PIK3CA Inhibitors Research Articles

Abstract P4-09-11: PIK3CA somatic alterations in 412 chinese invasive breast cancers: Higher frequency of mutant H1047R detected by next generation sequencing compared to breast cancer in caucasians

Abstract Purpose: Somatic alterations of PIK3CA gene is an important therapeutic target in breast cancer (BC). The PI3Kα-specific inhibitor alpelisib was remarkably active against PIK3CA-mutated, HR-positive/HER2-negative BC in the SOLAR-1 trial. We hypothesized that PIK3CA alterations in Chinese BC patients across different molecular subtypes might differ from other ethnic groups and this information would be useful for selecting anti-PI3K therapy. Methods: The molecular profile of the PIK3CA gene was analyzed in 412 Chinese untreated invasive BC patients with ER/HER2 molecular subtypes, using a 540 gene next-generation sequencing panel. The results were compared to the molecular profile of Caucasian breast cancer patients in The Cancer Genome Atlas(TCGA-white). Results: Compared to wild type, PIK3CA alterations were more frequent in the ER+ subtype (49.3%, p=0.024), and tumors with low ki67 proliferation (58.3%, p=0.007) and low histological grade (grade I/II/III 80%, 53.4%, 35.9%, p<0.001). Compared to TCGA Caucasian race (TCGA-white), Chinese BC patients had a higher alteration frequency (45.6% vs. 34.7%, p<0.001). The p.H1047R mutation predominantly occurred among three hot spots (p.E545K, p.E542K and p.H1047R) for Chinese BC compared to that of the TCGA-white cohort (66.1% vs 43.7%, p=0.01). Nine novel mutation sites of PIK3CA were observed in the Chinese cohort that was absent among Caucasian BC patients. Among the four ER/HER2 molecular subtypes, ER+/HER2+ tumors harbored the most PIK3CA alterations (51.6%), while ER-/HER2- harbored the least (30.0%). However the latter presented the highest frequency of copy number amplification (19.05%). Conclusion: PIK3CA alterations prevail in nearly half of Chinese BC patients and has some different molecular features compared to that of Caucasian BC patients. The PIK3CA distribution patterns differed among four ER/HER2 subtypes. The results provide more insights for evaluating the results of PIK3CA inhibitors. Citation Format: Minghan Jia, Ning Liao, Bo Chen, Guochun Zhang, Yulei Wang, Xiaoqing Chen, Liping Guo, Li Cao, Hsiaopei Mok, Chongyang Ren, Kai Li, Cheukfai Li, Lingzhu Wen, Jiali Lin, Guangnan Wei, Zhou Zhang, Charles M Balch. PIK3CA somatic alterations in 412 chinese invasive breast cancers: Higher frequency of mutant H1047R detected by next generation sequencing compared to breast cancer in caucasians [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 P4-09-11.

Molecular profiling in breast cancer—ready for clinical routine?

SummaryThe herald of genomic testing opened novel diagnostic and therapeutic possibilities for many tumor entities. For breast cancer, molecular profiling has become an integral part of disease management on multiple levels. Genetic testing allows for the identification of hereditary cancer syndromes in patients with a family history of malignancies and contributes to the successful prevention of breast cancer. In early breast cancer, several prospective randomized trials demonstrated the prognostic significance of commercially available mRNA-based gene expression analyses, which now have become part of standard of care in the adjuvant setting. In advanced breast cancer, testing for targetable mutations ensures personalized cancer treatment. Poly-ADP-ribose polymerase (PARP) inhibitors provide the first targeted alternative for patients with BRCA 1/2-associated breast cancer. In advanced breast cancer of luminal type, the detection of Phosphatidylinositol-4,5-Bisphosphate 3-Kinase Catalytic Subunit Alpha (PIK3CA) mutations provides a novel treatment option with alpelisib, a PIK3CA inhibitor. Further targetable mutations include NTRK3 in rare cases of secretory breast carcinoma and human epidermal growth factor receptor 2 (HER2). Recent data support the importance of the analysis of circulating tumor cells and cell-free DNA. These “liquid biopsies” open novel possibilities of molecular profiling. However, clinical benefit of such analyses remains to be confirmed.

Evidence-Based Network Approach to Recommending Targeted Cancer Therapies.

PURPOSEIn this work, we introduce CDGnet (Cancer-Drug-Gene Network), an evidence-based network approach for recommending targeted cancer therapies. CDGnet represents a user-friendly informatics tool that expands the range of targeted therapy options for patients with cancer who undergo molecular profiling by including the biologic context via pathway information.METHODSCDGnet considers biologic pathway information specifically by looking at targets or biomarkers downstream of oncogenes and is personalized for individual patients via user-inputted molecular alterations and cancer type. It integrates a number of different sources of knowledge: patient-specific inputs (molecular alterations and cancer type), US Food and Drug Administration–approved therapies and biomarkers (curated from DailyMed), pathways for specific cancer types (from Kyoto Encyclopedia of Genes and Genomes [KEGG]), gene-drug connections (from DrugBank), and oncogene information (from KEGG). We consider 4 different evidence-based categories for therapy recommendations. Our tool is delivered via an R/Shiny Web application. For the 2 categories that use pathway information, we include an interactive Sankey visualization built on top of d3.js that also provides links to PubChem.RESULTSWe present a scenario for a patient who has estrogen receptor (ER)–positive breast cancer with FGFR1 amplification. Although many therapies exist for patients with ER-positive breast cancer, FGFR1 amplifications may confer resistance to such treatments. CDGnet provides therapy recommendations, including PIK3CA, MAPK, and RAF inhibitors, by considering targets or biomarkers downstream of FGFR1.CONCLUSIONCDGnet provides results in a number of easily accessible and usable forms, separating targeted cancer therapies into categories in an evidence-based manner that incorporates biologic pathway information.

