Activating Mutations In PIK3CA Research Articles

Abstract P4-09-04: Prevalence of phosphatidylinositol-3-kinase (PI3K) pathway alterations and co-alteration of other markers in breast cancer

Abstract Background: PI3K/AKT signaling pathway is often activated in breast cancer (BC), through mutations in PIK3CA or AKT1, and alterations in PTEN, thus promoting cell survival. PI3K and AKT inhibitors have been shown to have significant activity against tumor progression and to overcome resistance in BC. We aim to explore the prevalence of PI3K pathway alterations and co-expression with other markers in different BC subtypes. This approach could allow identification of novel drug combinations that have the potential to elicit synergistic growth inhibition and be further explored in the clinical trial setting. Methods: Molecular profiles of 4895 female and male BC cases submitted to Caris Life Sciences were reviewed to identify pathogenic or presumed pathogenic mutations in PIK3CA, AKT1, PTEN, PIK3R1 and PIK3R2 using 592-gene next generation sequencing (NGS; average read depth 500 ×). Cases with loss of PTEN by IHC were also included. Co-mutation frequency with PIK3CA-AKT1-PTEN alterations were examined, including homologous recombination deficiency (HRD) genes and DNA damage response (DDR) pathways, markers of response to immune-oncology (IO) agents and RAS signaling pathway. Cases were classified in BC subtypes according to the ASCO-CAP guidelines. Results: The median age was 58 (range: 17-90). Gender frequency and primary/ metastatic site frequency were similar across BC subtypes. 3558 (72.7%) cases had at least one alteration in the PIK3CA-AKT1-PTEN pathway: 1472 (30.1%) cases harbored a PIK3CA mutation, 174 (3.6%) harbored an AKT1 mutation, and 2682 (54.8%) had PTEN alterations (PTEN mutation in 344, 7.0% and/or PTEN loss by IHC in 2516, 51.4% of cases). The most common hotspot mutations in PIK3CA were in the kinase domain (H1047R in 567 cases, 38.5% of all PIK3CA alterations) and in the helical domain (E545K in 304 cases, 20.7% of all PIK3CA alterations). Uncommon activating PIK3CA mutations were seen in 8.4% of breast tumors. The single hotspot mutation, E17K, was the most common AKT1 mutation (n=164, 94.3% of all AKT1 mutations). 81 (1.7%) tumors harbored a PIK3R1 mutation, with 66 unique alterations identified (4 pathogenic, 55 presumed pathogenic), and 4 (0.08%) cases harbored a PIK3R2 mutation (G373R mutation). With respect to the different BC subtypes, PIK3CA was the most frequent alteration in HER2 positive BC (present in 96.2% of mutated cases). Within HER2 negative subtypes, PTEN was most frequently altered and PTEN mutation or PTEN loss by IHC was present in 79.3% of mutated cases. Triple negative breast cancer (TNBC) was the subtype with the lowest frequency of PIK3CA mutations (18.0% in TNBC vs. 37% in other subtypes). The frequency of selected co-mutations with PIK3CA-AKT1-PTEN alterations is illustrated in table 1. Notable co-alterations in this cohort include increased PD-L1 expression and high tumor mutational burden (TMB). There were no significant increases in the frequency of mutations in DDR pathway mutations (not shown) in the PIK3CA-AKT1-PTEN altered cohort. Conclusions: We observed a high prevalence of expected hotspot mutations in PIK3CA and AKT1 across BC subtypes. There was a significant increase in PD-L1 expression in tumor cells, and high TMB in PIK3CA-AKT1-PTEN mutated cohorts. A similar association was seen with RAS signaling pathways. Further development of drugs that affect the PIK3CA-AKT1-PTEN pathway in all BC subtypes and combination with drugs that target the immune system may be of interest. Table 1. Selected co-alterations based on statistical significancePathwayGene/ ProteinAll subtypes (%)HR+ HER2+ (%)HR- HER2+ (%)HR+HER2- (%)TNBC (%)MTWTMTWTMTWTMTWTMTWTHomologous recombinationBRCA13.02.71.00.60.00.80.8*1.8*6.16.0BRCA24.15.41.02.53.62.34.1*7.9*4.43.0PALB20.7*1.3*0.00.00.00.00.5*2.5*0.90.3Possible predictors of IO benefitPD-149.850.038.552.266.766.737.541.766.058.1PD-L1 (SP142)6.9*4.2*3.30.78.14.93.33.011.68.1(Tumor Cells)PD-L1 (SP142)29.226.650.018.825.027.312.916.742.140.4(Immune Cells)MSI0.70.60.00.01.20.80.80.40.71.2TMB-High (≥ 10 mut/Mb)22.9*18.8*36.0*17.2*29.825.921.2*16.6*23.621.3Chromatin remodelingARID1A12.4*18.6*19.423.87.118.917.121.55.89.6ARID20.70.80.01.90.00.70.80.60.60.9RAS-RAF-MEK-ERK HRAS0.7*0.1*0.00.00.00.00.20.11.40.3KRAS2.0*1.1*1.00.00.00.01.91.22.22.0NRAS0.20.00.00.00.00.00.20.00.30.0BRAF0.50.11.00.01.20.00.60.30.40.0OthersTP5360.9*53.1*66.360.885.586.738.4*25.6*84.786.4CDH110.3*6.1*9.1*2.5*4.82.215.1*9.6*4.9*2.3*NF16.2*2.1*9.5*0.8*2.73.65.8*1.8*6.7*2.8*RB15.5*2.6*2.21.33.63.03.9*1.7*7.85.0ERBB22.3*3.4*3.03.13.56.73.23.51.0*2.3*Notes: MT = at least 1 pathogenic mutation in PIK3CA, AKT1, or PTEN or PTEN loss by IHC. WT = no pathogenic mutations in PIK3CA, AKT1, and PTEN.*statistically significant difference between MT and WT Citation Format: Katia Khoury, Antoinette Tan, Andrew Elliott, Joanne Xiu, Zoran Gatalica, Arielle L Heeke, Claudine Isaacs, Paula R Pohlmann, Lee S Schwartzberg, Michael Simon, Michael W Korn, Sandra M Swain, Filipa Lynce. Prevalence of phosphatidylinositol-3-kinase (PI3K) pathway alterations and co-alteration of other markers in breast cancer [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P4-09-04.

