PIK3CA Hotspot Mutations Research Articles

Detection of PIK3CA hotspot mutations in canine mammary tumors using droplet digital PCR: tissue validation and liquid biopsy feasibility

Domestic dogs (Canis lupus familiaris) serve as valuable translational models for human cancer research due to their biological similarities. Canine mammary tumors (CMTs), frequently diagnosed in female dogs, share various characteristics with human breast cancers. This study investigates the PIK3CA (H1047R) mutation in CMTs using droplet digital PCR (ddPCR) and explores the potential of liquid biopsy for non-invasive detection. We analyzed 80 formalin-fixed, paraffin-embedded (FFPE) CMT tissue samples and compared ddPCR results with next-generation sequencing (NGS) data, achieving high concordance. Plasma and serum samples were also assessed for mutation concordance with tissue results. Our findings indicate a higher frequency of the PIK3CA (H1047R) mutations in benign and grade I malignant CMTs compared to more aggressive malignancies. The ddPCR assay demonstrated high sensitivity and specificity, with plasma testing showing 78.6% sensitivity and 87.5% specificity, and serum testing showing 66.7% sensitivity and 90.0% specificity. These results highlight the viability of liquid biopsy as a minimally invasive method for monitoring PIK3CA mutations in canine patients. The study suggests that liquid biopsy techniques hold significant promise for improving the early detection and monitoring of canine cancers, warranting further research to refine these methods and explore their applications in canine cancer diagnostics and treatment.

Development and validation of a multi-marker liquid bead array assay for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in single circulating tumor cells (CTCs)

BackgroundPIK3CA and ESR1 mutations are associated with progression and therapy resistance in metastatic breast cancer (MBC). CTCs are highly heterogeneous and their analysis at single cell level can provide unique information for mutational profiling and the existence of different sub-clones related to tumor progression. We have developed a novel multi-marker liquid bead array assay based on combination of an enzymatic mutation enrichment method, multiplex PCR-based assay, and liquid bead array technology for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in liquid biopsy samples. We focus on single CTCs, however the assay can be used for bulk CTC and ctDNA analysis. Materials and methodsSingle CTCs were isolated from an ER+/HER2+ MBC patient from CellSearch® cartridges using the VyCAP Puncher System and subjected to whole genome amplification followed by nuclease-assisted minor-allele enrichment with probe-overlap (NaME-PrO) enrichment. The assay was validated for analytical sensitivity and specificity for the simultaneous detection of PIK3CA (E545K, E542K, H1047R, H1047L) and ESR1 (Y537S, Y537C, Y537N, D538G, L536H) mutations in single CTCs, while its clinical performance was evaluated on 22 single CTCs and three single white blood cells (WBCs). ResultsThe developed multi-marker liquid bead array assay is novel, highly specific and sensitive for both mutation panels. The assay can reliably detect mutation-allelic-frequencies (MAFs) as low as 0.1 %. The presence of PIK3CA and ESR1 mutations was detected in 13.6 % and 72.7 % of single CTCs, respectively. The developed assay is sample-saving since it requires only 2 μL of amplified DNA to check for nine hotspot PIK3CA and ESR1 mutations in a single cell. The developed liquid bead array assay (Luminex, US), based on a 96 microwell plate format, enables the simultaneous analysis of 96 single cells. ConclusionsThe developed novel multi-marker liquid bead array assay for the simultaneous detection of PIK3CA and ESR1 hotspot mutations in single CTCs is highly specific, highly sensitive, high-throughput, and sample-, cost-, and time-saving. This multi-marker liquid bead array assay can be extended to detect up to 100 mutations in many genes at once and can be applied for bulk CTC and ctDNA analysis.

Molecular Analysis of Renal/Adrenal Angiosarcomas Reveals High Frequency of Recurrent Genetic Alterations.

Angiosarcomas of the kidney and adrenal gland are rare, highly aggressive vascular neoplasms. Their genomic profile has not been systematically studied to date. We report the clinicopathologic and molecular features of six angiosarcomas centered in the kidney/adrenal gland. All patients were male adults, ranging from 58 to 77 years of age. Tumor sizes ranged from 2.5 to 22.5 cm. Half of the cases demonstrated hot spot mutations in the KDR gene, while one-third demonstrated mutations in the PIK3CA gene; both of these gene alterations being previously described, preferentially in breast angiosarcomas. In addition, two cases each demonstrated BRIP1 gene amplification, CTNNB1 and ETV6 mutations, which have not been previously reported in angiosarcoma. Notably, molecular studies were critical in establishing the correct diagnoses in three cases: one was an epithelioid angiosarcoma originally misdiagnosed as metastatic adenocarcinoma to the adrenal gland, the second was a vasoformative angiosarcoma that mimicked hemangioma, and the third was a collision tumor between a high-grade angiosarcoma and a chromophobe renal cell carcinoma which was originally diagnosed as a sarcomatoid renal cell carcinoma. In summary, angiosarcomas of the kidney and adrenal gland have a high frequency of recurrent genetic alterations, some of them being shared with other angiosarcoma subtypes, while other appear to be novel. In particular, activating hot spot KDR and PIK3CA mutations represent potential therapeutic targets for these highly aggressive cancers.

