94 Mb), following the manufacturer’s protocol, which assesses microsatellite instability (MSI) status, tumor mutation burden (TMB), recurrent somatic copy number variations (sCNV), somatic single nucleotide variants (SNVs). Libraries were sequenced on a NovaSeq 6000 instrument (Illumina) to reach a minimum of 500 × read depth. All samples were evaluated for RNA single cell transcriptional profile. 73 of 84 patients were treated with traditional neoadjuvant chemotherapy plus trastuzumab meanwhile 13 of 84 received neoadjuvant chemotherapy plus trastuzumab and pertuzumab. Statistical analysis was performed to detect the genes whose mutation involved in the progression and/or non-response of the disease using the Statistical Package for Social Science (SPSS), release 23.0. Continuous variables were expressed as mean ± SD or median [range], categorical variables were displayed as frequencies and the appropriate parametric (Student‘s t-test) non-parametric test (X2-test or Mann-Whitney test) was used to assess significance of the differences between subgroups (patients with or without pCR). Results In total we analyzed samples of 84 patients. The median age was 48 years. 64 of 84 (76.2%) were triple positive, 66 (78.6%) with G3 and 29 (34.5%) with stage III. The most common frequently mutated genes were PIK3CA (16/84, 19%) and BRCA1 (7/84, 8.3%). The pathogenic variant of BRCA1 (sBRCA1) had a significant association with resistance to treatment: we found a pCR in only 14.3% of sBRCA1 versus 62.3% in sBRCA1 wild type (wt) patients (p=0.014). We also identified 11 somatic mutations in hereditary genes (ATM, BRCA1, BRCA2, PALB2, CHEK2, RAD51C, RAD51D). From a germline standpoint we detected 7 pathogenic variants (two affecting BRCA1, two affecting CHEK2, one affecting PALB2, 7/84, 8.3%), which will be clinically confirmed. Among patients with a mutated PI3KCA, 43.8% obtained a pCR versus 61.8% of patients with PI3KCA wt (p=0.19). This data probably presents an imbalance due to the sample size A PTEN mutation was identified in 2% of pts (2/84) which obtained no benefit in terms of pCR after NAD versus 59.8% in wt patients (p=0.09). Conclusions In this preliminary report, genetic drivers such as BRCA1 status may have a clinical implication for prognosis and treatment response after NAD in locally advanced HER2 positive breast cancer. More samples are needed to evaluate the significance of PI3K and PTEN mutations in this patient setting. We are waiting for the results of the RNA single cell transcriptional profile of these samples. Event free survival data is not yet mature at this moment. We would like to acknowledge the contribution of Multi-specialistic Biobank Research Core Facility G-STeP, Fondazione Policlinico Universitario “A. Gemelli” IRCCS (Biobank-FPG) who provided the bio-resources. Citation Format: Ida Paris, Angelo Minucci, Daniele Generali, simona Nanni, Tatiana D'angelo, Francesco Pavese, Alessandra Fabi, Maria De Bonis, Katia Cannita, Alessia Piermattei, Giordana Tiberi, Paola Fuso, Luisa Carbognin, Silvia Rotondaro, Camilla Nero, Flavia Giacomini, Tina Pasciuto, Maria Marrazzo, Luciano Giaco', Antonino Mulè, Riccardo Masetti, Gianluca Franceschini, Giorgia Garganese, Diana Giannarelli, Giovanni Scambia. High throughput analysis in HER2 positive locally advanced breast cancer: pCR and mutational status [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO4-01-02.

Abstract A118: Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian breast cancer patients

Abstract Purpose: The phosphatidylinositol-4, 5-bisphosphate 3-kinase (PIK3CA), catalytic subunit alpha (c) is frequently mutated in breast cancer (BC). Although the biological impact of PIK3CA mutations in BC has been studied in various parts of the world, limited data is available from sub-Saharan Africa. In this study, the frequency and the prognostic role of PIK3CA mutations were investigated among BC patients from Ethiopia. Methods: Formalin-fixed paraffin-embedded blocks and fresh frozen BC tissue samples were collected from patients newly diagnosed with BC. Histopathological evaluation was carried out using immunohistochemistry (IHC). PIK3CA mutation profiling was carried out using TaqMan® Mutation detection assay. The association between PIK3CA mutation status and clinical and histopathological features was evaluated. A survival regression (Cox’s model) was employed to assess the effect of PIK3CA mutation and other variables on survival. Results: The prevalence of the PIK3CA mutations was 20.4%. Mutation of the PIK3CA gene was mainly observed among younger (24%), early pT stage (19.4%), and G1/G2 tumors (22.3%). The proportion of mutation was 24.4%, 27.3% and 20% in ER+, PR+ and HER2- tumors, respectively. A marked difference was observed in the PIK3CA mutation frequency across the four major tumor subgroups. However, most of the mutated tumors were found among HR+/HER2− (24.1%) followed by HR+/HER2+ tumors (27.8%). In his study, only TNBC was negatively associated with the proportion of mutation in the PIK3CA gene (p-value= 0.02) in comparison to HR+/HER2- tumors. In multivariate Cox’s regression analysis, the advanced pT stage and HR−/HER2- IHC group independently predicted worse overall survival. However, PIK3CA mutation status was not associated with survival. Conclusions: The PIK3CA mutation was relatively high in HR+ tumors. Mutation rates of PIK3CA in Ethiopian BC tumors are similar to those reported for other populations. Citation Format: Zelalem Desalegn Woldesonbet, Meron Yohannes, Adamu Addissie, Tamrat Abebe, Eva Johanna Kantelhardt, Martina Vetter. Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian breast cancer patients [abstract]. In: Proceedings of the AACR-NCI-EORTC Virtual International Conference on Molecular Targets and Cancer Therapeutics; 2023 Oct 11-15; Boston, MA. Philadelphia (PA): AACR; Mol Cancer Ther 2023;22(12 Suppl):Abstract nr A118.

