PIK3CA Alterations Research Articles

Lummus wins master licensor contract for DRPIC's new PC complex in Oman

The Lung Cancer Master Protocol (Lung-MAP; S1400) is a completed biomarker-driven master protocol designed to address an unmet need for better therapies for squamous non-small-cell lung cancer. Lung-MAP (S1400) was created to establish an infrastructure for biomarker screening and rapid regulatory intent evaluation of targeted therapies and was the first biomarker-driven master protocol initiated with the US National Cancer Institute (NCI).Lung-MAP (S1400) was done within the National Clinical Trials Network of the NCI using a public–private partnership. Eligible patients were aged 18 years or older, had stage IV or recurrent squamous non-small-cell lung cancer, had previously been treated with platinum-based chemotherapy, and had an Eastern Cooperative Oncology Group (ECOG) performance status of 0–2. The study included a screening component using the FoundationOne assay (Foundation Medicine, Cambridge, MA, USA) for next-generation sequencing, and a clinical trial component with biomarker-driven substudies and non-match substudies for patients who were ineligible for biomarker-driven substudies. Patients were pre-screened and received their substudy assignment upon progression, or they were screened at progression and received their substudy assignment upon completion of testing. Patients could enrol onto additional substudies after progression on a substudy. The study is registered with ClinicalTrials.gov, NCT02154490, and all research related to Lung-MAP (S1400) is completed.Between June 16, 2014, and Jan 28, 2019, 1864 patients enrolled and 1841 (98·9%) submitted tissue. 1674 (90·9%) of 1841 patients had biomarker results, and 1404 (83·9%) of 1674 patients received a substudy assignment. Of the assigned patients, 655 (46·7%) registered to a substudy. The biomarker-driven substudies evaluated taselisib (targeting PIK3CA alterations), palbociclib (cell cycle gene alterations), AZD4547 (FGFR alteration), rilotumumab plus erlotinib (MET), talazoparib (homologous recombination repair deficiency), and telisotuzumab vedotin (MET). The non-match substudies evaluated durvalumab, and nivolumab plus ipilimumab for anti-PD-1 or anti-PD-L1-naive disease, and durvalumab plus tremelimumab for anti-PD-1 or anti-PD-L1 relapsed disease. Combining data from the substudies, ten (7·0%) of 143 patients responded to targeted therapy, 53 (16·8%) of 315 patients responded to anti-PD-1 or anti-PD-L1 therapy for immunotherapy-naive disease, and three (5·4%) of 56 responded to docetaxel in the second line of therapy. Median overall survival was 5·9 months (95% CI 4·8–7·8) for the targeted therapy groups, 7·7 months (6·7–9·2) for the docetaxel groups, and 10·8 months (9·4–12·3) for the anti-PD-1 or anti-PD-L1-containing groups. Median progression-free survival was 2·5 months (95% CI 1·7–2·8) for the targeted therapy groups, 2·7 months (1·9–2·9) for the docetaxel groups, and 3·0 months (2·7–3·9) for the anti-PD-1 or anti-PD-L1-containing groups.Lung-MAP (S1400) met its goal to quickly address biomarker-driven therapy questions in squamous non-small-cell lung cancer. In early 2019, a new screening protocol was implemented expanding to all histological types of non-small-cell lung cancer and to add focus on immunotherapy combinations for anti-PD-1 and anti-PD-L1 therapy-relapsed disease. With these changes, Lung-MAP continues to meet its goal to focus on unmet needs in the treatment of advanced lung cancers.US National Institutes of Health, and AbbVie, Amgen, AstraZeneca, Bristol Myers Squibb, Genentech, and Pfizer through the Foundation for the National Institutes of Health.

TP53, SPOP and PIK3CA Genes Status in Prostate Cancer.