Acquired gene alterations in patients treated with ribociclib plus endocrine therapy or endocrine therapy alone using baseline and end-of-treatment circulating tumor DNA samples in the MONALEESA-2, -3, and -7 trials

A prior pooled analysis of the MONALEESA-2, -3, and -7 trials identified baseline markers predictive of sensitivity or resistance to ribociclib plus endocrine therapy (ET). We report the results of an analysis of paired baseline and end-of-treatment (EOT) circulating tumor DNA (ctDNA) samples across the MONALEESA trials. Paired baseline and EOT ctDNA samples from MONALEESA-2, -3, and -7 were sequenced using a targeted next-generation sequencing panel. Genes with an EOT alteration prevalence of >5% were included. A McNemar test was performed on paired samples and adjusted for multiple testing to control the false discovery rate. A Bayesian mixed-effects model was used to adjust for ctDNA fraction at both time points and for study differences. The analysis included 523 paired samples. At EOT, 21 genes had a >5% alteration prevalence. A trend for higher ctDNA fraction at EOT vs baseline (P=0.08) was observed. Prevalence of alterations was higher at EOT vs baseline in RB1, SPEN, TPR, PCDH15, and FGFR2 in the ribociclib arm; PBRM1 in the placebo arm; and ESR1 in both arms. The mixed-effects model demonstrated that the same trends for increased prevalence of these alterations at EOT were observed after adjusting for ctDNA fraction and that the increased rate of RB1 and SPEN alterations at EOT were specific to ribociclib plus ET. Analysis of ESR1 indicated a similar increase at EOT in both arms. The most common acquired ESR1 mutations at EOT included Y537C/N/S/D, D538G, E380Q, and L536H/R/P/LC. The prevalence of PIK3CA hotspot mutations at baseline and EOT was similar. This analysis identified acquired gene alterations in patients with HR+/HER2- advanced breast cancer treated with ribociclib plus ET or placebo plus ET. These data may support further studies on acquired resistance mechanisms and inform future systemic interventions in the post-CDK4/6 inhibitor setting.

A Multiplex Assay for Fast PIK3CA Hotspot Mutation Characterization in a Single Specimen by 3-Color Digital PCR Analysis.

Activating mutations in the phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) gene have been detected often in solid tumors. Targeted therapy for mutant PIK3CA is now available in the clinic, making molecular diagnostics pivotal. Our aim was to design a multiplex digital PCR (dPCR) assay to evaluate the 4 most common PIK3CA hotspot mutations simultaneously to characterize and quantify these in liquid biopsies. A multiplex assay was developed to detect exon 9 p.E542K and p.E545K mutations, and exon 20 p.H1047L and p.H1047R mutations using the Stilla 3-color dPCR Naica system. The assay was evaluated on stock and pre-amplified DNA from cell lines with the above mutations as single and pooled samples, and on cell-free DNA (cfDNA) from healthy blood donors (HBDs) and breast cancer patients, to determine detection thresholds and diagnostic accuracy. The assay distinguished all 4 PIK3CA mutations in (cf)DNA, and also when dual mutations were present. Detection thresholds of stock and pre-amplified cfDNA samples were 0.11 and 0.40 copies/uL (cp/uL) for mutant copies concentration, and 0.003% and 0.68% for variant allele frequencies (VAFs), respectively. The assay confirmed the PIK3CA (mutation) status as defined by targeted next-generation sequencing (NGS) in 82 out of 96 patients that were mutant for PIK3CA, and in 11 out of 12 patients with wild-type PIK3CA. Our designed multiplex dPCR assay detected PIK3CA mutations with high accuracy in stock and pre-amplified cfDNA. Furthermore, it is affordable and demands less cfDNA input when compared to available uniplex dPCR assays and NGS analyses.

Functional characterization of PI3K C2 domain mutations detected in breast cancer circulating tumor cells and metastatic cells

BackgroundIn breast cancer, over one third of all patients harbor a somatic mutation in the PIK3CA gene, encoding the p110α catalytic subunit of the phosphatidylinositol 3-kinase (PI3K) in their tumor cells. Circulating tumor cells (CTCs) are cells shed from the primary tumor into the blood stream. Recently, the long-term stable breast cancer CTC-ITB-01 cell line with tumorigenic and metastatic capacity was established from liquid biopsy derived cells. The oncogenic hotspot PIK3CA mutation H1047R (kinase domain) was detected in the primary tumor, CTCs and metastasis of the same patient. Other PIK3CA mutations located within the C2 domain (E418K and E453K) were detected in the CTCs and the vaginal metastasis but not in the primary tumor. The goal of our study was to functionally characterize the impact of the rare E418K and E453K mutations within the C2 domain that were not detected in the primary tumor. MethodsPIK3CA mutations E418K, E453K, H1047R were generated by site-directed mutagenesis and stably overexpressed in breast cancer cells by lentiviral transduction. Subsequent signaling pathway activation was examined by western blot analysis. The impact of PIK3CA mutations on biological processes was studied by live cell imaging using the Incucyte Zoom system. Structural modeling was conducted in Pymol. The membrane localization of the mutants was evaluated by separating the cytosolic and membrane fraction using ultracentrifugation. Drug susceptibility of CTC-ITB-01 cells was analyzed by live cell imaging. ResultsWestern blot analysis of human MDA-MB-231, MCF-7 and T47D breast cancer cells stably overexpressing either the PIK3CA wildtype (WT) or one of the E418K, E453K or H1047R mutants revealed a significant increase in AKT phosphorylation in both C2 mutants (E418K and E453K) and the kinase domain mutant H1047R. Functional analysis showed a significantly increased proliferation of MDA-MB-231 cells overexpressing the E453K and H1047R mutants. Migration was increased in all cells overexpressing WT and each of the mutants. Interestingly, invasion and chemotaxis were only enhanced in the MDA-MB-231 cells overexpressing the C2 domain mutants, i.e. E418K and E453K. In addition, membrane localization of the two C2 domain mutants was increased. Structural modeling of the E453K mutation suggests a disruption of the interaction between the negative regulatory domain of the p85α subunit and the p110α catalytic subunit as a potential mechanism leading to the observed activation of PI3K/AKT/mTOR signaling. Dual targeting of AKT/mTOR pathway by MK2206 and RAD001 leads to very strong synergistic effects (IC50 MK2206: 148 nM, IC50 RAD001: 15 nM) with respect to proliferation in the CTC-ITB-01 line through apoptosis induction. ConclusionsOur results demonstrate that PIK3CA C2 domain mutations activate PI3K downstream AKT signaling and can increase proliferation, migration and invasion after stable lentiviral transduction. Although both investigated mutations - E418K and E453K - are located within the C2 domain, a different molecular mechanism can be proposed. The PIK3CA mutated CTC-ITB-01 shows a high susceptibility against dual inhibition of AKT/mTOR. Further studies are required to fully elucidate the oncogenic potential of rare PIK3CA mutations.