PIK3CA gene aberrancy and role in targeted therapy of solid malignancies.

Phosphoinositide kinases (PIKs) are a group of lipid kinases that are important upstream activators of various signaling pathways that drive oncogenesis. Hyperactivation of the PI3K/AKT/mTOR pathways-either via mutations or genomic amplification-confers key oncogenic activity, essential for the development and progression of several solid tumors. Alterations in the PIK3CA gene are associated with poor prognosis of solid malignancies. Contradictory reports exist in the literature regarding the prognostic value of PIK3CA in aggressive cancers, but most available data highlights an important role of PIK3CA mutation in mediating tumorigenesis via increased signaling of the PI3K/AKT/mTOR survival pathway. Several inhibitors of PI3K/AKT/mTOR pathways have been investigated as potential therapeutic options in solid malignancies. This article reviews the role of PIK3CA mutations and inhibitors of the PI3K/AKT/mTOR pathway in cancer and examines association with the clinico-pathological parameters and prognosis.

Phase II evaluation of copanlisib, a selective inhibitor of Pi3kca, in patients with persistent or recurrent endometrial carcinoma harboring PIK3CA hotspot mutations: An NRG Oncology study (NRG-GY008)

PurposeNRG Oncology conducted a phase II trial to assess the antitumor activity and tolerability of copanlisib, a selective inhibitor of PIK3CA, in persistent or recurrent endometrial carcinoma harboring hotspot PIK3CA mutations. Patients and methodsEligible patients had endometrial cancer with endometrioid, serous or mixed histology, a somatic PIK3CA gene mutation, measurable disease, and GOG performance status ≤2. Treatment consisted of IV copanlisib (60 mg weekly, day 1, 8 and 15 of 28-day cycle) until disease progression or prohibitive toxicity. The primary endpoints of the study were objective tumor response as assessed by RECIST 1.1 and to determine the nature and degree of toxicity of copanlisib as assessed by CTCAE version 4. The study used a 2-stage group sequential design. ResultsEleven patients were enrolled onto stage I of the treatment trial. Five patients had endometrioid, four serous and two had a tumor of mixed histology. The most common PIK3CA mutation was Q546X (n = 3) in exon 9. The most common grade 3 or 4 AE was hyperglycemia. No grade 5 adverse events were reported. No clinical responses were detected. Six patients had a best overall response of stable disease. Of 11 who initiated treatment, 10 progressed on treatment. One patient with stable disease on copanlisib withdrew from treatment secondary to relocation. The median progression-free survival (PFS) was 2.8 months; at 6 months 27% were alive, progression-free. The median overall survival (OS) was 15.2 months. Due to the lack of CR/PR continuation of accrual to the second stage of accrual was not warranted. ConclusionCopanlisib is well tolerated but has limited activity as a single agent in this population.

PIK3CA Gene Mutations in Solid Malignancies: Association with Clinicopathological Parameters and Prognosis.

Phosphoinositide kinases (PIKs) are a group of lipid kinases that are important upstream activators of various significant signaling pathways. Hyperactivation of the PI3K/AKT/mTOR pathways—either via mutations or genomic amplification—confers key oncogenic activity, essential for the development and progression of several solid tumors. Alterations in the PIK3CA gene are associated with poor prognosis of solid malignancies. Although the literature reports contradictory prognostic values of PIK3CA in aggressive cancers, most of the available data highlight the important role of PIK3CA mutation in mediating tumorigenesis via increased signaling of the PI3K/AKT/mTOR survival pathway. Several inhibitors of PI3K/AKT/mTOR pathways are investigated as potential therapeutic options in solid malignancies. This article reviews the role of PIK3CA mutations and inhibitors of PI3K/AKT/mTOR pathways in major cancer types and examines its association with clinicopathological parameters and prognosis.

Overactivation of Akt Contributes to MEK Inhibitor Primary and Acquired Resistance in Colorectal Cancer Cells.

RAS and BRAF-mutated colorectal cancers are associated with resistance to chemotherapy and poor prognosis, highlighting the need for new therapeutic strategies. Although these cancers sometimes respond to mitogen activated protein kinase kinase (MEK) inhibitor treatment, they often acquire resistance via mechanisms, which are poorly understood. Here, we investigated the mechanism of MEK inhibitor resistance in primary- and acquired-resistant cells. Cell viability was examined using the trypan blue dye exclusion assay. Protein expression was analyzed by western blotting. Somatic mutations in colorectal cancer cells were investigated using the polymerase chain reaction array. PD0325901 and trametinib induced cell death in LoVo and Colo-205 cells but not in DLD-1 and HT-29 cells, which have a PIK3CA mutation constitutively activating Akt and NF-κB. Treatment with PD0325901 and trametinib suppressed ERK1/2 activation in all four cell lines but only induced Akt and NF-κB activation in DLD-1 and HT-29 cells. Inhibition of Akt but not NF-κB, overcame MEK inhibitor resistance in DLD-1 and HT-29 cells. Acquired-resistant LoVo/PR, Colo-205/PR and LoVo/TR cells have constitutively active Akt due to a M1043V mutation in the kinase activation loop of PIK3CA and Akt inhibitor resensitized these cells to MEK inhibitor. These results demonstrate that the overactivation of Akt plays a critical role in MEK inhibitor primary and acquired resistance and implicate combined Akt/MEK inhibition as a potentially useful treatment for RAS/BRAF-mutated colorectal cancer.