Recent advances in molecular biology make the identification of prostate cancer (PC) subsets a priority for more understanding of the molecular pathogenesis and treatment options. Genetic alterations in many genes such as TP53, SPOP and PIK3CA genes have been reported in PC with variable frequencies worldwide. We aimed to investigate genetic alterations in the hotspot lesions of TP53, SPOP and PIK3CA genes by direct sequencing and the expression of TP53 and PIK3CA by RT-PCR in prostate cancer, and to explore the correlation between TP53, SPOP and PIK3CA alterations and tumorigenesis of prostate cancer. Seventy-nine FFPE prostate samples from patients who underwent radical prostatectomy were obtained, subjected to genomic DNA extraction and sequenced for mutations in exons 5, 6, 7 and 8 of TP53 gene, exons 4 and 5 of SPOP gene and exons 9 and 20 of PIK3CA gene. RT-PCR was performed for the expression evaluation of the PIK3CA gene. Our results showed a high frequency of TP53 mutations (11/79, 13.9 %) in the selected population. On the other hand, SPOP and PIK3CA genes did not show any genetic alteration in the sequenced exons. PIK3CA gene overexpression was detected in 6% of the cohort by RT-PCR. TP53 mutation is the most frequent genetic alteration and likely has a major role in the pathogenesis of PC in the Jordanian population.

103P Comprehensive genomic landscape in younger and older Chinese patients with colorectal cancer

The incidence of colorectal cancer (CRC) in young patients is increasing in recent years. However, the difference of genomic landscape between younger and older patients with CRC are poorly investigated and has never been reported in Chinese population. A total of 75 CRC patients were enrolled. All kinds of genetic alterations were analyzed by next-generation sequencing (NGS) with Acornmed panel. Genomic landscape exhibited notable differences between younger and older CRC groups. APC and PIK3CA alterations were more commonly altered in older tumors (p < 0.05), while SMAD4 mutations tended to occur in younger tumors (p = 0.054). Notably, mutational distributions of KRAS in younger group differed from those in older group, and a higher prevalence of KRAS codon 12 alterations was potentially associated with young age (p = 0.076). Furthermore, the majority of patients (77.3%) harbored at least one clinically actionable alteration, and targeted genetic profiles between younger and older patients were significantly different (p < 0.05). Additionally, in patients with mismatch repair-proficient and mscirosatellite-stable (pMMR/MSS) CRC, tumor mutational burden (TMB) was positively correlated with age (p < 0.05), and a significantly association was found between high TMB and DNA damage response (DDR) pathway alterations (p < 0.05). This study revealed different molecular profiles between younger and older Chinese patients with CRC, which provided novel insights into the personalized therapy in CRC.

An evaluation of buparlisib for the treatment of head and neck squamous cell carcinoma

ABSTRACT Introduction Five-year overall survival for head and neck squamous cell carcinoma (HNSCC) is relatively poor at around 50–66%, and there has been little improvement over the past several decades. PIK3CA alterations are common in HNSCC and offer a promising therapeutic target. Areas covered The authors discuss the PIK3 pathway and the use of PIK3 inhibitors in cancer, with a particular focus on HNSCC. A summary of the safety and efficacy of buparlisib, a class I pan-PI3K inhibitor, from several phase I and phase II HNSCC trials is provided. Expert opinion With a maximum tolerated dose of 100 mg/day and an acceptable toxicity profile, buparlisib may be effective in HNSCC, irrespective of PIK3CA mutational status. On-going clinical trials will help determine the developmental strategy of buparlisib while novel combinatory strategies including combination with immune checkpoint inhibitors should be considered. Importantly, biomarker strategies, including wider use of tumor sequencing and circulating tumor DNA, should be utilized to improve patient selection.

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

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

Evolution of Mutational Landscape and Tumor Immune-Microenvironment in Liver Oligo-Metastatic Colorectal Cancer.