An analysis of PIK3CA hotspot mutations and response to neoadjuvant therapy in breast cancer patients from four prospective clinical trials.

The PI3K signaling pathway is frequently dysregulated in breast cancer (BC), and mutations in PIK3CA, are relevant for therapy resistance in HER2pos BC. Mutations in exons 9 or exon 20 may have different impact on response to neoadjuvant chemotherapy-based treatment regimens. We investigated PIK3CA mutations in 1691 early BC patients, randomized in four neoadjuvant multicenter trials: GeparQuattro (NCT00288002), GeparQuinto (NCT00567554), GeparSixto (NCT01426880) and GeparSepto (NCT01583426). The role of different PIK3CA exons and hotspots for pathological complete response (pCR) after neoadjuvant chemotherapy (NACT) and patient survival was evaluated for distinct molecular subgroups and anti-HER2 treatment procedures. A total of 302 patients (17.9%) of the full cohort of 1691 patients had a tumor with a PIK3CA mutation, with a different prevalence in molecular subgroups: luminal/HER2neg 95 of 404 patients (23.5%), HER2pos 170 of 819 patients (20.8%) and TNBC 37 of 431 patients (7.9%). We identified mutations in PIK3CA exon 20 to be linked with worse response to anti-HER2 treatment (OR=0.507, 95%CI 0.320-0.802, p=0.004), especially in HR positive HER2 positive BC (OR=0.445, 95%CI 0.237-0.837, p=0.012). In contrast, exon 9 hotspot mutations p.E452K and p.E545K revealed no noteworthy differences in response therapy response. Luminal/HER2neg patients show a trend to have worse treatment response when PIK3CA was mutated. Interestingly, patients with residual disease after neoadjuvant treatment, have better survival when PIK3CA was mutated. PIK3CA hotspot mutation p.H1047R are associated with worse pCR rates after NACT in HER2pos BC, while hotspot mutations in exon 9 seems to have less impact.

Identification of an HLA-A*11:01-restricted neoepitope of mutant PIK3CA and its specific T cell receptors for cancer immunotherapy targeting hotspot driver mutations

Hotspot driver mutations presented by human leukocyte antigens might be recognized by anti-tumor T cells. Based on their advantages of tumor-specificity and immunogenicity, neoantigens derived from hotspot mutations, such as PIK3CAH1047L, may serve as emerging targets for cancer immunotherapies. NetMHCpan V4.1 was utilized for predicting neoepitopes of PIK3CA hotspot mutation. Using in vitro stimulation, antigen-specific T cells targeting the HLA-A*11:01-restricted PIK3CA mutation were isolated from healthy donor-derived peripheral blood mononuclear cells. T cell receptors (TCRs) were cloned using single-cell PCR and sequencing. Their functionality was assessed through T cell activation markers, cytokine production and cytotoxic response to cancer cell lines pulsed with peptides or transduced genes of mutant PIK3CA. Immunogenic mutant antigens from PIK3CA and their corresponding CD8+ T cells were identified. These PIK3CA mutation-specific CD8+ T cells were subsequently enriched, and their TCRs were isolated. The TCR clones exhibited mutation-specific and HLA-restricted reactivity, demonstrating varying degrees of functional avidity. Identified TCR genes were transferred into CD8+ Jurkat cells and primary T cells deficient of endogenous TCRs. TCR-expressing cells demonstrated specific recognition and reactivity against the PIK3CAH1047L peptide presented by HLA-A*11:01-expressing K562 cells. Furthermore, mutation-specific TCR-T cells demonstrated an elevation in cytokine production and profound cytotoxic effects against HLA-A*11:01+ malignant cell lines harboring PIK3CAH1047L. Our data demonstrate the immunogenicity of an HLA-A*11:01-restricted PIK3CA hotspot mutation and its targeting therapeutic potential, together with promising candidates of TCR-T cell therapy.

Serial analysis of ESR1 and PIK3CA mutations in cell-free DNA from metastatic breast cancer during 1st line endocrine therapy.

e13060 Background: Activating mutations ofESR1 and PIK3CA genes are known mechanisms of endocrine resistance. Recent analysis supported benefit of early intervention at presence of ESR1 mutation in blood (bESR1) before clinical progression. We aimed to investigate ESR1 and PIK3CA mutations detected in cell-free DNA (cfDNA) from patients with hormone receptor-positive, HER2-negative metastatic breast cancer (MBC) and its impact on progression-free survival (PFS). Methods: Thirty patients undergoing 1st line endocrine therapy (ETx) were identified from a prospective cohort. Seven ESR1 hotspot mutations in the ligand binding domain were tested in cfDNA with droplet digital polymerase chain reaction (ddPCR) assay (Genopeaks Co., Ltd). Eleven PIK3CA hotspot mutations were tested using amplicon-targeted sequencing method (Genopeaks Co., Ltd) in both tumor and cfDNA. PFS analyses were performed using Kaplan-Meier methods and compared with the log-rank test. Results: We examined serial cfDNA samples from 26 patients collected every 3-6 months. ESR1 mutations were found in 61.5% (16/26) patients at any timepoint during 1st line endocrine therapy, with D538G being the most common followed by Y537C and 68.8% (11/16) being polyclonal. Among the 50.0% (8/16) bESR1 positive patients with clinical progression, 4 had bESR1 detected before clinical progression while 4 were diagnosed clinical progression concurrently, suggesting the necessity of closer intervals of cfDNA analyses. While presence of bESR1 did not affect PFS overall, 18.8% of patients with bESR1 detected within 6 months after 1st line ETx, displayed worse outcome (median PFS 5 vs 52 months). Also, patients with clearance of bESR1 mutation in subsequent cfDNA (81.3%, 13/16) were shown to have a better outcome (median PFS 52 vs 41 months). Among 14 patients with clinical progression, 8 had bESR1 mutation. Median PFS between patients with bESR1 positive vs negative was 14 vs 9 months. PIK3CA mutations were detected in 69.5% (16/23) of cfDNA at diagnosis of distant metastasis, among them 53.3% (8/15) had co-occurrence with bESR1 mutations. While presence of PIK3CA mutation in primary tumor tissue did not affect disease-free survival nor PFS, patients with blood PIK3CA mutation at diagnosis of metastasis displayed significantly worse outcome (p = 0.041). Conclusions: Substantial number of hormone receptor-positive, HER2-negative MBC patients were detected with ESR1 and PIK3CA mutation in plasma. Though it was a small-sized analysis to accurately assess statistical significance, we observed worse outcome in patients with 1) early detection (<6 months) of bESR1 and with 2) sustained bESR1 during palliative ETx. Patients with clinical progression without bESR1 mutation displayed shorter PFS than patients with bESR1. PIK3CA mutations in cfDNA were prognostic supporting the benefit of combined targeted therapy.