Abstract C074: Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian breast cancer patients

Abstract Purpose: The phosphatidylinositol-4, 5-bisphosphate 3-kinase (PIK3CA), catalytic subunit alpha (c) is frequently mutated in breast cancer (BC). Although the biological impact of PIK3CA mutations in BC has been studied in various parts of the world, limited data is available from sub-Saharan Africa. In this study, the frequency and the prognostic role of PIK3CA mutations were investigated among BC patients from Ethiopia. Methods: Formalin-fixed paraffin-embedded blocks and fresh frozen BC tissue samples were collected from patients newly diagnosed with BC. Histopathological evaluation was carried out using immunohistochemistry (IHC). PIK3CA mutation profiling was carried out using TaqMan® Mutation detection assay. The association between PIK3CA mutation status and clinical and histopathological features was evaluated. A survival regression (Cox’s model) was employed to assess the effect of PIK3CA mutation and other variables on survival. Results: The prevalence of the PIK3CA mutations was 20.4%. Mutation of the PIK3CA gene was mainly observed among younger (24%), early pT stage (19.4%), and G1/G2 tumors (22.3%). The proportion of mutation was 24.4%, 27.3% and 20% in ER+, PR+ and HER2- tumors, respectively. A marked difference was observed in the PIK3CA mutation frequency across the four major tumor subgroups. However, most of the mutated tumors were found among HR+/HER2− (24.1%) followed by HR+/HER2+ tumors (27.8%). In his study, only TNBC was negatively associated with the proportion of mutation in the PIK3CA gene (p-value= 0.02) in comparison to HR+/HER2- tumors. In multivariate Cox’s regression analysis, the advanced pT stage and HR−/HER2- IHC group independently predicted worse overall survival. However, PIK3CA mutation status was not associated with survival. Conclusions: The PIK3CA mutation was relatively high in HR+ tumors. Such relatively higher molecular aberrations among HR+ tumors can provide a benefit in choosing the best therapeutic option for breast cancer. Citation Format: Zelalem Desalegn Woldesonbet, Meron Yohannes, Adamu Addissie, Tamrat Abebe, Eva Johanna Kantelhardt, Martina Vetter. Somatic mutations in the PIK3CA gene and its prognostic implications among Ethiopian breast cancer patients [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr C074.

PIK3CA mutations in breast cancer: A Tunisian series.

The aim of this study was to analyze PIK3CA mutations in exons 9 and 20 in breast cancers (BCs) and their association with clinicopathological characteristics. Mutational analysis of PIK3CA exon 9 and 20 was performed by Sanger sequencing in 54 primary BCs of Tunisian women. The associations of PIK3CA mutations with clinicopathological characteristics were analyzed. Fifteen exon 9 and exon 20 PIK3CA variants were identified in 33/54 cases (61%). PIK3CA mutations including pathogenic (class 5/Tier I) or likely pathogenic (class 4/Tier II) occurred in 24/54 cases (44%): 17/24 cases (71%) in exon 9, 5/24 cases (21%) in exon 20 and 2/24 cases (8%) in both exons. Of these 24 cases, 18 (75%) carried at least one of the three hot spot mutations: E545K (in 8 cases), H1047R (in 4 cases), E542K (in 3 cases), E545K/E542K (in one case), E545K/H1047R (in one case) and P539R/H1047R (in one case). Pathogenic PIK3CA mutations were associated with negative lymph node status (p = 0.027). Age distribution, histological SBR tumor grading, estrogen and progesterone receptors, human epidermal growth factor receptor 2, and molecular classification were not correlated with PIK3CA mutations (p > 0.05). The frequency of somatic PIK3CA mutations in BCs of Tunisian women is slightly higher than that of BCs of Caucasian women and more observed in exon 9 than in exon 20. PIK3CA mutated status is associated with negative lymph node status. These data need to be confirmed in larger series.

Thr presence of PIK3CA gene mutations and possible implications in breast cancer

Breast cancer is one of the most common types of cancer worldwide, which predominantly affects women. Histology-based classification is one of the most used methods to identify it nowadays. Histologic subtypes include ductal, lobular,mucinous and medullary. The development of breast cancer may be driven by environmental and genetic factos. Mutations in the PIK3CA gene are one of the most common genetic risk factors. There are two main exons, 9 and 20, where the mutation predominantly takes place. To describe the presence of p.E545K, p.E542K and p.H1047R mutations in different histologic types of breast cancer, with the aim that future investigations might find some uses in the clinical setting. A recompilation of data was conducted by the research of specific keywords (PIK3CA mutation, PIKaCA breast cancer prognosis, presence of PIK3CA mutation in breast cancer and different histologic types of breast cancer) in clinical key, google scholar and PubMed databases. PIK3KCA expression is increased in breast cancer compared to notmal tissue. Mutations were more prevalent in lobular breast cancer than other subtypes. Mucinous show the less rate of mutations. Exon 9 mutation were related with early death and exon 20 with goog prognosis. Also, mutations in found between the presence of the mutations and cancer parameter like nodes metastasis but is was demonstrated the importance od the piK3CA mutations in the development of breast cancer, based on histological classification