The Angiosarcoma Project: enabling genomic and clinical discoveries in a rare cancer through patient-partnered research.

Despite rare cancers accounting for 25% of adult tumors1, they are difficult to study due to the low disease incidence and geographically dispersed patient populations, which has resulted in significant unmet clinical needs for patients with rare cancers. We assessed whether a patient-partnered research approach using online engagement can overcome these challenges, focusing on angiosarcoma, a sarcoma with an annual incidence of 300 cases in the United States. Here we describe the development of the Angiosarcoma Project (ASCproject), an initiative enabling US and Canadian patients to remotely share their clinical information and biospecimens for research. The project generates and publicly releases clinically annotated genomic data on tumor and germline specimens on an ongoing basis. Over 18 months, 338 patients registered for the ASCproject, which comprises a large proportion of all patients with angiosarcoma. Whole-exome sequencing (WES) of 47 tumors revealed recurrently mutated genes that included KDR, TP53, and PIK3CA. PIK3CA-activating mutations were observed predominantly in primary breast angiosarcoma, which suggested a therapeutic rationale. Angiosarcoma of the head, neck, face and scalp (HNFS) was associated with a high tumor mutation burden (TMB) and a dominant ultraviolet damage mutational signature, which suggested that for the subset of patients with angiosarcoma of HNFS, ultraviolet damage may be a causative factor and that immune checkpoint inhibition may be beneficial. Medical record review revealed that two patients with HNFS angiosarcoma had received off-label therapeutic use of antibody to the programmed death-1 protein (anti-PD-1) and had experienced exceptional responses, which highlights immune checkpoint inhibition as a therapeutic avenue for HNFS angiosarcoma. This patient-partnered approach has catalyzed an opportunity to discover the etiology and potential therapies for patients with angiosarcoma. Collectively, this proof-of-concept study demonstrates that empowering patients to directly participate in research can overcome barriers in rare diseases and can enable discoveries.

Torin2 Exploits Replication and Checkpoint Vulnerabilities to Cause Death of PI3K-Activated Triple-Negative Breast Cancer Cells.

Frequent mutation of PI3K/AKT/mTOR signaling pathway genes in human cancers has stimulated large investments in targeted drugs but clinical successes are rare. As a result, many cancers with high PI3K pathway activity, such as triple-negative breast cancer (TNBC), are treated primarily with chemotherapy. By systematically analyzing responses of TNBC cells to a diverse collection of PI3K pathway inhibitors, we find that one drug, Torin2, is unusually effective because it inhibits both mTOR and other PI3K-like kinases (PIKKs). In contrast to mTOR-selective inhibitors, Torin2 exploits dependencies on several kinases for S-phase progression and cell-cycle checkpoints, thereby causing accumulation of single-stranded DNA and death by replication catastrophe or mitotic failure. Thus, Torin2 and its chemical analogs represent a mechanistically distinct class of PI3K pathway inhibitors that are uniquely cytotoxic to TNBC cells. This insight could be translated therapeutically by further developing Torin2 analogs or combinations of existing mTOR and PIKK inhibitors.

Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors.

Activating mutations in PIK3CA are frequent in human breast cancer, and phosphoinositide 3-kinase alpha (PI3Kα) inhibitors have been approved for therapy. To characterize determinants of sensitivity to these agents, we analyzed PIK3CA-mutant cancer genomes and observed the presence of multiple PIK3CA mutations in 12 to 15% of breast cancers and other tumor types, most of which (95%) are double mutations. Double PIK3CA mutations are in cis on the same allele and result in increased PI3K activity, enhanced downstream signaling, increased cell proliferation, and tumor growth. The biochemical mechanisms of dual mutations include increased disruption of p110α binding to the inhibitory subunit p85α, which relieves its catalytic inhibition, and increased p110α membrane lipid binding. Double PIK3CA mutations predict increased sensitivity to PI3Kα inhibitors compared with single-hotspot mutations.

Genotype correlates with clinical severity in PIK3CA-associated lymphatic malformations.