PIK3CA Hotspot Mutations in Saliva as a Diagnostic Marker in Oral Squamous Cell Carcinoma Patients.

This study aimed at the analogous detection of PIK3CA mutations, common in oral squamous cell carcinoma (OSCC), in matched tumor and saliva samples. Tissue and saliva samples were obtained from 29 patients diagnosed with primary OSCC. Saliva samples were obtained preoperatively; tissue specimens were acquired during tumor resection. Tumor DNA was extracted from both tissue and saliva samples. All samples were controlled for DNA quantity and quality and genetic matching of sample pairs was confirmed using the iPlex Pro Exome QC Panel. Variant detection was performed using the MassARRAY® System, a mass-spectrometry based detection system. Mutational analysis in tissue tumor DNA was made using the multiplexed ClearSEEK™ PIK3CA v1.0 Panel covering 20 hotspot mutations in PIK3CA. In saliva samples, variants were analyzed using both the ClearSEEK™ and the UltraSEEK® Lung v1.1 Panel, with a higher limit of detection but covering less PIK3CA variants. Overall, a PIK3CA variant was found in seven of the 29 tumor tissue samples (24%) by ClearSEEK™; UltraSEEK® additionally confirmed the variant in four of these seven positive samples. Of the three variants not detected by UltraSEEK®, two were not included in the panel and one was included but not detected. Of the seven variants found in tissue, five could also be detected in the matching saliva samples (71%), either by utilizing ClearSEEK™ or UltraSEEK® Conclusion: The detection of PIK3CA hotspot mutations in OSCC and their simultaneous occurrence in saliva underline the potential benefit of liquid biopsies for non-invasive cancer detection and follow-up care of OSCC patients.

Genomic dissection and mutation-specific target discovery for breast cancer PIK3CA hotspot mutations

BackgroundRecent advancements in high-throughput genomics and targeted therapies have provided tremendous potential to identify and therapeutically target distinct mutations associated with cancers. However, to date the majority of targeted therapies are used to treat all functional mutations within the same gene, regardless of affected codon or phenotype.ResultsIn this study, we developed a functional genomic analysis workflow with a unique isogenic cell line panel bearing two distinct hotspot PIK3CA mutations, E545K and H1047R, to accurately identify targetable differences between mutations within the same gene. We performed RNA-seq and ATAC-seq and identified distinct transcriptomic and epigenomic differences associated with each PIK3CA hotspot mutation. We used this data to curate a select CRISPR knock out screen to identify mutation-specific gene pathway vulnerabilities. These data revealed AREG as a E545K-preferential target that was further validated through in vitro analysis and publicly available patient databases.ConclusionsUsing our multi-modal genomics framework, we discover distinct differences in genomic regulation between PIK3CA hotspot mutations, suggesting the PIK3CA mutations have different regulatory effects on the function and downstream signaling of the PI3K complex. Our results demonstrate the potential to rapidly uncover mutation specific molecular targets, specifically AREG and a proximal gene regulatory region, that may provide clinically relevant therapeutic targets. The methods outlined provide investigators with an integrative strategy to identify mutation-specific targets for the treatment of other oncogenic mutations in an isogenic system.

What Do German Molecular Tumor Boards Recommend in Patients with PIK3CA-Mutated Tumors? Launch and First Results from the German Transsectoral Molecular Tumor Board Exchange Platform Deutschland

Introduction: Comprehensive molecular tumor profiling is widely used in the management of patients with cancer. Molecular tumor boards devise treatment strategies based on testing results. In this setting, the Transsectoral Molecular Tumor Board exchange platform Deutschland (TEAM-D) aims to drive peer-to-peer exchange to connect experts in the field. Methods: During the first virtual TEAM-D meeting, participants from 16 German universities and 5 nonacademic institutions discussed five cases with PIK3CA hotspot mutations. Furthermore, an illustrative case vignette was presented. Results: Overall, German caregivers show restraint in administering off-label PIK3CA inhibitor and favor clinical trials in this setting. Conclusion: In the setting of precision oncology, TEAM-D enables virtual case discussion across the different sectors of the German healthcare system. Based on the example of PIK3CA hotspot mutations, TEAM-D demonstrated the value of integrating knowledge from different healthcare professionals.