PIK3CA mutations in breast cancer with low HER2 / neu expression

Introduction. Disturbances in the PI3K-dependent (PI3K – phosphoinositide 3‑kinase) cascade are characteristic of all types of breast cancer. In particular, 30–40 % of patients with advanced / metastatic hormone-positive HER2‑negative (HER2 – human epidermal growth factor receptor 2) breast cancer carry PIK3CA mutations in tumor cells. The detection of these mutations in patients with hormone-positive HER2‑negative breast cancer is of great clinical importance, since they are a predictor of tumor sensitivity to the PI3K inhibitor alpelisib. According to the HER2 / neu protein expression status, all patients with hormone-positive HER2‑negative breast cancer can be divided into two groups – with low expression of HER2 / neu (scores 0, 1+ or 2+ per immunohistochemical analysis and negative result of in situ hybridization) and with a complete lack of expression of this protein.Aim. To establish whether there are differences in the nature and prevalence of PIK3CA mutations in patients in these two groups.Materials and methods. The study was carried out on 32 breast cancer samples with a luminal HER2‑negative immunophenotype, which were divided into two groups – with low HER2 / neu expression (n = 15) and with a complete absence of HER2 / neu expression (n = 17). PIK3CA mutations were determined using the commercially available cobas PIK3CA MutationTest kit (Roche, Switzerland) by real-time polymerase chain reaction on paraffin block material (tissue biopsy).Results. Mutations of the PIK3CA gene were detected in 37.5 % of cases, of which p.E542K mutation was detected in 2 cases; p.E545X – in 3, p.H1047X – in 6 and p.N345K – in 1. Analysis of the mutational status of both groups revealed statistically significant differences in the quantitative distribution of PIK3CA mutations. The frequency of PIK3CA mutations was significantly higher in tumors with low expression of HER2 / neu (p = 0.0268). Thus, characteristic genetic changes have been identified for a group of patients with HER2‑low breast cancer. These changes are potential targets for therapy, which is important for clinical practice, as it opens up new therapeutic possibilities for breast cancer patients with low HER2 / neu expression.

PIK3CA-mutations in breast cancer

PurposePhosphatidylinositide-3-kinase (PI3K) regulates proliferation and apoptosis; somatic PIK3CA-mutations may activate these processes. Aim of this study was to determine the prevalence of PIK3CA-mutations in a cohort of early stage breast cancer patients and the association to the course of disease.Patients and methodsFrom an unselected cohort of 1270 breast cancer patients (PiA, Prognostic Assessment in routine application, NCT 01592825) 1123 tumours were tested for the three PIK3CA hotspot-mutations H1047R, E545K, and E542K by qPCR. Primary objectives were the prevalence of somatic PIK3CA-mutations and their association to tumour characteristics. Secondary objective was the association of PIK3CA-mutations to recurrence-free interval (RFI) and overall survival.ResultsPIK3CA-mutation rate was 26.7% (300 of 1123). PIK3CA-mutations were significantly more frequent in steroid hormone-receptor (SHR)-positive HER2-negative (31.4%), and G1 and G2 tumours (32.8%). Overall, we did not observe a significant association of PIK3CA-mutations to RFI. In SHR-positive BCs with PIK3CA-mutations, a strong trend for impaired RFI was observed (adjusted HR 1.64, 95% CI 0.958–2.807), whilst in SHR-negative BCs PIK3CA-mutations were insignificantly associated with improved RFI (adjusted HR 0.49; 95% CI 0.152–1.597). Of note, we observed a significantly detrimental prognostic impact of PIK3CA-mutations on RFI in SHR-positive, HER2-negative BCs if only aromatase inhibitors were administered as adjuvant therapy (adjusted HR 4.44, 95% CI 1.385–13.920), whilst no impact was observed in tamoxifen treated patients.ConclusionThis cohort study speficies the overall mutation rate of PIK3CA in early breast cancer. The impact of PIK3CA-mutations on RFI and OS was heterogeneous. Our results suggest that estrogen deprivation failes to be active in case of PIK3CA-mutation.

Clinicopathological characteristics and prognostic analysis of PIK3CA mutation in breast cancer patients in Northwest China

PurposeMultiple studies on PIK3CA mutations in breast cancer (BC) had been performed, which showed the controversial results among different countries and races even those from the same country. The present study aimed to explore the PIK3CA gene mutation status in BC patients in Northwest China and reveal the relationship between PIK3CA mutations and clinicopathological features along with prognosis. Materials and methods1002 BC patients from Northwest China were recruited in this study, genomic DNA was extracted from formalin-fixed paraffin-embedded (FFPE) tumor tissues, and hotspot mutations in the exon 9 and 20 of PIK3CA gene were detected by ARMS-PCR. ResultsPIK3CA mutations were found in 31.2% (313/1002) of BC patients, among them 66.1% were mutations in exon 20% and 32.6% were mutations in exon 9. H1047R was the most common mutation type, accounting for 56.5% of the total mutated samples. Significant correlations were observed between PIK3CA mutation status and age (P = 0.035), histopathologic types (P = 0.004), pathological grade (P = 0.013), ER positivity (P < 0.001), PR positivity (P < 0.001), molecular subtypes (P = 0.004) and family history (P = 0.007). Cox multivariate analysis showed that patients with mutations in exon 9 or 20 had shorter DFS and OS than wild-type patients. Those with exon 9 mutations subgroup had the worst prognosis. Interestingly, patients with H1047L mutation had the best prognosis than others. ConclusionPIK3CA mutations could be used as an indicator of clinical outcome or targeted therapy for multiple breast cancer subgroups in Northwest China.