Lymphatic malformations (LMs) are congenital, nonneoplastic vascular malformations associated with postzygotic activating PIK3CA mutations. The mutation spectrum within LMs is narrow, with the majority having 1 of 3 hotspot mutations. Despite this relative genetic homogeneity, clinical presentations differ dramatically. We used molecular inversion probes and droplet digital polymerase chain reaction to perform deep, targeted sequencing of PIK3CA in 271 affected and unaffected tissue samples from 81 individuals with isolated LMs and retrospectively collected clinical data. Pathogenic PIK3CA mutations were identified in affected LM tissue in 64 individuals (79%) with isolated LMs, with variant allele fractions (VAFs) ranging from 0.1% to 13%. Initial analyses revealed no correlation between VAF and phenotype variables. Recognizing that different mutations activate PI3K to varying degrees, we developed a metric, the genotype-adjusted VAF (GVAF), to account for differences in mutation strength, and found significantly higher GVAFs in LMs with more severe clinical characteristics including orofacial location or microcystic structure. In addition to providing insight into LM pathogenesis, we believe GVAF may have broad applicability for genotype-phenotype analyses in mosaic disorders.

A Phase 1b Study of Cetuximab and BYL719 (Alpelisib) Concurrent with Intensity Modulated Radiation Therapy in Stage III-IVB Head and Neck Squamous Cell Carcinoma

Activation of the PI3K/mTOR signaling pathway is common in head and neck squamous cell carcinoma (HNSCC). BYL719 is an α-specific PI3K inhibitor that is synergistic and efficacious when combined with cetuximab, a Food and Drug Administration-approved radiosensitizing agent in the treatment of HNSCC. The agent independently has been shown to enhance radiosensitivity. This study evaluates the addition of BYL719 to cetuximab and radiation in the treatment of locally advanced HNSCC. This is a single-institution, phase 1 study. Patients with American Joint Committee on Cancer seventh edition stage III to IVB HNSCC received standard cetuximab (400 mg/m2 intravenous loading dose) before intensity modulated radiation therapy (IMRT) followed by 250 mg/m2 weekly infusions during IMRT. BYL719 was given orally during IMRT in 3 dose levels: (1) 200 mg/d, (2) 250 mg/d, or (3) 300 mg/d in a standard 3 + 3 dose-escalation design. Eleven patients were evaluable. Dose level 2 was the maximum tolerated dose for BYL719. Two patients on dose level 3 had dose-limiting toxicities of oral mucositis that required a dose reduction of BYL719. One patient on dose level 2 had a dose-limiting toxicity of nausea that led to withdrawal of on-study treatment. Related grade 3 or higher adverse events consisted of decreased lymphocyte count, oral mucositis, dysphagia, hyperglycemia, maculopapular rash, and palmar-plantar erythrodysesthesia syndrome. All 11 patients had a complete response on posttreatment imaging, and 10 remain disease free. Of the 8 patients with mutational analysis, 1 had an activating PIK3CA mutation associated with a rapid response on serial intratreatment magnetic resonance imaging scans. The recommended phase 2 dose of BYL719 is 250 mg/d in combination with cetuximab and IMRT in patients with locally advanced HNSCC. Further evaluation of the addition of BYL719 to the platinum-sparing regimen of cetuximab and IMRT in the treatment of locally advanced HNSCC is warranted.

318P - Association between PIK3CA mutation status and development of brain metastases in HR+/HER2- metastatic breast cancer

BackgroundCNS metastases is a devastating complication of breast cancer, occurring in approximately 10%–15% of patients with metastatic breast cancer (MBC) and resulting in median survival of less than one year in historic cohorts. Biological factors that govern metastases to the brain, including the role of activating PIK3CA mutations, the most common actionable alterations in HR+/HER2- MBC, are poorly understood. MethodsIn this retrospective cohort study, we determined the cumulative incidence of brain metastasis in PIK3CA mutant and PIK3CA non-mutant HR+/HER2- MBC patients treated at the Massachusetts General Hospital and genotyped during their routine clinical care with a highly sensitive multiplexed assay for real time mutation profiling of clinical samples. ResultsIn the overall cohort of 307 patients, 120 patients (39.1%) had PIK3CA mutant disease and 187 patients (60.9%) had PIK3CA non-mutant disease, comparable to previously published results. Median OS from the time of diagnosis of metastatic disease was 3.96 yrs (95% CI 3.40-4.87 yrs) for PIK3CA mutant patients and 4.43 yrs (95% CI 3.82-5.32 yrs) for PIK3CA non-mutant patients, p=0.6. 22.44% of patients with HR+/HER2- disease developed brain metastases; 30.83% of PIK3CA mutant patients and 17.11% of PIK3CA non-mutant patients developed CNS metastases, p=0.0049. Median time to the development of CNS disease was 8.61 yrs for PIK3CA mutant subset and not reached (NR) for PIK3CA non-mutant subset, p=0.0086. Among patients with CNS metastases, median OS for PIK3CA mutant patients was 0.48 yrs (95% CI 0.27-0.74) and for PIK3CA non-mutant it was 1.09 yrs (95% CI 0.39-2.27), p=0.019). ConclusionsBrain metastases are common in HR+/HER2- MBC. This incidence of brain metastases is particularly high among patients with HR+/HER2- tumors harboring a PIK3CA mutation, where it approaches the incidence historically seen in HER2+ MBC. Early recognition of symptoms potentially related to brain metastases is important even in HR+/HER2- subtype of breast cancer. High incidence of brain metastases in PIK3CA mutant HR+/HER2- MBC warrants development of blood-brain barrier penetrant agents targeting the PI3K/AKT/mTOR pathway. Legal entity responsible for the studyThe authors. FundingHas not received any funding. DisclosureS. Isakoff: Advisory / Consultancy, Research grant / Funding (institution): Myriad; Advisory / Consultancy, Research grant / Funding (institution): Puma; Advisory / Consultancy, Research grant / Funding (institution): Immunomedics; Advisory / Consultancy, Research grant / Funding (institution): Mylan; Advisory / Consultancy, Research grant / Funding (institution): Genentech; Advisory / Consultancy, Research grant / Funding (institution): Pharmamar; Advisory / Consultancy, Research grant / Funding (institution): Abbvie; Advisory / Consultancy, Research grant / Funding (institution): OncoPep; Advisory / Consultancy, Research grant / Funding (institution): Merck; Advisory / Consultancy, Research grant / Funding (institution): AstraZeneca. A. Bardia: Advisory / Consultancy, Research grant / Funding (institution): Genentech/Roche; Advisory / Consultancy, Research grant / Funding (institution): Immunomedics; Advisory / Consultancy, Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Pfizer; Advisory / Consultancy, Research grant / Funding (institution): Merck; Advisory / Consultancy, Research grant / Funding (institution): Radius Health; Advisory / Consultancy, Research grant / Funding (institution): Specturm; Advisory / Consultancy, Research grant / Funding (institution): Taiho Pharmaceutical; Research grant / Funding (institution): Mersana; Research grant / Funding (institution): Innocrin; Research grant / Funding (self): Biothernostics. P.K. Brastianos: Research grant / Funding (institution): Merck; Research grant / Funding (institution): Pfizer; Research grant / Funding (institution): Bristol-Myer Squibb; Advisory / Consultancy: Genentech-Roche; Advisory / Consultancy: Merck; Advisory / Consultancy: Lily; Advisory / Consultancy: TESARO; Advisory / Consultancy: AngioChem. D. Juric: Advisory / Consultancy, Research grant / Funding (self), Research grant / Funding (institution): Novartis; Advisory / Consultancy, Research grant / Funding (institution): Genentech; Advisory / Consultancy, Research grant / Funding (institution): Eisai; Advisory / Consultancy, Research grant / Funding (institution): EMD Serono; Advisory / Consultancy, Research grant / Funding (institution): Syros; Advisory / Consultancy: Ipsen; Research grant / Funding (institution): Takeda; Research grant / Funding (institution): Celgene; Research grant / Funding (institution): Placon Therapeutics. All other authors have declared no conflicts of interest.