Abstract PO1-26-03: Activity of alpelisib in a panel of breast XPDX models harboring hotspot and uncommon PIK3CA mutations

Abstract Background: Therapies targeting mutated phosphoinositide 3-kinase (PI3K) p110α catalytic subunit (PIK3CA) cancers remain an active field of research. Alpelisib was approved in combination with fulvestrant in ER+/HER2- breast cancer patients harboring PIK3CA mutations on hotspot amino acids E542, E545 Q546 or H1047. While mutation at these sites have been widely studied, they only comprise ~25% of identified variants in this protein. Recent studies have reported other mutations, including those at the c-terminus, which can lead to constitutive activation of PIK3CA; however, whether these variants are sensitive to agents like alpelisib is unclear. To better understand these variants and their role in PIK3CA-mediated breast cancer, we established a panel of PIK3CA-mutated ER+ and ER- breast XPDX models and evaluated each in vivo with single agent alpelisib. Methods: Ninety previously developed XPDX models representing PIK3CA-mutated ER+ and ER- breast cancer were evaluated in this study. Models were grown subcutaneously in female athymic nude mice supplemented with estradiol in drinking water when necessary and ER expression confirmed at multiple passes; PIK3A variants were determined by WES and RNAseq. For in vivo studies, alpelisib was administered once daily by oral gavage at 35 mg/kg through study completion. Endpoints included tumor volume and time from treatment initiation with %T/C values and tumor regression reported at study completion; a T/C of ≤ 20% versus control was considered sensitive. Tumor regression (%T/C< 0%) versus Day 0 tumor volume was also reported. Results: 60% of PIK3CA-mutated models were found ER+ with 40% also HER2+ while 20% of ER- PIK3CA-mutated models were also HER2+. H1047X mutations accounted for 40% of all PIK3CA variants, 75% of which were single or dual PIK3CAH1047R. Several hotspot-mutated models were sensitive to alpelisib some with regressions including ST986 (E542K), ST1097 (E454K) and STF040 (H1047R), as well as ST1245C (R88Q/N1044H), ST2076 (102-103ins/R357Q) and ST4176 (E726K/H1047R). HER2+ models were less sensitive to alpelisib although STM148D (H1047L) reported tumor regressions. Interestingly, ST1799/PBR (E542K/H1065L), a palbociclib resistant clone of the ER+ parent ST1799 model was resistant to alpelisib while the parent was found sensitive. Conclusion: We have benchmarked a panel of PIK3CA-mutated breast XPDX models with alpelisib and compared activity of models harboring hotspot versus uncommon PIK3CA mutations with ER and HER2 expression. This data is a valuable tool in further developing PIK3CA inhibitors and identifying new variant targets in breast cancer. Citation Format: Mercedes Castaneda, Alyssa Simonson, Johnnie Flores, Maci DeBoer, Jim Lund, Tahmi Rouzbahan, Kyriakos P. Papadopoulos, Amy Lang, Gladys Rodriguez, Maryam Elmi, Arthur Rosenthal, Drew Rasco, Victor Moreno, Amita Patnaik, Tatiana Hernandez, Emiliano Calvo, Lon Smith, Manish Sharma, Muralidhar Beeram, Michael Wick. Activity of alpelisib in a panel of breast XPDX models harboring hotspot and uncommon PIK3CA mutations [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 PO1-26-03.

Abstract PO5-21-10: Efficacy and Safety of Alpelisib in PIK3CA-mutated, hormone receptor-positive advanced breast cancer after a CDK4/6 inhibitor: An Open-label, Multi-centre, Prospective, Single Arm Clinical Trial

Abstract Introduction: Currently, patients with luminal metastatic breast cancer receive a CDK4/6 inhibitor in combination with endocrine therapy as a first or second line of treatment. When tumors become resistant to the CDK4/6 inhibitors, treatment with alpelisib (PI3K inhibitor) in combination with an endocrine agent can be a next treatment option if an activating PIK3CA mutation is confirmed (cfr. SOLAR-1 trial). However, limited data is available after treatment with CDK4/6 inhibitors (cfr. BYLieve trial) and even less about alpelisib in later lines of therapy. Therefore, we aim to investigate the therapeutic efficacy and safety of alpelisib in combination with an endocrine agent in PIK3CA-mutated advanced breast cancer patients in later lines after prior CDK4/6i treatment. Methods: This is an open-label, prospective, multi-centre, single arm clinical trial enrolling patients from both the University Hospital of Leuven (UHL) and Ghent University Hospital (GUH). For each patient, metastatic tumor was tested for PIK3CA mutations using the UHL 96 gene panel. Our endpoints are clinical benefit rate, progression-free survival, time to treatment discontinuation (defined as the date of starting alpelisib to the date of treatment discontinuation or death) and safety. Descriptive statistics were used. Results: Between June 18th 2019 and August 23rd 2021, 38 patients have been included with confirmed PIK3CA hotspot mutations. All patients had CDK4/6 inhibitor in an earlier treatment line. Median age at alpelisib initiation was 64 years (range: 39-82 years). Included patients had a median of four lines of systemic therapy for advanced disease prior to starting alpelisib (range: 1- 11). Clinical benefit rate (patients receiving ³ 6 months of treatment) was 26.3% (10/38). The median progression-free-survival as well as time to treatment discontinuation were 3 months (range: 1 – 18). Dose reduction due to toxicity occurred in 11 patients (29%), of which 7 due to hyperglycemia grade 3, 2 due to diarrhea grade 3, 1 due to rash grade 2 and 1 due to anorexia. Finally, 84% of patients (32/38) stopped alpelisib treatment because of progressive disease, 8% (3/38) because of intolerance, one patient died because of cerebral hemorrhage during treatment, one patient withdrew their informed consent and one patient is still ongoing with the treatment. Conclusion: Our trial demonstrates activity of alpelisib in patients with PIK3CA mutated advanced breast cancer in later lines of treatment after treatment with CDK4/6 inhibitors with a clinical benefit rate of 26.3%. Discontinuation of therapy due to toxicity was seen in only 8% of patients, although toxicity induced dose reduction was needed in 29% of patients. These findings support the results of the BYLieve trial and additionally show efficacy of alpelisib in later lines of treatment for hormone receptor-positive advanced breast cancer. Citation Format: Rik Van Severen, Anne-Sofie De Crem, Hava Izci, Laurence Slembrouck, Isabelle Vanden Bempt, Hans Wildiers, Kevin Punie, Eline Naert, Ingeborg Hilderson, Ann Smeets, Ines Nevelsteen, Anne Deblander, Nynke Willers, Patrick Berteloot, Ignace Vergote, Sileny Han, Adriaan Vanderstichele, Giuseppe Floris, Christine Desmedt, Hannelore Denys, Patrick Neven. Efficacy and Safety of Alpelisib in PIK3CA-mutated, hormone receptor-positive advanced breast cancer after a CDK4/6 inhibitor: An Open-label, Multi-centre, Prospective, Single Arm Clinical Trial [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 PO5-21-10.