Patient-derived organoid models of metastatic colorectal cancer to study response to PIK3CA inhibitors

Abstract Background More than 70% of patients diagnosed with colorectal cancer with liver metastasis have unresectable disease, so the available treatment is systemic chemotherapy that has limited efficacy and causes harmful side-effects. Thus novel and more effective drugs are needed to improve patients’ survival and quality of life. Recent studies have identified several genomic alterations in CRLM that can theoretically be targeted by novel cancer-specific drugs. Among those is the gain-of-function mutations in PIK3CA – the gene encoding the p110a catalytic subunit of PI3K – that are present in 18% of metastatic colorectal tumours. Following the recent FDA-approval of Alpelisib (a PI3Ka-specific inhibitor) HR-positive breast cancer, there is increasing interest to test this drug efficacy to treat CRLM patients with PIK3CA mutations. Although widely used to test cancer cell response, immortalized cell lines fail to represent tumour genomic alterations and heterogeneity. Our goal is to develop patient-derived primary cell models that can be used to reliably test patients’ drug response. Methods Fresh colorectal cancer liver metastasis surgical specimens were dissociated and digested into single cells and seeded in matrigel with appropriate culture media. Originated organoid cultures were then submitted to a minimum of 5 passages followed by a freeze-thaw cycle before deemed established culture. To validate organoid tumour origin, we then performed whole-genome sequencing of paired organoid and respective fresh tumour. Results The established patient-derived organoids from colorectal liver metastasis add an overall mutation match of > 80% when compared to with the original tumour. We have found so far two CRLM organoid lines with mutations in the helical domain of PIK3CA (E545A and E542K). Conclusions We have demonstrated patient-derived organoids recapitulate the genome of their tumour of origin. Libraries of these primary cell models should in the near future be used to more accurately determine drug effectiveness prior to clinical trials. Ongoing testing of Alpelisib alone or in combination with other PI3K pathway target genes will determine whether these patients could benefit from these drugs. Legal entity responsible for the study Barros-Silva, J.D. Funding Cancer Research UK. Disclosure All authors have declared no conflicts of interest.

Whole-exome sequencing of cervical carcinomas identifies activating ERBB2 and PIK3CA mutations as targets for combination therapy

The prognosis of advanced/recurrent cervical cancer patients remains poor. We analyzed 54 fresh-frozen and 15 primary cervical cancer cell lines, along with matched-normal DNA, by whole-exome sequencing (WES), most of which harboring Human-Papillomavirus-type-16/18. We found recurrent somatic missense mutations in 22 genes (including PIK3CA, ERBB2, and GNAS) and a widespread APOBEC cytidine deaminase mutagenesis pattern (TCW motif) in both adenocarcinoma (ACC) and squamous cell carcinomas (SCCs). Somatic copy number variants (CNVs) identified 12 copy number gains and 40 losses, occurring more often than expected by chance, with the most frequent events in pathways similar to those found from analysis of single nucleotide variants (SNVs), including the ERBB2/PI3K/AKT/mTOR, apoptosis, chromatin remodeling, and cell cycle. To validate specific SNVs as targets, we took advantage of primary cervical tumor cell lines and xenografts to preclinically evaluate the activity of pan-HER (afatinib and neratinib) and PIK3CA (copanlisib) inhibitors, alone and in combination, against tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway (71%). Tumors harboring ERBB2 (5.8%) domain mutations were significantly more sensitive to single agents afatinib or neratinib when compared to wild-type tumors in preclinical in vitro and in vivo models (P = 0.001). In contrast, pan-HER and PIK3CA inhibitors demonstrated limited in vitro activity and were only transiently effective in controlling in vivo growth of PIK3CA-mutated cervical cancer xenografts. Importantly, combinations of copanlisib and neratinib were highly synergistic, inducing long-lasting regression of tumors harboring alterations in the ERBB2/PI3K/AKT/mTOR pathway. These findings define the genetic landscape of cervical cancer, suggesting that a large subset of cervical tumors might benefit from existing ERBB2/PIK3CA/AKT/mTOR-targeted drugs.

306PD - PIK3CA alterations in metastatic breast cancer (mBC)