PIK3CA mutations in lipomatosis of nerve with or without nerve territory overgrowth.

Lipomatosis of nerve is a rare malformation characterized by a fibrolipomatous proliferation within peripheral nerve. Lipomatosis of nerve most frequently involves the median nerve, and manifests clinically as a compressive neuropathy. However, 30-60% of cases are associated with tissue overgrowth within the affected nerve's territory (e.g., macrodactyly for lipomatosis of nerve in the distal median nerve). Somatic activating PIK3CA mutations have been identified in peripheral nerve from patients with lipomatosis of nerve with type I macrodactyly, which is now classified as a PIK3CA-related overgrowth spectrum disorder. However, the PIK3CA mutation status of histologically confirmed lipomatosis of nerve, including cases involving proximal nerves, and cases without territory overgrowth, has not been determined. Fourteen histologically confirmed cases of lipomatosis of nerve involving the median (N = 6), brachial plexus (N = 1), ulnar (N = 3), plantar (N = 2), sciatic and superficial peroneal nerves (N = 1 each) were included. Ten cases had nerve territory overgrowth, ranging from macrodactyly to hemihypertrophy; and four cases had no territory overgrowth. Exome sequencing revealed "hotspot" activating PIK3CA missense mutations in 6/7 cases. Droplet digital polymerase chain reaction for the five most common PIK3CA mutations (p.H1047R, p.H1047L, p.E545K, p.E542K, and p.C420R) confirmed the exome results and identified an additional six cases with mutations (12/14 total). PIK3CA mutations were found in 8/10 cases with territory overgrowth (N = 7 p.H1047R and N = 1 p.E545K), including two proximal nerve cases with extremity overgrowth, and 4/4 cases without territory overgrowth (p.H1047R and p.H1047L, N = 2 each). The variant allele frequency of PIK3CA mutations (6-32%) did not correlate with the overgrowth phenotype. Three intraneural lipomas had no detected PIK3CA mutations. As PIK3CA mutations are frequent events in lipomatosis of nerve, irrespective of anatomic site or territory overgrowth, we propose that all phenotypic variants of this entity be classified within the PIK3CA-related overgrowth spectrum and termed "PIK3CA-related lipomatosis of nerve".

Practical Treatment Strategies and Future Directions After Progression While Receiving CDK4/6 Inhibition and Endocrine Therapy in Advanced HR+/HER2− Breast Cancer

Cyclin-dependent kinase 4/6 inhibitors (CDK4/6i) in combination with backbone endocrine therapy have markedly improved progression-free survival and overall survival over endocrine therapy alone in advanced hormone receptor–positive, HER2-negative (HR+/HER2−) breast cancer and are the standard of care in the first- or second-line setting. There are few data to drive decision making for subsequent treatment strategies after inevitable disease progression after CDK4/6i. Information about the genomic landscape of CDK4/6i-resistant disease is emerging. Resistance mechanisms appear to be varied, but mutations in PIK3CA and ESR1, which can be acquired while receiving treatment, are frequent. Activating PIK3CA mutations are present in up to 35% of patients and are now the most actionable genomic alteration in HR+/HER2− advanced breast cancer with the recent approval of alpelisib and fulvestrant. Everolimus-based combinations and chemotherapy appear to have continued efficacy after progression while receiving CDK4/6i, although historical data on benefit include CDK4/6i-naive patients. Use of selective estrogen down-regulators over aromatase inhibitors is best once the patient has an acquired ESR1 mutation. Tumor biopsy with genomic sequencing and repeat biomarker analysis in patients with CDK4/6i- and endocrine-resistant disease will be integral to guide subsequent treatment strategies and to inform clinical trial eligibility. Promising novel therapeutics in CDK4/6i-resistant disease including oral selective estrogen down-regulators, fibroblast growth factor receptor antagonists, and immunotherapy will be discussed.