Using an Improved Residual Network to Identify PIK3CA Mutation Status in Breast Cancer on Ultrasound Image.

BackgroundThe detection of phosphatidylinositol-3 kinase catalytic alpha (PIK3CA) gene mutations in breast cancer is a key step to design personalizing an optimal treatment strategy. Traditional genetic testing methods are invasive and time-consuming. It is urgent to find a non-invasive method to estimate the PIK3CA mutation status. Ultrasound (US), one of the most common methods for breast cancer screening, has the advantages of being non-invasive, fast imaging, and inexpensive. In this study, we propose to develop a deep convolutional neural network (DCNN) to identify PIK3CA mutations in breast cancer based on US images.Materials and MethodsWe retrospectively collected 312 patients with pathologically confirmed breast cancer who underwent genetic testing. All US images (n=800) of breast cancer patients were collected and divided into the training set (n=600) and test set (n=200). A DCNN-Improved Residual Network (ImResNet) was designed to identify the PIK3CA mutations. We also compared the ImResNet model with the original ResNet50 model, classical machine learning models, and other deep learning models.ResultsThe proposed ImResNet model has the ability to identify PIK3CA mutations in breast cancer based on US images. Notably, our ImResNet model outperforms the original ResNet50, DenseNet201, Xception, MobileNetv2, and two machine learning models (SVM and KNN), with an average area under the curve (AUC) of 0.775. Moreover, the overall accuracy, average precision, recall rate, and F1-score of the ImResNet model achieved 74.50%, 74.17%, 73.35%, and 73.76%, respectively. All of these measures were significantly higher than other models.ConclusionThe ImResNet model gives an encouraging performance in predicting PIK3CA mutations based on breast US images, providing a new method for noninvasive gene prediction. In addition, this model could provide the basis for clinical adjustments and precision treatment.

Ultrasonic Features and Molecular Subtype Predict Somatic Mutations in TP53 and PIK3CA Genes in Breast Cancer

To predict mutations in TP53 and PIK3CA genes in breast cancer using ultrasound (US) signatures and clinicopathology. In this study, we developed and trained a model in 386 breast cancer patients to predict TP53 and PIK3CA mutations. The clinicopathological and US characteristics (including two-dimensional and color Doppler US) were investigated. Statistically significant variables were used to build predictive models, then a combined model was developed using the multivariate logistic regression analysis. Univariate and multivariate analyses revealed that calcifications on US was an independent predictor of TP53 mutation (p < 0.05), whereas diameter on US and US type were independent predictors of PIK3CA mutation in breast cancer (all p < 0.05). Meanwhile, Luminal B/Human epidermal growth factor receptor two-positive (HER2+), HER2+/estrogen receptor-negative (ER-), and triple-negative breast cancer (TNBC) subtypes were strong predictors of TP53 mutation (odds ratio [OR]=3.13, 3.18, 3.44, respectively, all p < 0.05). HER2+/ER- and TNBC subtypes were negative predictors of PIK3CA mutation (OR=0.223, 0.241, respectively, all p < 0.05). The areas under curves (AUCs) for PIK3CA mutation in the training set increased from 0.553-0.610 to 0.741 in the multivariate model that combined US features and molecular subtype, with a sensitivity and specificity of 80.6% and 58.7%, respectively. The application of the multivariate model in the validation set achieved acceptable discrimination (AUC=0.715). For TP53 mutation, the AUC was 0.653. US is a non-invasive modality to recognize the presence of TP53 and PIK3CA mutation. The models combined with US features and molecular subtype have implications for the practical application of predicting gene mutation for individual decision-making regarding treatment planning.

Abstract 2231: Utility of plasma tumor fraction (TF) to inform sensitivity of FoundationOne Liquid CDx (F1LCDx)