Detection of hotspot PIK3CA mutations in primary tumors and plasma-cfDNA of breast cancer patients using a novel highly sensitive CE-IVD KIT

Detection of hotspot PIK3CA mutations in primary tumors and plasma-cfDNA of breast cancer patients using a novel highly sensitive CE-IVD KIT

Abstract CT042: NCI10217: Phase Ib biomarker-driven tumor-agnostic combination (Combo) trial of copanlisib (Copa) and olaparib (Ola) in molecularly-selected patients (pts) with advanced cancers with PIK3CA hotspot, PTEN and DNA damage response (DDR) mutations

Abstract Background: Preclinically, PI3K and PARP inhibition synergize in cancers with DDR and PI3K pathway alterations. NCI10217 assessed the combo of Copa (pan-PI3K inhibitor) and Ola (PARP inhibitor) in tumors harboring mutations in PI3K/AKT or DDR pathways. Materials and Methods: Eligible pts had tumors with pathogenic PIK3CA hotspot, PTEN and DDR mutations. Copa was administered at 45 mg to 60 mg IV on Days (D) 1 and 15 or 1, 8 and 15 with Ola at 200 mg to 300 mg twice daily (BID) orally in 28-days cycles. Prior PARP and PI3K inhibitors were permitted. Fresh tumor biopsies and ctDNA were mandated at baseline and C1D15 and optional at the end of trial. Study objectives were safety, RP2D, pharmacokinetics, antitumor activity and translational analyses of serial tumor (WES; RNA-Seq; RPPA) and ctDNA samples. Results: 28 pts (M:F 8:20; ECOG PS 0:1 9:19; mean age 58y (28-76y) with breast (n=6), colorectal (n=5), prostate (n=4), endometrial (n=2), gastric (n=2), vaginal (n=2), appendix, cervix, head and neck, leiomyosarcoma, ovarian, peritoneal, and renal (n=1) cancers were enrolled. Pts with BRCA1/2 (n=12), PTEN (n=10), PIK3CA hotspot (n=6), ARID1A (n=4), CHEK2 (n=3), PALB2 (n=3), ATM (n=2), CDK12, CHEK1, MRE11A, RAD51C (n=1 each) mutations were enrolled. 10 pt tumors harbored >1 qualifying mutation. 17 (61%)/28 pts had ≥3 prior lines of therapy; 2 (7%)/28 had prior PARP inhibitors and 1 (4%)/28 had prior PI3K inhibitor. Common treatment-related toxicities included G1/2 mucositis (43%), nausea (43%), diarrhea (36%), anorexia (29%), fatigue (29%), maculo-papular rash (29%), hyperglycemia (25%), vomiting (25%); G3 transient hypertension (29%). Dose-limiting toxicities occurred in 3 (11%)/28 pts: 1 pt (G3 elevated transaminases) at Copa 45 mg (D1, D8 and D15) + Ola 200 mg BID, and 2 pts (G2 mucositis and maculo-papular rash, and G4 hyperglycemia) at Copa 60 mg (D1, D8, and D15) + Ola 300 mg BID. Of 22 pts evaluable for RECISTv1.1 criteria, 6 (27%)/22 pts achieved RECISTv1.1 partial responses (PR): 2 pts with BRCA1 mutation breast cancer; 1 pt with PIK3CA + PTEN + ARID1A mutation breast cancer; 1 pt with PTEN + PALB2 mutation breast cancer and prior PARP inhibitor exposure; 1 pt with BRCA2 mutation prostate cancer; 1 pt with BRCA2 + PTEN mutation prostate cancer. 8 (36%)/22 pts achieved RECISTv1.1 stable disease (SD); 2 (25%)/8 pts had SD≥6 months, including a pt with CA125 response (>50% reduction). Clinical benefit rate (SD≥6 months + PR) was 36%. Responses were deep (up to -100%) and durable (up to 37+ months). Based on these data, the RP2D was established at Copa 60 mg D1 and D15 + Ola 300 mg BID. Conclusion: Copa + Ola was safe and well-tolerated with clinical benefit observed in 36% of pts with advanced cancers with PIK3CA hotspot, PTEN and/or DDR mutations. Translational analyses are ongoing. Citation Format: Timothy A. Yap, Ecaterina E. Dumbrava, Jordi Rodon Ahnert, Apostolia M. Tsimberidou, David Hong, Sarina A. Piha-Paul, Daniel D. Karp, Siqing Fu, Aung Naing, Paula Pohlmann, Jessica R. Rhudy, Sheila B. Berenji-Jalaei, Ashley A. Cole, Christian Valladolid, Desirae Dufner, Bruno B. Bockorny, Andrea Bullock, Daniel Fein, Elizabeth Buchbinder, Atish Choudhury, Candace Haddox, Elizabeth Lee, Gerburg Wulf, Percy Ivy, Rabih Said, Geoffrey Shapiro, Funda Meric-Bernstam. NCI10217: Phase Ib biomarker-driven tumor-agnostic combination (Combo) trial of copanlisib (Copa) and olaparib (Ola) in molecularly-selected patients (pts) with advanced cancers with PIK3CA hotspot, PTEN and DNA damage response (DDR) mutations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 2 (Late-Breaking, Clinical Trial, and Invited Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(7_Suppl):Abstract nr CT042.