BackgroundThe anticipated approval of the first specific PIK3CA inhibitor, apelisib, has increased interest in the frequency and range of PIK3CA genomic alterations (GA) in the major subtypes of mBC. MethodsDNA was extracted from 3,871 mBC: 1,259 ER+/HER2-, 1,969 HER2 amplified (amp) and 643 TNBC. GA, tumor mutational burden (TMB) and microsatellite instability (MSI) were identified by hybrid-capture. PD-L1 was determined by IHC. ResultsPIK3CA GA were significantly higher in ER+(39%) and HER2amp (37%) and lower in TNBC (21%) groups and dominated by point mutations and indels (mut) (Table). The H1047R was the most frequent PIK3CA GA in all groups. ESR1 GA were highest in ER+ and BRCA1 GA were most frequent in PIK3CAmut- TNBC and BRCA2 GA were most frequent in PIK3CAmut- ER+. FGFR1 GA were significantly more frequent in PIK3CAmut- ER+ and EGFR and BRAF GA were most frequent in PIK3CAmut+ TNBC. Biomarkers of potential immunotherapy benefit including CD274amp and PD-L1 expression in immunocytes were most frequent in the TNBC patients, while TMB was highest in the PIK3CAmut+ cohort, regardless of subtype.Table306PDTableER+/HER2- (1,249)HER2 Amp (1,922)TNBC (925)PIK3CAmut+PIK3CAmut-PIK3CAmut+PIK3CAmut-PIK3CAmut+PIK3CAmut-481 (39%) CN 4% Mut 96% H1047R 30% E545K 17% E542K 15% N345K 5%768 (61%)715 (37%) CN 8% Mut 92% H1047R 34% E545K 15% E542K 10% N345K 3%1,207 (63%)192 (21%) CN 17% Mut 83% H1047R 30% E545K 8% E542K 7% N345K 3%733 (79%)Age (range in years)57 (23-89+)53 (22-89)55 (25-88)53 (20-89+)56.5 (30-89+)53 (20-89+)PIK3CA GA100%0%100%0%100%0%TP53 GA39%47%75%68%74%88%PTEN GA9%12%3%6%15%15%CDH1 GA11%5%5%3%9%3%ESR1 GA16%16%7%6%2%<1%BRCA1/2 GA1%/3%4%/7%1%/2%3%/3%3%/3%8%/4%HER2 amp0%0%100%100%0%0%HER2 mut2%3%7%6%5%2%Other Kinase GAFGFR1 14% EGFR 1% BRAF 1%FGFR1 21% EGFR 2% BRAF 2%FGFR1 11% EGFR 3% BRAF 1%FGFR1 11% EGFR 3% BRAF 1%FGFR1 9% EGFR 11% BRAF 3%FGFR1 8% EGFR 3% BRAF 3%AR amp<1%<1%2%1%3%<1%MSI High<1%<1%<1%<1%0%<1%CD274 (PD-L1) amp<1%1%1%1%3%3%TMB > 10/20 mut/Mb11%/5%5%/1%11%/3%8%/1%11%/3%6%/1%PD-L1 TILs low/high9%/0% n=3311%/0% n=5711%/0% n=459%/0% n=7920%/0% n=1517%/1% n=75 ConclusionsA wide variety of PIK3CA GA are identified in mBC and appear to influence other important biomarkers such as BRCA1/2 GA and TMB status. The PIK3CA GA distribute differently among the ER+, HER2+ and TNBC cohorts and may impact the initial and future use of PIK3CA inhibitors in the treatment of the disease. Legal entity responsible for the studyFoundation Medicine. FundingFoundation Medicine. DisclosureE.S. Sokol: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. L.A. Albacker: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. J.A. Elvin: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. J. Vergilio: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. J..K. Killian: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. N. Ngo: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. D. Lin: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. S. Ramkissoon: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. E. Severson: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. S.M. Ali: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. A.B. Schrock: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. J. Chung: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. P. Reddy: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. V.A. Miller: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. B.M. Alexander: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment, Officer / Board of Directors: Foundation Medicine. K. McGregor: Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. J.S. Ross: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Foundation Medicine. All other authors have declared no conflicts of interest.

Helical and kinase domain mutations of PIK3CA, and their association with hormone receptor expression in breast cancer.

Breast cancer is one of the major causes of female morbidity and mortality, accounting for ~25% of the total cancer cases in women. Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic α subunit (PIK3CA) mutations serve a major role in downstream signaling of receptor tyrosine kinases. The present study aimed to elucidate the frequency of exon 9 and 20 mutations of PIK3CA and their role in disease progression. A total of 118 tumor samples from confirmed breast cancer patients were collected from the histopathology laboratory at King Fahd Hospital of the University (Al-Khobar, Saudi Arabia). Sanger sequencing was performed on extracted DNA to identify the mutations on exons 9 and 20 of PIK3CA. The results were further validated by competitive allele-specific TaqMan polymerase chain reaction. Three mutations, namely E542K and E545K within exon 9, and H1047R within exon 20, were observed in 25 patients (21.2%). Among these, 18 patients carried the H1047R mutation of the kinase domain, while the remaining 7 patients carried mutations in the helical domain. PIK3CA mutations were associated with the estrogen receptor-positive/progesterone receptor-positive (ER+/PR+) group of tumors in contrast to the ER−/PR− group (P=0.021). Furthermore, it was observed that the PIK3CA mutation was associated with a poor disease prognosis. Taken together, the current study emphasized the potential of PIK3CA mutations as an important biomarker for breast cancer classification and the possible use of PIK3CA inhibitor as targeted therapy for breast cancer.