Abstract Background: F1LCDx is an FDA-approved liquid biopsy test offering pan-tumor profiling of &amp;gt;300 genes with CDx indications for multiple cancer types. One key limitation is that sensitivity for detection of genomic alterations in ctDNA is impaired when the plasma tumor fraction (TF) is low. TF is known to vary in advanced cancer and has been correlated with overall survival (Stover, JCO, 2018). While some ctDNA assays use variant allele fraction (VAF) to quantify tumor content, such methods may be prone to interference from germline variants, copy number alterations and a limited number of mutations. We studied SNP aneuploidy to develop a variant-independent measure of TF which we hypothesized could inform assay sensitivity. Methods: For each liquid sample, coverages from heterozygous SNPs, across the genome, were used to measure allelic deviations from normal via a root-mean-square (RMS) metric. The relationship between RMS and TF was established based on a training data set of clinical samples with known TF that were diluted in silico. In this way, the RMS metric for any sample could be linked to a distribution of TF values. TF is reported when the lower bounds of the predicted TF distribution is &amp;gt;0%. Positive percentage agreement (PPA) of liquid NGS versus tissue genotype was studied in those with a TF reported vs TF not quantified. Results: For a pilot concordance analysis, we studied a real-world cohort of NSCLC patients where NGS was performed on both tissue and on a 70-gene ctDNA assay (FoundationOne®Liquid (F1L), median 314 days between results). Among 251 cases with tissue NGS showing an EGFR L858R or 19del mutation and a F1L result available, the EGFR mutation was detected 90% of the time (57/63) when TF was reported (range 13-74%) but was detected 51% of the time (96/188) when TF was not quantified. Next, we analyzed a cohort of 3 clinical trials in advanced cancers where tissue genotype was known and with F1LCDx results available, including studies of activating PIK3CA mutations in breast cancer, MET exon 14 mutations in NSCLC and BRCA1/2 mutations in prostate cancer. For the subset of patients with TF reported (range 9.6-72%), PPA was 94.7% (breast, n=38), 100% (NSCLC, n=19), and 90.1% (prostate, n=46), versus 66.7% (breast, n=33), 66.7% (NSCLC, n=45) and 89.6% (prostate, n=48) for TF not quantified. Conclusions: We describe a novel method to measure TF in plasma ctDNA based on aneuploidy, which may overcome some limitations of TF measurement based on VAF. When TF confirms tumor content, sensitivity of F1LCDx for short variant detection is excellent (90%-100%), suggesting reduced value from a reflex to tissue genotyping in the absence of a targetable genomic alteration. When TF is not quantified, sensitivity can be lower and the value of reflex to tissue genotyping may be heightened. Citation Format: Meijuan Li, Bernard Fendler, Lei Yang, Russell Madison, Brennan Decker, Ole Gjoerup, Kimberly McGregor, Aparna Aiyer, Jason Hughes, Priti Hegde, Christine Vietz, Geoffrey R. Oxnard. Utility of plasma tumor fraction (TF) to inform sensitivity of FoundationOne Liquid CDx (F1LCDx) [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2231.

Investigation of alterations in PIK3CA and OCT-4 gene expression in breast cancer

Breast cancer (BCa) is one of the most prevalent cancer amongst women and PIK3CA mutations have a crucial role in carcinogenesis. On the other hand, Octamer-Binding Transcription Factor 4 (OCT-4) is common biomarkers of cancer stem cells, which provide to the pathological processes of numerous carcinomas. In this study, we evaluated the association of OCT-4 gene expression levels with the PIK3CA mutation in BCa patients.The mRNA expression level of the OCT-4 gene was detected by qPCR in 44 BCa patients and 30 BCa patients control have positive PIK3CA mutations. Exon 9 and exon 20 of PIK3CA mutations were identified by sequencing. OCT-4 gene expression and PIK3CA mutations were also clinically evaluated in BCa patients.The frequency of PIK3CA mutation in 44 new cases were 32%. PIK3CA mutations were significantly associated with HER2-positive (p = 0.0271) status, Ki-67 status (p = 0.0434) and patient age (p = 0.0149). OCT-4 mRNA expression was significantly higher in the BCa tissue in comparison to normal breast tissue (p = 0.0305). A significant correlation was found between expression of OCT-4 and node status (p = 0.0190). OCT-4 mRNA expression was higher in the PIK3CA mutation tissue than the wild type tissue. However, no association was found between the expression of OCT-4 and the PIK3CA mutation or wild type samples (p = 0.7908).Our results provided that OCT-4 gene and PIK3CA mutations may have a role in development of BCa. OCT-4 mRNA expression level and PIK3CA mutations have a potential important for BCa diagnosis or treatment.

Frequency and spectrum of PIK3CA somatic mutations in breast cancer

PurposeThe therascreen PIK3CA mutation assay and the alpha-specific PI3K inhibitor alpelisib are FDA-approved for identifying and treating patients with advanced PIK3CA-mutated (PIK3CAmut) breast cancer (BC). However, it is currently unknown to what extend this assay detects most PIK3CA mutations in BC. This information is critical as patients and clinicians are using this and other genomic assays to indicate alpelisib.MethodsData from 6338 patients with BC was explored across 10 publicly available studies. The primary objective was to evaluate the proportion and distribution of PIK3CA mutations in BC. Secondary objectives were (1) to evaluate in silico the spectrum of PIK3CA mutations in BC that would be captured by the therascreen panel; (2) to evaluate the proportion and distribution of PIK3CA mutations in hormone receptor-positive/HER2-negative (HR+/HER2−), HER2+, and triple-negative BC (TNBC); and (3) to explore the identification of PIK3CA mutations in a cohort of 48 HR+/HER2− advanced BC patients by the Guardant B360 circulating tumor DNA (ctDNA) assay.ResultsPatients with PIK3CAmut tumors represented 35.7% (2261/6338). Five PIK3CA mutations comprised 73% of all PIK3CA mutations: H1047R (35%), E545K (17%), E542K (11%), N345K (6%), and H1047L (4%). Therascreen gene list would capture 72% of all PIK3CA mutations and 80% of patients with a known PIK3CAmut BC. Among patients with double PIK3CAmut tumors (12% of all PIK3CAmut), the therascreen panel would capture 78% as harboring 1 single PIK3CA mutation, 17% as PIK3CAmut undetected, and 5% as PIK3CA double-mut. PIK3CA mutation rates were lower in TNBC (16%) compared to HR+/HER2 (42%) and HER2+ (31%) BC; however, the distribution of the 4 main PIK3CA mutations across subtypes was similar. Finally, 28% of PIK3CA mutations identified in ctDNA in 48 patients with advanced HR+/HER2− BC were not part of the therascreen panel.ConclusionPIK3CA mutations in BC are heterogenous and ~ 20% of patients with a known PIK3CA mutation, and 95% with a known double PIK3CAmut tumor, would not be captured by the therascreen panel. Finally, the clinical utility of PIK3CA mutations not present in the therascreen companion diagnostic assay or identified by other sequencing-based assays needs further investigation.