MAPK- and AKT-activated thyroid cancers are sensitive to group I PAK inhibition.

The number of individuals who succumb to thyroid cancer has been increasing and those who are refractory to standard care have limited therapeutic options, highlighting the importance of developing new treatments for patients with aggressive forms of the disease. Mutational activation of MAPK signaling, through BRAF and RAS mutations and/or gene rearrangements, and activation of PI3K signaling, through mutational activation of PIK3CA or loss of PTEN, are well described in aggressive thyroid cancer. We previously reported overactivation and overexpression of p21-activated kinases (PAKs) in aggressive human thyroid cancer invasive fronts and determined that PAK1 functionally regulated thyroid cancer cell migration. We reported mechanistic crosstalk between the MAPK and PAK pathways that are BRAF-dependent but MEK independent, suggesting that PAK and MEK inhibition might be synergistic. In the present study, we tested this hypothesis. Pharmacologic inhibition of group I PAKs using two PAK kinase inhibitors, G-5555 or FRAX1036, reduced thyroid cancer cell viability, cell cycle progression and migration and invasion, with greater potency for G-5555. Combination of G-5555 with vemurafenib was synergistic in BRAFV600E-mutated thyroid cancer cell lines. Finally, G-5555 restrained thyroid size of BRAFV600E-driven murine papillary thyroid cancer by >50% (P < 0.0001) and reduced carcinoma formation (P = 0.0167), despite maintenance of MAPK activity. Taken together, these findings suggest both that group I PAKs may be a new therapeutic target for thyroid cancer and that PAK activation is functionally important for BRAFV600E-mediated thyroid cancer development.

Abstract 3172: Prognostic and therapeutic implication of programmed death ligand 1 (PD-L1), microsatellite instability, and PIK3CA gene in lipoarcoma

Abstract Background: With the promising efficacies with personalized approach, we tested clinically relevant molecular target programmed death ligand 1 (PD-L1), microsatellite Instability (MSI), and PIK3CA molecules in liposarcoma to provide practical guide. Methods: A consecutive series of 74 liposarcoma patients who underwent curative resection between 2005 and 2016 were assessed using immuno-molecular panels: PD-L1 (22C3 pharmDx assay) and mismatch repair proteins (MLH1, PMS2, MSH2, and MSH6) by immunohistochemistry (IHC), MSI using PCR, and PIK3CA mutation/amplification using pyrosequencing and fluorescence in situ hybridization. Results: For all the cases, PD-L1 was positive only in tumor infiltrating lymphocytes (TILs), while no PD-L1 expression was found on tumor cell and 23% were tumors with PD-L1+ TILs. PD-L1+ TILs was significantly predominant in abdominal site (P=0.004) and had significantly longer overall survival than PD-L1- TILs (5 year OS 84.4% vs 60.8%, P=0.007). Regarding the MSI status, 2 well differentiated liposarcoma showed MSI [MSI-H (n=1) and MSI-L (n=1)]. For concordance with mismatch repair protein using IHC, only 1 out of 8 with concurrent loss of MLH1, MSH6, and PMS2 showed MSI-H (D2S123, D17S250). Activating PIK3CA mutation was detected in 7 patients [9.5%, exon 9 (n=4) and exon 20 (n=3) mutation] and 6 cases were PD-L1-TIL group. PIK3CA copy number gain were detected in 18 (24.3%) cases and significantly associated with PD-L1+TIL tumors (P=0.045). Conclusions: With our comprehensive immuno-moleuclar panel, liposarcoma need to be categorized based on the molecular genomic subtype and this may facilitate the development of successful future clinical trials using molecular agents. Citation Format: Hyo Song Kim, Hyae Min Jeon, Jae Seok Lee, Soo Hee Kim, Young Han Lee, Hyuk Hur, Sung Hoon Kim, Seung Hyun Kim, Hei-Cheul Jeung. Prognostic and therapeutic implication of programmed death ligand 1 (PD-L1), microsatellite instability, and PIK3CA gene in lipoarcoma [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 3172.