Abstract 5149: Subclonal sociability: Interactions of HER2 and PIK3CAmutant cells in breast cancer

Abstract Background: Tumor heterogeneity is a common characteristic of many cancers and plays an important role in their development and eventual metastasis. The traditional clonal evolution model describes cancer cells as descendants of a single progenitor that has accumulated a stepwise series of mutations. However, recent sequencing studies have revealed the presence of genetically distinct subclones in numerous tumors. PIK3CA is the most commonly mutated gene in breast cancer while HER2 is overexpressed in ~20% of breast cancers. Activating missense mutations in the gene that encodes HER2 have also been discovered, and our lab has previously shown the effects of these mutations and their synergy with PIK3CA mutations in a double-mutant cell. This project explores the interactions between cells with either a HER2 or a PIK3CA mutation when they are present as genetically distinct subclones in co-cultures. Methods: Isogenic MCF-10A cells containing mutations in PIK3CA, HER2, or no mutation were co-cultured in growth factor-deprived conditions. In these conditions, PIK3CA mutant cells are known to be able to grow, while HER2 mutant and wild-type (WT) cells arrest. The cellular makeup of the co-cultures was determined using droplet digital PCR (ddPCR) with probes against the respective mutations. Cells were tagged with stable expression of either zsGreen (PIK3CA mutants) or tdTomato (HER2 and WT) and observed under fluorescent microscopy. Further imaging was performed using the IncuCyte live cell imaging system (Essen Bioscience), which allowed for periodic imaging of cells in culture. Co-cultures were treated with Neratinib or Alpelisib (BYL719), which are HER1/2/4 and PIK3CA inhibitors, respectively. Cells in each condition were counted and ddPCR was performed to determine allelic fractions of the co-cultures. Results: When cultured together, PIK3CA mutant cells can induce proliferation in HER2 mutant cells, but not WT cells. Over time, HER2 mutant cells grow to make up &amp;gt;50% of the co-cultures. Imaging and transwell assay data (not included on poster) implicate cell-cell contact rather than paracrine factors as the primary driving factor of this phenotype. HER2 and PIK3CA inhibitors can effectively target the co-cultures and inhibiting the growth of the PIK3CA cells appears to halt the growth of the HER2 mutants as well. Conclusions: PIK3CA mutant cells can induce proliferation of quiescent HER2 mutant cells in growth-factor deprived conditions. This effect appears to the cell-cell contact mediated rather than driven by secreted factors. Co-cultures that contain PIK3CA and HER2 mutant cells have therapeutic vulnerabilities that can be exploited using drugs that are currently approved or in clinical trials. These results have important implications in understanding early tumor development and suggest that therapeutic approaches that target subclonal populations may be effective in certain tumors. Citation Format: Ian Waters, Swathi Karthikeyan, Lauren Dennison, David Chu, Ben Ho Park. Subclonal sociability: Interactions of HER2 and PIK3CAmutant cells in breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 5149.

Abstract 3916: Unbiased phospho-proteomic profiling of mouse breast cancer models with DIA mass spectrometry refines CanPath prototype, a platform for predictive cancer pathway modeling

Abstract Background CanPathPro is designed to build and validate a combined experimental and systems biology platform, which will be used in testing cancer signaling hypotheses. It combines highly defined mouse and organotypic experimental systems, high-dimensional data including next generation sequencing and quantitative proteomics, and computational models for data integration, visualization and modelling. Mouse cancer models are characterized by quantitative transcriptome, quantitative mass spectrometry including phospho-proteome, histopathology and histochemistry. Phospho-proteomic data has been obtained using data independent acquisition (DIA) and used to refine signaling models in the mouse cell lines. Currently, the model integrates modules of the signal transduction pathways Egfr/Erbb2, Fgfr, insulin, Akt, Mtor, Myc, Ras, Hippo, Met, Tgfbr, Il6, integrin, Wnt, apoptosis and cell cycle regulation integrating in total about 380 different genes as well as related proteins and phospho-proteins Methods Two mouse mammary gland model cell lines, (Cdh1-fl/AKT1[E17K] and Cdh1-fl + PTEN-fl) were each treated with DMSO, a Pik3ca inhibitor (Wortmannin), or an Akt inhibitor (MK-2206). Cells were lysed and proteins were denatured, followed by reduction, alkylation and digestion with trypsin. The resulting peptides were desalted and enriched for phosphopeptides with TiO2 beads and cleaned up for mass spectrometry. A phosphopeptide library was generated from pooled phosphoenriched samples using LC-MS/MS shotgun measurements and included 22,893 phosphosites from 3,549 protein groups. DIA data was acquired on a Q Exactive HF mass spectrometer with a gradient length of 60 - 120 minutes on a C18 Easy LC 1200 nano-liquid chromatography system. The DIA data was extracted and processed with Spectronaut 11 (Biognosys) for analysis. Results In the AKT1[E17K] samples, 13,396 peptides (21,862 phospho-peptides) were quantified in the DIA runs and 12,297 peptides (19,928 phospho-peptides) were quantified in PTEN-fl samples. Under treatment with MK2206 and Wortmanin, 859 phosphopeptides from 548 protein groups were significantly changed across all comparisons in the AKT1[E17K] samples and with the same treatments 2,276 phosphopeptides from 976 proteins were significantly changed in the PTEN-fl cells. Based on this data 11 functionally relevant new phosphosites have been added to the model including ones on: EIF4B, FOX03, MAP2K4, PAK1, RAF1, and ULK1. Conclusions Phospho-proteomic profiling of cell lines using DIA mass spectrometry enables deep characterization of the phospho-signaling cascades modulated through small molecule inhibitors. Citation Format: Magdalena Bober, Monika Banko-Bielecka, Daniel Heinzmann, Oliver Rinner, Nicholas Dupuis, Christoph Wierling, Huaibiao Li, Thomas Kessler, Artur Muradyan, Louisa Krützfeldt, Moritz Schütte, Felix Dreher, Aspasia Ploubidou, Bodo Lange. Unbiased phospho-proteomic profiling of mouse breast cancer models with DIA mass spectrometry refines CanPath prototype, a platform for predictive cancer pathway modeling [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 3916.