PIK3CA mutation profiling in Vietnamese patients with breast cancer

Activating mutations in phosphoinositide-3-kinase, catalytic, alpha polypeptide (PIK3CA) gene frequently occur in breast cancer, and are important for the survival of patients with breast cancer. Although PIK3CA mutations have been studied widely in many countries, the relationships between PIK3CA mutations and clinicopathological features are still inconsistent. Moreover, information about PIK3CA mutations in Vietnamese breast cancer has not been investigated. In the present study, we identified PIK3CA mutations in 27.2% of 162 human breast tumors, including 31 exon 9 mutations and 13 exon 20 mutations. In addition, PIK3CA mutations were associated with larger tumor size and low Ki67 level. Moreover, the distribution of PIK3CA mutations in the breast cancer subtypes was analyzed. The PIK3CA mutations was not equally distributed among different intrinsic subtypes, in which the rate of mutations in hormone (HR)-positive subtypes was somewhat higher than that in human epidermal growth factor receptor-2 (HER2)-positive subtypes. Overall, this study provides more information about PIK3CA mutations and suggests prognostic and predictive values for breast cancer management in Vietnamese population.

Liquid Biopsy in Breast Cancer: A Focused Review.

The role of liquid biopsy in cancer management has been gaining increased prominence in the past decade, with well-defined clinical applications now being established in lung cancer. Recently, the US Food and Drug Administration also approved the Therascreen PIK3CA RGQ polymerase chain reaction assay as a companion diagnostic assay to detect PIK3CA mutations in breast cancer for both tissue and liquid biopsies, bringing the role of liquid biopsy in breast cancer management to the fore. Its utility in other aspects of breast cancer, however, is yet to be clearly defined. To review the studies that looked at liquid biopsies in breast cancer and examine their potential for clinical application in the areas of early diagnosis, prognostication, monitoring disease response, detecting minimal residual disease, and predicting risk of progression or relapse. We focus mainly on circulating tumor cells and circulating tumor DNA. Peer-reviewed articles in PubMed. Liquid biopsies in breast cancers have yielded promising results, especially in the areas of monitoring treatment response and predicting disease progression or relapse. With further study, and hopefully coupled with continued improvements in technologies that isolate tumor-derived materials, liquid biopsies may go on to play a greater role in the breast cancer clinic.

Evaluation of TP53/PIK3CA mutations using texture and morphology analysis on breast MRI

PurposeSomatic mutations in TP53 and PIK3CA genes, the two most frequent genetic alternations in breast cancer, are associated with prognosis and therapeutic response. This study predicted the presence of TP53 and PIK3CA mutations in breast cancer by using texture and morphology analyses on breast MRI. Materials and methodsA total of 107 breast cancers (dataset A) from The Cancer Imaging Archive (TCIA) consisting of 40 TP53 mutation cancer and 67 cancers without TP53 mutation; 35 PIK3CA mutations cancer and 72 without PIK3CA mutation. 122 breast cancer (dataset B) from Seoul National University Hospital containing 54 TP53 mutation cancer and 68 without mutations were used in this study. At first, the tumor area was segmented by a region growing method. Subsequently, gray level co-occurrence matrix (GLCM) texture features were extracted after ranklet transform, and a series of features including compactness, margin, and ellipsoid fitting model were used to describe the morphological characteristics of tumors. Lastly, a logistic regression was used to identify the presence of TP53 and PIK3CA mutations. The classification performances were evaluated by accuracy, sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV). Taking into account the trade-offs of sensitivity and specificity, the overall performances were evaluated by using receiver operating characteristic (ROC) curve analysis. ResultsThe GLCM texture feature based on ranklet transform is more capable of recognizing TP53 and PIK3CA mutations than morphological feature, especially for the TP53 mutation that achieves statistically significant. The area under the ROC curve (AUC) for TP53 mutation dataset A and dataset B achieved 0.78 and 0.81 respectively. For PIK3CA mutation, the AUC of ranklet texture feature was 0.70. ConclusionTexture analysis of segmented tumor on breast MRI based on ranklet transform is potential in recognizing the presence of TP53 mutation and PIK3CA mutation.