Abstract 336: A recombinant human protein targeting HER2 overcomes drug resistance in HER2-positive breast cancer

Abstract Background &amp; Goals: HER2 is an oncogenic receptor tyrosine kinase (RTK) implicated in several types of human cancer. It is strongly expressed in about 20% of breast cancer (BC), known as HER2-positive BC (HER2-BC), due to gene amplification. HER2 amplification or overexpression is a strong predictor of poor disease prognosis. Several HER2-targeting drugs are available for treating HER2-BC, including monoclonal antibodies trastuzumab (Ttzm) and pertuzumab, T-DM1 (Ttzm coupled to a microtubule inhibitor), and tyrosine kinase inhibitors (TKIs) lapatinib and neratinib. While these agents have greatly improved disease outcomes, primary and acquired drug resistance, including cross-resistance, is common. Overcoming drug resistance remains a major unmet medical need in HER2-BC. Notably, HER2 remains overexpressed in drug-resistant HER2-BC cells. We recently found that recombinant human peptidase D (PEPD), also known as prolidase, strongly downregulates HER2 and EGFR in cancer cells in vitro and in vivo via its binding to HER2 and EGFR. The enzymatic activity of PEPD plays no role in its modulation of HER2 and EGFR, and we subsequently focused on recombinant PEPDG278D, an enzymatically inactive mutant (point mutation at codon 278). Our objective in the present study is to determine whether PEPDG278D is active in preclinical models of HER2-BC resistant to clinically available HER2 inhibitors and if so, its mechanism of action. Results: PEPDG278D was exceedingly effective against HER2-BC cells that are resistant to Ttzm and other HER2 inhibitors. The cells carried activating PIK3CA mutations, low expression of PTEN, and/or cyclin E overexpression. All the cell lines also overexpressed MUC4 which shields HER2 from Ttzm and stabilizes HER2. However, PEPDG278D rapidly bound to and freed HER2 from MUC4, and rapidly disrupted the interaction of HER2 with other RTKs, including MET and IGF1R. PEPDG278D subsequently induced persistent downregulation of HER2 via internalization and lysosomal degradation. PEPDG278D also downregulated EGFR. Thus, PEPDG278D suppresses multiple RTKs either directly or indirectly in HER2-BC cells. In contrast, Ttzm cannot perform any of these functions of PEPDG278D. PEPDG278D was highly active in mouse tumor models of HER2-BC resistant to Ttzm and also enhanced the therapeutic efficacy of paclitaxel. However, adverse effects of PEPDG278D were not detected in the animal studies. Conclusions &amp; Therapeutic Relevance: The therapeutic activity of PEPDG278D highlights that HER2 remains a critical target in drug-resistant HER2-BC. The strong therapeutic activity of PEPDG278D in preclinical models of drug-resistant HER2-BC, which carry clinically relevant molecular changes that confer resistance to current HER2 inhibitors provides the scientific premise for potential evaluation of this recombinant human protein in patients with drug-resistant HER2-BC. Citation Format: Lu Yang, yun Li, Arup Bhattacharya, yuesheng Zhang. A recombinant human protein targeting HER2 overcomes drug resistance in HER2-positive 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 336.

Abstract 4895: Natural history and outcome of patients presenting a metastatic breast cancer with PIK3CA mutation

Abstract BACKGROUND: Activating PIK3CA mutations occur in 20-30% of patients with metastatic breast cancer (mBC). A recent study showed that alpha selective PI3K inhibitors improve outcome in patients with PIK3CA mutation, HR+/Her2- mBC. There is a need to better understand the natural history of PIK3CA mutant mBC to optimally position of this drug family. PATIENTS AND METHODS: 649 patients from SAFIR02 trial (NCT02299999), for which mutational profile was available and with clinical data entered in a database, were selected for this analysis. Associations between PIK3CA mutation, clinical characteristics and outcome were analyzed. RESULTS: 143 patients (22%) harbor PIK3CA mutation in tumor sample. 10% (n=27) and 34% (n=104) of TNBC and HR+/Her2- mBC presented a PIK3CA mutation respectively (p&amp;lt;0.001). In patients with HR+/Her2- mBC, there is no significant association between PIK3CA mutation and site of metastases or number of metastases (p&amp;lt;0.01). In the same group, patients with PIK3CA mutations were less sensitive to chemotherapy (stable disease or response: 51.3% vs. 69.2% in PIK3CA wild type; p=0.005) (Odds ratio multivariate: 0.40 [95% CI: 0.22-0.71] p=0.002). The median overall survival (OS) for patients with PIK3CA mutated HR+/Her2- mBC was of 19.6 months vs. 23.5 for patients with PIK3CA wild type (p=0.048) (HR multivariate: 1.44 [95% CI: 1.02-2.03] p=0.039). HR+/Her2- mBC with PIK3CA mutations presented more frequently a MAP3K1 mutation (16% vs. 4%, p=0.0002). In the TNBC group, the median OS in patients with PIK3CA mutated cancer was of 24.2 months vs. 14 months in the wild type group (p=0.028). CONCLUSION: Patients with PIK3CA mutated, HR+/Her2- mBC are less sensitive to chemotherapy and present a shorter survival. These data emphasize the need for new therapies in this setting, and to position these therapies earlier than chemotherapy in the treatment sequences. Citation Format: Fernanda Mosele, Benjamin Verret, Amelie Lusque, Thomas Filleron, Thomas Bachelot, Monica Arnedos, Mario Campone, Florence Dalenc, Claudia Lefeuvre, Marie Paule Sablin, Hervé Bonnefoi, Ludovic Lacroix, Ivan Bièche, Anthony Gonçalves, William Jacot, Marta Jimenez, Amelie Jacquet, Fabrice Andre, Fabrice Andre. Natural history and outcome of patients presenting a metastatic breast cancer with PIK3CA mutation [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 4895.