Abstract 2407: Detection of hotspot PIK3CA mutations in primary tumors and plasma-cfDNA of breast cancer patients using a novel highly sensitive CE-IVD kit

Abstract Introduction: Detection of PIK3CA mutations in primary tumors (FFPEs) and liquid biopsy samples is of increasing importance for treatment decisions in breast cancer. Oncolipsy PIK3CA kit (Pharmassist Ltd, Greece) is based on the combination of allele-specific priming, asymmetric PCR, and melting curve analysis. The CE-IVD kit can detect the presence of four PIK3CA hotspot mutations (E542K, E545K, E545Q, H1047R). The aim of the present study was to: a) evaluate the performance of this novel CE-IVD kit both in FFPEs and plasma-cfDNA samples from patients with metastatic breast cancer (MBC) and b) directly compare the derived results using the Oncolipsy PIK3CA kit with the cobas® PIK3CA mutation test (CE-IVD, Roche Diagnostics, Germany) in identical gDNAs isolated from FFPEs samples. Patients and methods: We analyzed 42 primary tumors (FFPEs) and 29 plasma-cfDNA samples from patients with estrogen receptor (ER) positive metastatic breast cancer. Genomic DNA was isolated from FFPEs using the QIAamp DNA FFPE Tissue Kit (Qiagen, Hilden, Germany), while cfDNA was extracted from 2.00 mL of plasma using the QIAamp DSP cNA Kit (Qiagen, Hilden, Germany). PIK3CA hotspot mutations were detected in the LightCycler® 2.0 (IVD instrument, Roche Diagnostics, Germany) using the highly sensitive Oncolipsy PIK3CA kit (analytical sensitivity 0.05%). A direct comparison study was performed using the cobas® PIK3CA Mutation Test on the cobas z 480 analyzer (IVD instrument, Roche Diagnostics, Germany). Results: In primary tumors the E545K mutation was detected in 22/42 (52.4%), the E542K and H1047R mutations were detected in 11/42 (26.2%) and 4/42 (9.5%) of primary tumor samples, respectively, while the E545Q mutation was not detected in any FFPE sample tested. At least one PIK3CA mutation was detected in 14/29 (48.3%) plasma-cfDNA samples. More specifically the E545K mutation was detected in 11/29 (38%), the H1047R mutation in 3/29 (10.4%) and the E542K mutation in 2/29 (6.9%) while the E545Q mutation was not detected in any plasma-cfDNA sample tested. In FFPEs, as expected, PIK3CA mutation frequency was higher compared to plasma-cfDNA. Direct comparison of the results derived using these two commercially available kits, the Oncolipsy CE-IVD kit and the cobas PIK3CA mutation test, using the same gDNA isolated from 42 FFPEs revealed a concordance of 34/42 (81%). Conclusions: The commercially available Oncolipsy PIK3CA CE-IVD kit is highly sensitive and specific for the detection of four PIK3CA hotspot mutations in primary tumors and plasma-cfDNA. Acknowledgement: This study has been financially supported by the European Union and Greek national funds through the Operational Program Competitiveness, Entrepreneurship and Innovation, under the call RESEARCH - CREATE - INNOVATE (project code: T1RCI-02935). Citation Format: Stavroula Smilkou, Dimitra Stergiopoulou, Eleni Tzanikou, Loukas Kaklamanis, Ioanna Balgkouranidou, Helena Linardou, Flora Zagouri, Evangelia Razi, Stylianos Kakolyris, Amanda Psyrri, Christos Papadimitriou, Ioanna Koukli, Athina Markou, Evi Lianidou. Detection of hotspot PIK3CA mutations in primary tumors and plasma-cfDNA of breast cancer patients using a novel highly sensitive CE-IVD kit [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 2407.

Abstract 582: Oncogenic PIK3CA fortifies immune determinants in vascular cancers

Abstract Angiosarcomas are a group of vascular cancers that form malignant blood vessels. These malignancies are seemingly inflamed primarily due to their pathognomonic nature, which consists of irregular endothelium and tortuous blood channels. The malignant vascular spaces host a variety of blood and immune components, where a controlled scavenging system is necessary for tumor maintenance. Oncogenes may convey molecular signals to foster the tumor immune niche, and PIK3CA mutations that induce continuous activation of the PI3K pathway occur in a subset of angiosarcomas. Despite the undoubtedly oncogenic properties of PIK3CA mutations, the mechanistic role of these mutations - particularly the potential for controlling the hemato-endothelial system in angiosarcomas - remains undetermined. In this study, we demonstrate the functional consequences of oncogenic PIK3CA and its molecular properties in angiosarcoma cells. We created isogenic cell clones from two angiosarcoma cell lines engineered to harbor hotspot mutations in PIK3CA using CRISPR/Cas9: two homozygous PIK3CA H1047R cell clones (C8 and C35) and one wild-type (WT) clone were generated from DHSA-1426 angiosarcoma cells; and one homozygous mutant clone was created from COSB cells. We found that PIK3CA mutant cells constitutively activated the PI3K/AKT/mTOR pathway at a greater level than that of WT cells. Bulk- and single cell(sc)-RNA-seq data revealed that mutant cells enriched gene sets associated with PI3K signaling and other oncogenic pathways including KRAS, MAPK, and TGF-beta. Also, mutant cells significantly increased cytokines regulating immune cell migration and chemotaxis such as IL-8 and MCP-1. In addition to the common features, we identified functional and molecular divergence between mutant clones. Noticeable changes in cellular morphology, growth kinetics, and tube-forming capacity were observed between two mutant clones. C35 mutant cells were more sensitive to both pan-PI3K and PI3K-alpha specific inhibitor, and DNA damage was greater than in the C8 clone. C35 cells enhanced activation of IL-6/STAT3 signaling compared to C8, despite the increment of the aforementioned immune cytokines in both mutants. Moreover, our comprehensive analysis of bulk- and sc-RNA-seq, ATAC-seq, and metabolomics data identified molecular signatures associated with metabolic vulnerabilities of C35 cells. In summary, we demonstrate that oncogenic PIK3CA perpetuates PI3K signaling activation and reinforces a supply for immune signaling. Furthermore, our data suggest that PIK3CA mutations contribute to establishing cellular heterogeneity that reveals a spectrum of vascular, immunogenic, and metabolic activities. Our ongoing work involves developing an experimental model of angiosarcoma using induced pluripotent stem cells to examine if oncogenic PIK3CA controls immune determinants during malignant endothelial transformation. Citation Format: Donghee Lee, Emma Kozurek, Md Abdullah, Rong Li, Erin B. Dickerson, Jong Hyuk Kim. Oncogenic PIK3CA fortifies immune determinants in vascular cancers [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 582.