Abstract 3917: Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer

Abstract Activating mutations in PIK3CA, the gene coding for the catalytic subunit (p110α) of phosphoinositide 3-kinase (PI3K), are the most frequent oncogenic alterations in all cancers, including estrogen receptor-positive (ER+) breast cancer. There are many distinct oncogenic PIK3CA mutations including major hotspot mutations (e.g. E542K, E545K, H1047R) which are predictive of response to PI3Kα inhibitors. While responses to PI3Kα inhibitors can be variable, some patients with single hotspot mutant tumors derive a deep and prolonged clinical benefit. In a comprehensive analysis of the genomic data available in breast cancer, we observed double PIK3CA mutations and investigated their potential biological relevance and potential correlation with sensitivity to PI3Kα inhibitors. We detected double PIK3CA mutations in 10-15% of all PIK3CA-mutant cancers including breast cancer. Double PIK3CA mutations in breast cancer are defined by a pattern of co-expression of a major hotspot mutation associated with a recurrent second-site PIK3CA mutation (‘minor mutation’). We have found that these double PIK3CA mutations are compound, that is in cis on the same allele, using single molecule real time sequencing (SMRT-seq) of fresh breast tumor samples. Double compound PIK3CA mutations result in increased PI3K activity and downstream signaling compared to single hotspot mutants in nontransformed cells and in ER+ breast cancer cells. Double compound mutations also increase cell proliferation and xenograft growth compared to single hotspot mutants. Biochemical experiments using recombinant PI3K compound mutant protein complexes reveal a combination mechanism of action, with simultaneous PI3K destabilization and increased membrane binding compared to single hotspot mutants, leading to increased kinase activity. Importantly, these compound mutations predict for increased sensitivity to PI3Kα inhibitors compared to single hotspot mutants in both preclinical models and also in patients with breast cancer. Together, our data support that double compound PIK3CA mutations enhance the oncogenicity of single hotspot PIK3CA mutations and this increased dependency results in increased sensitivity to PI3Kα inhibitors compared to single hotspot mutations. We propose that double compound activating mutations are an additional mechanism of oncogenic transformation in addition to other known mechanisms such as gene amplification, point mutation, or gene translocation. We speculate that double compound mutant PIK3CA may function as a clinical biomarker of increased sensitivity to PI3K-directed targeted therapies and may improve the therapeutic window of PI3K inhibitors in ER+ breast cancer and other PIK3CA-mutant tumor histologies. Citation Format: Neil Vasan, Pedram Razavi, Jared Johnson, Hong Shao, Hardik Shah, Alesia Antoine, Erik Ladewig, Alexander Gorelick, Eneda Toska, Guotai Xu, Abiha Kazmi, Matthew T. Chang, Barry S. Taylor, Maura N. Dickler, Komal Jhaveri, Raul Rabadan, Ed Reznik, Melissa L. Smith, Robert Sebra, Lewis C. Cantley, Maurizio Scaltriti, Jose Baselga. Double PIK3CA mutations in cis enhance oncogene activation and sensitivity to PI3K alpha inhibitors in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 3917.

Aspirin Treatment Effect and Association with PIK3CA Mutation in Breast Cancer: A Biomarker Analysis

BackgroundStudies suggest regular aspirin use decreases breast cancer (BRCA) risk, with high doses exerting an “anti-cancer” effect. Despite reports suggesting aspirin’s protective role in BRCA, no findings on aspirin dose association(s) with treatment outcomes have been reported, nor have any molecular subtype associations by which aspirin influences outcomes been elucidated. To interrogate aspirin’s effect and determine which populations may benefit from its use, we retrospectively explored data from 1227 patients with BRCA. In this population, 32 used high-dose aspirin (325 mg), 121 used low-dose aspirin (81 mg), and 1074 used no aspirin before and/or after diagnosis. Patients and MethodsSeveral association tests were performed to examine the correlations of clinical variables and PIK3CA mutations from 45 patients with BRCA who used 81 mg of aspirin daily. Kaplan-Meyer survival curves and the log-rank test were utilized to compare survival outcome differences for aspirin dose, usage history, and PIK3CA mutation status. Cox proportional hazards models were used to compute the multivariate hazard ratio (HR) for death. ResultsPatients who regularly used high-dose aspirin (325 mg) had better survival outcomes than those who used low-dose aspirin (81 mg) (HR, 0.094; 95% confidence interval [CI], 0.014-0.62; P = .014). Patients who used aspirin post-diagnosis only achieved significant benefits in overall survival (HR, 0.082; 95% CI, 0.023-0.3; P = 1.39E-04). Also, a subgroup of patients in the low-dose, long-term aspirin group with a PIK3CA mutation showed a small beneficial effect (HR, 0.37; 95% CI, 0.04-3.25; P = .37). ConclusionHigh-dose aspirin after diagnosis may confer BRCA treatment benefits. Future studies should assess the comprehensive mechanism of aspirin for the PIK3CA mutant subgroup in a large study.

Abstract P3-08-12: PIK3CA mutations in breast cancer: Mutational landscape and clinical implications in ER+/HER2- subtype