Abstract 3412: Genomic signature of trastuzumab neoadjuvant therapy predictive of patient survival in HER2-positive breast cancer

Abstract Although the adjuvant use of trastuzumab has significantly improved survival, therapy resistance still plagues HER2-positive breast cancer patients. A recent clinical trial study showed that tumors exposed to single dose trastuzumab have increased Immune index and PD-1 expression1, suggesting that trastuzumab not only blocks HER2 signaling but also alters the tumor immune microenvironment. In order to identify genomic signature(s) of tumors that correlate with trastuzumab-induced tumor immune response, we analyzed eight HER2-positive breast tumors samples from patients treated with 2 or more cycles of neoadjuvant trastuzumab. First, we assessed the tumor immune environment using immunohistochemistry (IHC) with a specific interest in PD-1, a T cell immune checkpoint marker. Second, we conducted DNA/RNA sequencing and identified gene mutations and expression signatures. Lastly, we used the gene signature to evaluate survival outcomes of breast cancer patients using the TCGA dataset. DNA sequencing detected that two tumors contained deleterious TP53 mutations, two tumors activating PIK3CA mutations, and one tumor a GATA1 inactivating mutation, closely reflecting the prevalent gene mutation frequencies previously reported in breast cancer. Unsupervised clustering of the RNA sequencing data revealed two distinct clades in this patient cohort. The pathway analysis showed the gene list that distinguished the two clades included inflammatory genes such as TNFα and CXCL10 as well as immune checkpoint genes, CTLA-4 and iCOS. IHC staining for immune cell markers was consistent with the RNA sequencing results showing the presence of a large number of T cells positive for CD4, CD8, or PD-1 in tumors expressing pro-inflammatory genes. Supervised clustering of the two clades identified a gene signature composed of 59 upregulated and 24 downregulated genes in the “pro-inflammatory” clade. The gene signature effectively stratified HER2 breast cancer patients in the TCGA dataset with a striking Hazard Ratio of 7.3 (n=182, p = 0.0026, 95% C.I. 2.01-27.23) and patients with the “pro-inflammatory” tumors had significantly favorable survival outcomes. This patient stratification by the gene signature was uniquely specific to HER2-positive breast cancer, indicating a functional relevance of the gene signature related to HER2 cancer biology and/or therapy. These results support the idea that trastuzumab elicits local immune response, which contributes to therapeutic efficacy. Furthermore, patients with tumors containing the “pro-inflammatory” gene signature may benefit from immune checkpoint inhibitor therapy in combination with trastuzumab. 1Varadan et al (2016) Clin Cancer Res 22(13):3249-99 Citation Format: Natalia Briones, Salvatore Facista, Rebecca Halperin, Paul Heaton, Daruka Mahadevan, Wiiliam Hendricks, Suwon Kim. Genomic signature of trastuzumab neoadjuvant therapy predictive of patient survival in HER2-positive 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 3412.

The Dual PI3K/mTOR Pathway Inhibitor GDC-0084 Achieves Antitumor Activity in PIK3CA-Mutant Breast Cancer Brain Metastases.

Previous studies have shown that the PI3K/Akt/mTOR pathway is activated in up to 70% of breast cancer brain metastases, but there are no approved agents for affected patients. GDC-0084 is a brain penetrant, dual PI3K/mTOR inhibitor that has shown promising activity in a preclinical model of glioblastoma. The aim of this study was to analyze the efficacy of PI3K/mTOR blockade in breast cancer brain metastases models.Experimental Design: The efficacy of GDC-0084 was evaluated in PIK3CA-mutant and PIK3CA wild-type breast cancer cell lines and the isogenic pairs of PIK3CA wild-type and mutant (H1047R/+) MCF10A cells in vitro. In vitro studies included cell viability and apoptosis assays, cell-cycle analysis, and Western blots. In vivo, the effect of GDC-0084 was investigated in breast cancer brain metastasis xenograft mouse models and assessed by bioluminescent imaging and IHC. In vitro, GDC-0084 considerably decreased cell viability, induced apoptosis, and inhibited phosphorylation of Akt and p70 S6 kinase in a dose-dependent manner in PIK3CA-mutant breast cancer brain metastatic cell lines. In contrast, GDC-0084 led only to growth inhibition in PIK3CA wild-type cell lines in vitro. In vivo, treatment with GDC-0084 markedly inhibited the growth of PIK3CA-mutant, with accompanying signaling changes, and not PIK3CA wild-type brain tumors. The results of this study suggest that the brain-penetrant PI3K/mTOR targeting GDC-0084 is a promising treatment option for breast cancer brain metastases with dysregulated PI3K/mTOR signaling pathway conferred by activating PIK3CA mutations. A national clinical trial is planned to further investigate the role of this compound in patients with brain metastases.

Phosphatidylinositol-3-kinase (PI3K)/Akt Signaling is Functionally Essential in Myxoid Liposarcoma.

Myxoid liposarcoma (MLS) is an aggressive soft-tissue tumor characterized by a specific reciprocal t(12;16) translocation resulting in expression of the chimeric FUS-DDIT3 fusion protein, an oncogenic transcription factor. Similar to other translocation-associated sarcomas, MLS is characterized by a low frequency of somatic mutations, albeit a subset of MLS has previously been shown to be associated with activating PIK3CA mutations. This study was performed to assess the prevalence of PI3K/Akt signaling alterations in MLS and the potential of PI3K-directed therapeutic concepts. In a large cohort of MLS, key components of the PI3K/Akt signaling cascade were evaluated by next generation seqeuncing (NGS), fluorescence in situ hybridization (FISH), and immunohistochemistry (IHC). In three MLS cell lines, PI3K activity was inhibited by RNAi and the small-molecule PI3K inhibitor BKM120 (buparlisib) in vitro An MLS cell line-based avian chorioallantoic membrane model was applied for in vivo confirmation. In total, 26.8% of MLS cases displayed activating alterations in PI3K/Akt signaling components, with PIK3CA gain-of-function mutations representing the most prevalent finding (14.2%). IHC suggested PI3K/Akt activation in a far larger subgroup of MLS, implying alternative mechanisms of pathway activation. PI3K-directed therapeutic interference showed that MLS cell proliferation and viability significantly depended on PI3K-mediated signals in vitro and in vivo Our preclinical study underlines the elementary role of PI3K/Akt signals in MLS tumorigenesis and provides a molecularly based rationale for a PI3K-targeted therapeutic approach which may be particularly effective in the subgroup of tumors carrying activating genetic alterations in PI3K/Akt signaling components.