Abstract PD9-12: Integrative molecular profiling of breast cancer brain metastasis and patient-derived xenograft organoids from resected breast cancer brain metastases to interrogate and prioritize therapeutic personalized strategies

Abstract Background: Breast cancer brain metastasis (BM) is an area of unmet need in metastatic breast cancer patients. Novel therapeutic interventions to help prevent and treat BM are warranted. We conducted integrative molecular profiling of BM and matched primary tumors (PT) using next-generation DNA and RNA sequencing to examine the molecular landscape. In addition, we established patient-derived xenograft/organoid (PDX/PDO) to examine drug sensitivity according to the molecular and clinical features of the BM. Methods: Archived, formalin fixed paraffin-embedded BM was collected retrospectively. BM were also collected prospectively at the time of clinically indicated surgical resection through the central nervous system tissue banking and the Michigan Oncology Sequencing Center (MI-ONCOSEQ) protocols. Matched archived PT tissues were collected when available. Integrative next-generation sequencing was conducted using the MI-ONCOSEQ platform. The prospectively collected BM were further used to establish PDXs/ PDOs. Successfully established PDXs/PDOs were used for ex vivo drug testing via MiDrugScreen, a novel drug sensitivity testing platform, where testing was performed in a dose-response format with drug selection prioritized by clinical scenario and molecular alterations if known a priori. Results: 12 matched BM-PT pairs were analyzed: 6 triple negative, 5 HER2 positive, and 1 ER positive HER2 negative. All except one (11/12) had TP53 mutations. When present, TP53 mutations in BM were also found in PT (except for 1 unknwon case in PT due to low coverage). ER+HER2- was the only one without TP53 mutation but had hyper-mutation (APOBEC signature). Driver mutations and unique copy number alterations (CDKN2A loss in 1/12, mutations in PIK3CA in 1/12 and ESR1 in 1/12, CCNE1 amplification in 1/12) were noted in BMs. In 75% of cases, mutational burden was higher in BM vs. PT. 2 PDX/PDO were available for drug testing. PDO-BC9 was noted to have RB1 (splice acceptor) and LOH. As predicted by this alteration, PDO-BC9 was insensitive to CDK4/6 inhibitors (palbociclib, abemaciclib) tested on MiDrugScreen panel. PDX-BC4 was established from PIK3CA and ESR1 mutated BM from an ER+HER2- patient who had previously progressed on endocrine therapy with a CDK4/6 inhibitor. As predicted, the PDX-BC4 was resistant to CDK4/6 inhibitor but interestingly sensitive to PIK3CA, ERK, and MEK inhibitors. Conclusions: TP53 mutation was highly prevalent and may be a biomarker for increased risk of BM. Further study is warranted to see if specific TP53 mutations are associated with a risk of BM development and can be used in risk stratification for BM specific intervention. Unique molecular alterations in BM compared to matched PT may have a therapeutic implication as a target or resistance biomarker. Conducting drug testing in addition to molecular profiling has the strong potential of being informative in tailoring or prioritizing therapeutic agents in the era of precision medicine. Additional BM PDXs/PDOs from breast and other solid tumors are being examined using this novel therapeutic tailoring approach with the combination of MIONCOSEQ and MiDrugScreen. Citation Format: Morikawa A, Robinson DR, Soellner M, Wu Y-M, Lonigro R, Gilani R, Cheng X, Lachacz E, Thomas D, McMurray K, Smerage J, Henry NL, Heth J, Chinnaiyan A, Hayes DF, Merajver S. Integrative molecular profiling of breast cancer brain metastasis and patient-derived xenograft organoids from resected breast cancer brain metastases to interrogate and prioritize therapeutic personalized strategies [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr PD9-12.

PI3K oncogenic mutations mediate resistance to afatinib in HER2/neu overexpressing gynecological cancers

ObjectiveAberrant expression of HER2/neu and PIK3CA gene products secondary to amplification/mutations are common in high-grade-serous-endometrial (USC) and ovarian-cancers (HGSOC). Because scant information is currently available in the literature on the potential negative effect of PIK3CA mutations on the activity of afatinib, in this study we evaluate for the first time the role of oncogenic PIK3CA mutations as a potential mechanism of resistance to afatinib in HGSOC and USC overexpressing HER2/neu. MethodsWe used six whole-exome-sequenced primary HGSOC/USC cell-lines and three xenografts overexpressing HER2/neu and harboring mutated or wild-type PIK3CA/PIK3R1 genes to evaluate the role of PI3K-mutations as potential mechanism of resistance to afatinib, an FDA-approved pan-c-erb-inhibitor in clinical trials in USC. Primary-USC harboring wild-type-PIK3CA gene was transfected with plasmids encoding oncogenic PIK3CA-mutations (H1047R/E545K). The effect of afatinib on HER2/PI3K/AKT/mTOR pathway was evaluated by immunoblotting. ResultsWe found PI3K wild-type cell-lines to be significantly more sensitive (lower IC50) than PI3K-mutated cell-lines p = 0.004). In vivo, xenografts of primary cell-line USC-ARK2, transfected with the PIK3CA-H1047R or E545K hotspot-mutations, exhibited significantly more rapid tumor growth when treated with afatinib, compared to mice harboring ARK2-tumors transfected with wild-type-PIK3CA (p = 0.041 and 0.001, respectively). By western-blot, afatinib effectively reduced total and phospho-HER2 proteins in all cell-lines. However, H1047R/E545K-PIK3CA-transfected-ARK2-cells demonstrated a greater compensatory increase in phosphorylated-AKT proteins after afatinib exposure when compared to controls ARK2. ConclusionsOncogenic PI3K mutations may represent a major mechanism of resistance to afatinib. Combinations of c-erb with PIK3CA, AKT or mTOR inhibitors may be necessary to more efficiently block the PIK3CA/AKT/mTOR pathway.