Abstract Introduction: PIK3CA mutation is one of the most frequent genomic alterations in breast cancer. We evaluated PIK3CA mutational status including spatial and temporal heterogeneity, clinical characteristics and prognostic impact focused on ER+/HER2- subtype. Methods: We performed targeted ultra-deep sequencing (CancerSCAN™) of breast cancer tissue in a prospective cohort. Burden of disease was assessed by metabolic tumor volume(MTV) in 18F-FDG-PET scan. Association with clinical characteristics or survival were tested in ER+/HER2- subtype, using Chi square test or Kaplan-Meier method. Results: PIK3CA analyses were performed in 1274 breast cancer specimens from 1091 patients. 957 patients had early breast cancer. PIK3CA alterations were found in 397 patients(36.3%), and frequency of PIK3CA mutation was significantly lower in triple negative breast cancer(19.0%), compared with 40.4% in ER+/HER2-, 40.9% in ER+/HER2+, and 45.2% in ER-/HER2+ subtype(p&amp;lt;0.0001). 158 patients had more than two biopsies. Among 92 patients with second biopsy within one month, 11%(10/92) had spatial heterogeneity of PIK3CA mutation. After neoadjuvant chemotherapy, 10%(3/30) of patients had change of PIK3CA mutational status. Serial biopsy at time of recurrence revealed loss or gain of PIK3CA mutation in 10 out of 59 patients (17%). In ER+/HER2- subtype, PIK3CA had a trend toward longer distant disease free survival without statistical significance. In patients with stage IV ER+/HER2- disease, PIK3CA hotspot mutations were associated with significant longer overall survival(OS) (71.0 vs. 37.8 months, p=0.048) and better progression free survival(PFS) at 1st line palliative treatment (37.7 vs. 9.4 months, p = 0.0004). Frequency of symptomatic recurrence, recurrence as oligometastases, and specific metastatic sites were not associated with PIK3CA mutational status, except that bone metastases at first distant metastases was less prevalent in patients with PIK3CA hotspot mutations(35.6% vs. 53.8% in PIK3CA wt, p=0.048). Metabolic tumor volume(MTV) at time of first distant metastases was not associated with presence of PIK3CA mutation. Conclusion: We observed variations in PIK3CA mutational status in more than 10% of patients with &amp;gt;1 repeated biopsy. In stage IV ER+/HER2- disease, PIK3CA hotspot mutation seemed to be associated with longer PFS and OS, however metabolic tumor burden was not associated with PIK3CA alterations. Citation Format: Ahn HK, Park S, Hyun SH, Park K, Lee E, Kim J-Y, Nam SJ, Kim SW, Lee JE, Lee SK, Yu JH, Ahn JS, Im Y-H, Park YH. PIK3CA mutations in breast cancer: Mutational landscape and clinical implications in ER+/HER2- subtype [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P3-08-12.

Abstract 1772: PIK3CA C2 domain deletions hyperactivate PI3K, generate oncogene dependence and are exquisitely sensitive to PI3Kα inhibitors

Abstract Background: A 63 year old postmenopausal woman with advanced ER+ breast cancer resistant to endocrine therapy exhibited an exceptional response to the PI3Kα inhibitor alpelisib (BYL719) and the aromatase inhibitor letrozole (Mayer et al. Clin Cancer Res 2016). Targeted capture next generation sequence (NGS) of DNA from a liver metastasis identified a P447_L455 deletion in the C2 domain of PIK3CA. About 80% of PIK3CA activating mutations are in ‘hot spots’ within the helical and kinase domains. C2 domain mutations make up ~10% of all PIK3CA mutations in breast cancer (TCGA, Foundation Medicine) and are frequently not reported by tumor and plasma cell-free DNA NGS panels. Deletions and mutations in this domain cluster in a region encompassing amino acids 446-460 of PIK3CA. We investigated herein the functional role of PIK3CA C2 domain mutations and their response to PI3K inhibitors. Methods: V5-tagged lentiviral vectors encoding wild type, delP447-L455, and delH450-P458 were stably transduced into MCF10A non-tumorigenic human breast epithelial cells. Cell viability and acini formation in 3D Matrigel were examined in media ± EGF or insulin or alpelisib. Markers of PI3K activation were examined by immunoblot and phosphoflow analysis. The Rosetta software suite was used to construct a structural model that would predict the change in stability of the p85/p110α complex. Physical association of p85α and p110α was determined by precipitation with V5 antibodies and immunoblot analysis. Results: MCF10A cells stably expressing V5-tagged PIK3CAdelP447-L455 and PIK3CAdelH450-P458 exhibited EGF- and insulin-independent growth and higher phosphorylation of AKT, ERK and S6 when compared to parental MCF10A cells. In 3D Matrigel, MCF10A cells with PIK3CA C2 domain deletions formed invasive acini with increased protrusions, spindling, and bridging between acini. All these changes were ablated upon the addition of 1 µM of alpelisib whereas parental MCF10A cells were unaffected by alpelisib. We hypothesized that delP447-L455 would reduce the binding affinity of p110α with the p85 regulatory subunit of PI3K. A structural model of PIK3CAdelP447-L455 in the context of the regulatory complex revealed specific favorable inter-residue contacts that would be lost as a result of the deletion, predicting a significant decrease in binding energy. Consistent with this structural analysis, coimmunoprecipitation of p85 with V5 antibodies showed reduced binding of the C2 domain deletion mutants with p85 compared to wild type p110α. Conclusions: These data suggest that C2 domain deletions in PIK3CA are activating mutations and generate oncogene dependence. As a result, tumors expressing these mutations are exquisitely sensitive to PI3Kα inhibitors. Thus, in addition to PIK3CA ‘hot spot’ mutations, C2 domain mutations should also be considered biomarkers of sensitivity to PI3K inhibitors. Citation Format: Sarah Croessmann, Jonathan Sheehan, Gregory Sliwoski, Nalin Leelatian, Jie He, Rebecca Nagy, Justin M. Balko, Ingrid A. Mayer, Richard B. Lanman, Vincent Miller, Lewis C. Cantley, Jonathan M. Irish, Jens Meiler, Carlos L. Arteaga. PIK3CA C2 domain deletions hyperactivate PI3K, generate oncogene dependence and are exquisitely sensitive to PI3Kα inhibitors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1772. doi:10.1158/1538-7445.AM2017-1772