Genomic landscape of a metastatic malignant proliferating tricholemmal tumor and its response to PI3K inhibition

Proliferating tricholemmal tumors (PTTs) are rare benign neoplasms that arise from the outer sheath of a hair follicle. Occasionally, these PTTs undergo malignant transformation to become malignant proliferating tricholemmal tumors (MPTTs). Little is known about the molecular alterations, malignant progression, and management of MPTTs. Here, we describe the case of a 58-year-old female that had a widely metastatic MPTT that harbored an activating PIK3CA mutation and was sensitive to the PI3K inhibitor, alpelisib (BYL719). We review the available literature on metastatic MPTT, detail the patient’s course, and present a whole genome analysis of this rare tumor.

Cloves syndrome: A rare disorder of overgrowth with unusual features – An uncommon phenotype?

CLOVES syndrome characterized by Congenital Lipomatous Overgrowth, Vascular malformations, Epidermal nevi, and Skeletal anomalies is a recently described sporadic syndrome from postzygotic activating mutations in PIK3CA. This 3-year-old boy, born to nonconsanguineous and healthy parents, had epidermal verrucous nevus, lower limb length discrepancy and bilateral genuvalgum, anterior abdominal wall lipomatous mass, central beaking of L2 and L3, and fibrous dysplasia of the left frontal bone. Ocular and dental abnormalities (ptosis, esotropia, delayed canine eruption, dental hypoplasia), ipsilateral asymmetrical deformity of skull, and large left cerebral hemisphere with mild ipsilateral ventriculomegaly were peculiar to him denoting an uncommon phenotype. The parents did not consent for magnetic resonance imaging and genetic studies because of financial constraints. The CLOVES syndrome has emerged as an uncommon yet distinct clinical entity with some phenotypic variations. Its diagnosis is usually from cutaneous, truncal, spinal, and foot anomalies in clinical and radioimaging studies. Proteus syndrome remains the major differential.

The Space-Time Continuum of Cortical Dysplasia.

Somatic Mutations Activating the mTOR Pathway in Dorsal Telencephalic Progenitors Cause a Continuum of Cortical Dysplasias D’Gama AM, Woodworth MB, Hossain AA, Bizzotto S, Hatem NE, LaCoursiere CM, Najm I, Ying Z, Yang E, Barkovich AJ, Kwiatkowski DJ, Vinters HV, Madsen JR, Mathern GW, Blümcke I, Poduri A, Walsh CA. Cell Rep. 2017;21:3754-3766. doi:10.1016/j.celrep.2017.11.106Focal cortical dysplasia (FCD) and hemimegalencephaly (HME) are epileptogenic neurodevelopmental malformations caused by mutations in mTOR pathway genes. Deep sequencing of these genes in FCD/HME brain tissue identified an etiology in 27 (41%) of 66 cases. Radiographically indistinguishable lesions are caused by somatic activating mutations in AKT3, MTOR, and PIK3CA and germline loss-of-function mutations in DEPDC5, NPRL2, and TSC1/2, including TSC2 mutations in isolated HME demonstrating a “two-hit” model. Mutations in the same gene cause a disease continuum from FCD to HME to bilateral brain overgrowth, reflecting the progenitor cell and developmental time when the mutation occurred. Single-cell sequencing demonstrated mTOR activation in neurons in all lesions. Conditional Pik3ca activation in the mouse cortex showed that mTOR activation in excitatory neurons and glia, but not interneurons, is sufficient for abnormal cortical overgrowth. These data suggest that mTOR activation in dorsal telencephalic progenitors, in some cases specifically the excitatory neuron lineage, causes cortical dysplasia.

Somatic activating mutations in PIK3CA cause generalized lymphatic anomaly.

Generalized lymphatic anomaly (GLA) is a vascular disorder characterized by diffuse or multifocal lymphatic malformations (LMs). The etiology of GLA is poorly understood. We identified four distinct somatic PIK3CA variants (Glu542Lys, Gln546Lys, His1047Arg, and His1047Leu) in tissue samples from five out of nine patients with GLA. These same PIK3CA variants occur in PIK3CA-related overgrowth spectrum and cause hyperactivation of the PI3K-AKT-mTOR pathway. We found that the mTOR inhibitor, rapamycin, prevented lymphatic hyperplasia and dysfunction in mice that expressed an active form of PIK3CA (His1047Arg) in their lymphatics. We also found that rapamycin reduced pain in patients with GLA. In conclusion, we report that somatic activating PIK3CA mutations can cause GLA, and we provide preclinical and clinical evidence to support the use of rapamycin for the treatment of this disabling and deadly disease.