Abstract 2841: Her2/neu expression as potential marker of regorafenib resistance in CRC

Abstract Nature Reviews Clinical Oncology, (2017). doi:10.1038/nrclinonc.2017.43 Jason J. Luke 0 0 2017-03-27T13:39:00Z 2017-11-29T14:35:00Z 1 312 1781 14 4 2089 14.0 Normal 0 false false false EN-US JA X-NONE /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-priority:99; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin-top:0cm; mso-para-margin-right:0cm; mso-para-margin-bottom:8.0pt; mso-para-margin-left:0cm; line-height:107%; mso-pagination:widow-orphan; font-size:11.0pt; font-family:Calibri; mso-ascii-font-family:Calibri; mso-ascii-theme-font:minor-latin; mso-hansi-font-family:Calibri; mso-hansi-theme-font:minor-latin; mso-ansi-language:EN-US;} Regorafenib is a multikinase inhibitor currently approved for the treatment of chemorefractory mCRC patients. No predictive biomarkers of efficacy have been identified. We recently reported that amplification or mutations in HER-2/neu might predict resistance to regorafenib in a small cohort of patients treated with Regorafenib. We therefore sought to better investigate the role of HER-2/neu in response to Regorafenib in preclinical and clinical models. Short-term proliferation assay with Regorafenib was performed in a panel of CRC cell lines. Basal protein expression of total and phospho Her2 were analized by WB analysis. RPPA data from MD Anderson cell lines project were used for external validation of total and phospho HER-2/neu. Sperman correlation was applied to correlate the expression levels of total and phospo HER2/neu and IC50 to Regorafenib. HT29 CRC cell line (HT29) was made resistant to Regorafenib (HT29R). WB analysis of basal levels of proteins of the EGFR and Her2 axis were investigated in both HT29 and HT29R. Moreover, HT29 and HT29R were treated with EGFR inhibitors, Her2/neu inhibitors, MAPK and PIk3Ca inhibitors. Apoptosis was perfromed by FACs analysis by using Annexin-V staining. We found a negative correlation between pHer2 expression and response to Regorafenib in both our data set of CRC cell lines and in the MD Anderson panel. Overexpression of all the epitelial markers of the EGFR and HER2/neu axis was observed in HT29R as compared to HT29. This translated to an increased sensitivity and apoptosis to Trastuzumab in HT29R as compared to HT29 (IC50 with 50 times fold change) and PIk3Ca inhibitor (IC50 with 5 times fold change). No differences of IC50 were observed with other inhibitors. Moreover, combined treatment with Trastuzumab and PIk3Ca inhibitor induced significantly early and late apoptosis in HT29R as compared to HT29. Our preliminary data indicate pHer2 levels to be predictive of resistance to Regorafenib in CRC. Functional work and IHC analysis of CRC patients treated with Regorafenib is ongoing and will be presented. Citation Format: Loredana Vecchione, Stefania Napolitano, Valentina Belli, Erika Martinelli, Nunzia Matrone, Christophe Hapke, Ulrich Keilholz, Josep Tabernero, Fortunato Ciardiello, Teresa Troiani. Her2/neu expression as potential marker of regorafenib resistance in CRC [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 2841.

Signaling pathway screening platforms are an efficient approach to identify therapeutic targets in cancers that lack known driver mutations: a case report for a cancer of unknown primary origin

Precision medicine aims to tailor cancer therapies to target specific tumor-promoting aberrations. For tumors that lack actionable drivers, which occurs frequently in the clinic, extensive molecular characterization and pre-clinical drug efficacy studies will be required. A cell line maintained at low passage and a patient- derived xenograft model (PDX) were generated using a fresh biopsy from a patient with a poorly-differentiated neuroendocrine tumor of unknown primary origin. Next-generation sequencing, high throughput signaling network analysis, and drug efficacy trials were then conducted to identify actionable targets for therapeutic intervention. No actionable mutations were identified after whole exome sequencing of the patient’s DNA. However, whole genome sequencing revealed amplification of the 3q and 5p chromosomal arms, that include the PIK3CA and RICTOR genes, respectively. We then conducted pathway analysis, which revealed activation of the AKT pathway. Based on this analysis, efficacy of PIK3CA and AKT inhibitors were evaluated in the tumor biopsy-derived cell culture and PDX, and response to the AKT inhibitor AZD5363 was observed both in vitro and in vivo indicating the patient would benefit from targeted therapies directed against the serine/threonine kinase AKT. In conclusion, our study demonstrates that high throughput signaling pathway analysis will significantly aid in identifying actionable alterations in rare tumors and guide patient stratification into early-phase clinical trials.