Abstract 3700: Genomic alterations on first-line panitumumab plus FOLFIRI in metastatic colorectal cancer

Abstract Background: IMPROVE is a randomized, non-comparative multicenter, phase 2 study evaluating continuous or intermittent FOLFIRI/PANI, in first-line in patients (pts) with unresectable RAS/BRAF wild-type metastatic colorectal cancer (mCRC). In this trial intermittent FOLFIRI/PANI strategy produced a longer progression-free survival (PFS) on treatment, 17.6 months (mts) vs 11.3 mts, a reduced skin severe toxicity, 18% vs 30%, without any detrimental effect on overall survival (OS), 36.2 mts vs 36.2 mts. The trial also included a prospective genomic alterations (GAs) analysis on circulating tumor DNA with the aim to explore emergence of GAs under the selective pressure of FOLFIRI/PANI. Methods: We analyzed paired plasma samples (basal and PD) by a commercially available NGS panel enabled to simultaneously analyze KRAS, NRAS, BRAF and PIK3CA hotspot mutations from blood samples. Among them, inspecting default calling parameters on proprietary analysis software (Ion Reporter software 5.2.0), only variants with ⩾5X allele coverage and a quality score ⩾20, within an amplicon that covered at least 1000X alleles was considered. As clonality, the threshold of 0.5% of variant allele frequency (VAF) was established to classify mutations as clonal (VAF⩾0.5%) or subclonal (VAF<0.5%). Results: Of the 137 pts enrolled in the trial, GAs basal analyses were available for 84 pts. Among these, in 55 (65.5%) no GAs were detected (ND). In the remaining cases, the analysis relieved the presence of mutations for PIK3CA (N=14), KRAS (N=12), NRAS (N=2) and BRAF (N=1). According to the clonality threshold, these GAs were classified as subclonal (SC) in 12 cases (14.3%) and clonal (CL) in 17 (20.2%) cases. Survival analysis according to basal GAs clonality showed a median PFS of 16.6 mts (95% IC 13.0-20.2), 12 mts (95% IC 9.1-14.9) and 25.8 mts (95% IC 17.2-34.5) for ND, CL and SC group, respectively. Median OS was 47.7 mts for ND group (95% IC 34.9-60.5), 26.8 mts for CL (95% IC 25.8-27.8) and not reached for SC group. Moreover, we performed GAs analysis on 61 cases of which basal and PD samples were available. Forty-two cases (68.9%) resulted ND, 7 (11.5%) with SC and 12 (19.7%) with CL GAs.At PD, among 42 ND basal cases, 29 remained ND (69%), 8 (19%) and 5 cases (11.9%) developed SC and CL GAs, respectively. In the SC group, 1 kept SC (14.3%), 4 (57.1%) and 2 (28.6%) cases became ND and CL GAs, respectively. In the CL group, 10 (83.3%) kept CL GAs, 1 (8.3%) case became ND and 1 (8.3%) CL. Conclusions: These findings suggest that classical GAs associated with anti-EGFR resistance are infrequent with up-front use of anti-EGFR/chemotherapy. Moreover, our data show that basal SC GAs rarely evolve to CL GAs at progression disease and do not affect survival of pts with anti-EGFR/chemotherapy treatment. An update will be provided at the congress. NCT04425239 Citation Format: Antonio Avallone, Francesco Giuliani, Guglielmo Nasti, Vincenzo Montesarchio, Giuseppe Santabarbara, Silvana Leo, Umberto Malapelle, Gerardo Rosati, Claudio Lotesoriere, Emiliano Tamburini, Alfredo Colombo, Francesco Pepe, Claudia Cardone, Alessandra Leone, Carlo Vitagliano, Gianluca Russo, Giancarlo Troncone, Diana Giannarelli, Alfonso De Stefano, Alfredo Budillon. Genomic alterations on first-line panitumumab plus FOLFIRI in metastatic colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3700.

C-MET-positive circulating tumor cells and cell-free DNA as independent prognostic factors in hormone receptor-positive/HER2-negative metastatic breast cancer

BackgroundEndocrine therapy resistance in hormone receptor-positive/HER2-negative (HR+/HER2−) breast cancer (BC) is a significant clinical challenge that poses several unmet needs in the management of the disease. This study aimed to investigate the prognostic value of c-MET-positive circulating tumor cells (cMET+ CTCs), ESR1/PIK3CA mutations, and cell-free DNA (cfDNA) concentrations in patients with hormone receptor-positive (HR+) metastatic breast cancer (mBC).MethodsNinety-seven patients with HR+ mBC were prospectively enrolled during standard treatment at Samsung Medical Center. CTCs were isolated from blood using GenoCTC® and EpCAM or c-MET CTC isolation kits. PIK3CA and ESR1 hotspot mutations were analyzed using droplet digital PCR. CfDNA concentrations were calculated using internal control copies from the ESR1 mutation test. Immunocytochemistry was performed to compare c-MET overexpression between primary and metastatic sites.ResultsThe proportion of c-MET overexpression was significantly higher in metastatic sites than in primary sites (p = 0.00002). Survival analysis showed that c-MET+ CTC, cfDNA concentration, and ESR1 mutations were significantly associated with poor prognosis (p = 0.0026, 0.0021, and 0.0064, respectively) in HR+/HER2− mBC. By contrast, EpCAM-positive CTC (EpCAM+ CTC) and PIK3CA mutations were not associated with progression-free survival (PFS) in HR+/HER2− mBC. Multivariate analyses revealed that c-MET+ CTCs and cfDNA concentration were independent predictors of PFS in HR+/HER2− mBC.ConclusionsMonitoring c-MET+ CTC, rather than assessing c-MET expression in the primary BC site, could provide valuable information for predicting disease progression, as c-MET expression can change during treatment. The c-MET+ CTC count and cfDNA concentration could provide complementary information on disease progression in HR+ /HER2− mBC, highlighting the importance of integrated liquid biopsy.