Screen for MicroRNA and Drug Interactions in Breast Cancer Cell Lines Points to miR-126 as a Modulator of CDK4/6 and PIK3CA Inhibitors.

Background: Breast cancer (BC) represents the most common cancer in women worldwide. Due to its heterogeneous nature, breast cancer management might benefit from differential treatments toward personalized medicine. Additionally, drug resistance is a common phenomenon. We systematically investigated the effect of 14 different drugs administered on BC cell lines in combination with microRNAs (miRNA, miR).Methods: Thirty-eight miRNAs, all associated with BC by clinical and molecular parameters including progression, prognosis and subtypes, were tested for their effects on the viability of 12 different BC cell lines. Four miRNAs with the strongest impact on viability were further assayed in combination with 14 BC drugs. Mann–Whitney U-test with Bonferroni correction was used for statistical analysis.Results: In a miRNA only pre-screen we observed effects on BC cell lines' viability for 34 out of 38 candidate miRNAs. We then identified 14 miRNA/drug combinations for which the combination IC50 was lower than that of both miRNA and drug as single agents. miR-181a, paired with GSK1070916, Doxorubicin, XL765 and AMG511, was the only miRNA active on the triple negative (TNBC) MDA-MB-468 cell line. miR-126 was the only miRNA (in combination with CDK4/6 or PIK3CA inhibitors) with significant effects on cell lines from different subtypes: MCF7 (Luminal) and MDA-MB-453 (HER2+). Because of its activity on different BC subtypes, we investigated the genome wide effects of miR-126 using transcriptomics and confirmed that expression of miR-126 in BC cell lines affected cell cycle and mitosis.Conclusion: Our results show that a combination treatment with miRNAs, in particular miR-181a, miR-326, miR-9 and miR-126, enhance the activity of specific BC drugs in vitro, even on the most aggressive BC subtypes, HER2+ and TNBC. Finally, as expected from its drug interactions, based on a whole transcriptome study we could confirm a role for miR-126 in cell cycle regulation.

Study of Imidazolium Salt Derivatives as PIK3CA Inhibitors Using a Comprehensive in Silico Method.

A series of imidazolium salt derivatives have demonstrated potent antitumor activity in prior research. A comprehensive in silicon method was carried out to identify the putative protein target and detailed structure-activity relationship of the compounds. The Topomer CoMFA and CoMSIA techniques were implemented during the investigation to obtain the relationship between the properties of the substituent group and the contour map of around 77 compounds; the Topomer CoMFA and CoMSIA models were reliable with the statistical data. The protein–protein interaction network was constructed by combining the Pharmmapper platform and STRING database. After generating the sub-network, the phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit α (PIK3CA with protein data bank ID: 3ZIM) was selected as the putative target of imidazolium salt derivatives. A docking study was carried out to correlate interactions of amino acids in protein active pockets surrounded by the ligand with contour maps generated by the structure-activity relationship method. Then the molecular dynamics simulations demonstrated that the imidazolium salt derivatives have potent binding capacity and stability to receptor 3ZIM, and the two ligand-receptor complex was stable in the last 2 ns. Finally, the ligand-based structure-activity relationship and receptor-based docking were combined together to identify the structural requirement of the imidazolium salt derivatives, which will be used to design and synthesize the novel PIK3CA inhibitors.

Abstract P1-13-14: Triple positive breast cancer ; a distictive subtype and consideration of systemic therapeutic approach

Abstract Introduction: Triple positive breast cancer is one of intrinsic subtype in breast cancer that is defined namely, ER/PR/Her2 positive tumors. It has multiple strategies for systemic therapy according to the characteristics of hormonal and anti-HER2 responsiveness. Each targeted therapy plays cross-talks between HER-2 and estrogen receptor signaling pathway resulting in endocrine resistance and anti Her2 resistance. Methods: We compared the triple positive subtype to the other breast cancer intrinsic subtypes to distinguish the uniqueness in their position among other breast cancer subtypes using retrospective analysis of two different cohorts; Korea Breast Cancer Society (KBCS) Breast cancer registry data (N=31266, Jan. 2006 – Dec. 2010) and database from St. Mary`s hospital Breast cancer registry (N=2216, Apr. 2009 – Mar. 2016). Results: Median follow up duration of 76 months in KBCS cohort (2006-2010) showed the overall survival graph of triple positive breast cancer located in the middle in between Luminal A intrinsic subtype and HER2 enriched subtype(P&amp;lt;.001). Also HER2 directed trastuzumab therapy did not improve the overall survival in triple positive breast cancer patients (P=.899) in contrast to the improved overall survival using trastuzumab therapy in HER2 enriched subtype (P=.018). Like the preceding results, CMC breast cancer data showed the similar results in recurrence free survival (P&amp;lt;.001). and no recurrence free survival improvement using trastuzumab therapy in triple positive breast cancer patient during the median follow up of 33 months (P=0.800). Conclusion: 1) Anti-HER2 therapy seems less beneficial in Triple positive breast cancer subtype regardless of breast cancer stage. 2) Triple positive breast cancer may require different therapeutic approaches 3) Other targeted agents (mTOR inhibitor, CDK4/6 inhibitor, PIK3CA inhibitor) can be a substitute option for the Trastuzumab therapy in triple positive breast cancer. Citation Format: Kim JS, Kim YS, You SH. Triple positive breast cancer ; a distictive subtype and consideration of systemic therapeutic approach [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P1-13-14.