Simple SummaryAbout 10% of colorectal cancer patients presents with oligo-metastatic disease. The aim of our study was to assess genetic and immunologic dynamics underlying the oligo-metastatic status, evaluating genotype-phenotype correlations in a clean and homogeneous clinical model of liver-limited metastatic colorectal cancer. We show that loss of KRAS and SMAD4 mutations characterizes the oligo-metastatic disease while a progressive mutational evolution (gain in KRAS, PI3KCA, BRAF and SMAD4) is observed in poly-metastatic evolving disease. Furthermore, high granzyme-B+ T-cells infiltration is found in oligo-metastatic lesions. This study can support innovative strategies to monitor clinical evolution and to induce regressive genetic trajectories in cancer.Genetic dynamics underlying cancer progression are largely unknown and several genes involved in highly prevalent illnesses (e.g., hypertension, obesity, and diabetes) strongly concur to cancer phenotype heterogeneity. To study genotype-phenotype relationships contributing to the mutational evolution of colorectal cancer (CRC) with a focus on liver metastases, we performed genome profiling on tumor tissues of CRC patients with liver metastatic disease and no co-morbidities. We studied 523 cancer-related genes and tumor-immune microenvironment characteristics in primary and matched metastatic tissues. We observed a loss of KRAS and SMAD4 alterations and a high granzyme-B+ T-cell infiltration when the disease did not progress. Conversely, gain in KRAS, PIK3CA and SMAD4 alterations and scarce granzyme-B+ T-cells infiltration were observed when the tumor evolved towards a poly-metastatic spread. These findings provide novel insights into the identification of tumor oligo-metastatic status, indicating that some genes are on a boundary line between these two clinical settings (oligo- vs. poly-metastatic CRC). We speculate that the identification of these genes and modification of their evolution could be a new approach for anti-cancer therapeutic strategies.

CDK 4/6 Inhibition Overcomes Acquired and Inherent Resistance to PI3Kα Inhibition in Pre-Clinical Models of Head and Neck Squamous Cell Carcinoma.

Activating alterations in PIK3CA, the gene coding for the catalytic subunit of phosphoinositide-3-kinase (PI3K), are prevalent in head and neck squamous cell carcinoma (HNSCC) and thought to be one of the main drivers of these tumors. However, early clinical trials on PI3K inhibitors (PI3Ki) have been disappointing due to the limited durability of the activity of these drugs. To investigate the resistance mechanisms to PI3Ki and attempt to overcome them, we conducted a molecular-based study using both HNSCC cell lines and patient-derived xenografts (PDXs). We sought to simulate and dissect the molecular pathways that come into play in PIK3CA-altered HNSCC treated with isoform-specific PI3Ki (BYL719, GDC0032). In vitro assays of cell viability and protein expression indicate that activation of the mTOR and cyclin D1 pathways is associated with resistance to PI3Ki. Specifically, in BYL719-resistant cells, BYL719 treatment did not induce pS6 and pRB inhibition as detected in BYL719-sensitive cells. By combining PI3Ki with either mammalian target of rapamycin complex 1 (mTORC1) or cyclin D1 kinase (CDK) 4/6 specific inhibitors (RAD001 and abemaciclib, respectively), we were able to overcome the acquired resistance. Furthermore, we found that PI3Ki and CDK 4/6 inhibitors have a synergistic anti-tumor effect when combined in human papillomavirus (HPV)-negative/PIK3CA-WT tumors. These findings provide a rationale for combining PI3Ki and CDK 4/6 inhibitors to enhance anti-tumor efficacy in HNSCC patients.

Molecular patterns in salivary duct carcinoma identify prognostic subgroups

Salivary duct carcinoma (SDCa) is a rare cancer with high rate of metastases and poor survival despite aggressive multimodality treatment. This study analyzes the genetic changes in SDCa, their impact on cancer pathways, and evaluates whether molecular patterns can identify subgroups with distinct clinical characteristics and outcome. Clinicopathologic details and tissue samples from 66 patients (48 males, 18 females) treated between 1995 and 2018 were obtained from multiple institutions. Androgen receptor (AR) was assessed by immunohistochemistry, and the Illumina TruSight 170 gene panel was used for DNA sequencing. Male gender, lympho-vascular invasion, lymph node metastasis, and smoking were significant predictors of disease-free survival. AR was present in 79%. Frequently encountered alterations were mutations in TP53 (51%), PIK3CA (32%) and HRAS (22%), as well as amplifications of CDK4/6 (22%), ERBB2 (21%), MYC (16%), and deletions of CDKN2A (13%). TP53 mutation and MYC amplifications were associated with decreased disease-free survival. Analysis of cancer pathways revealed that the PI3K pathway was most commonly affected. Alterations in the cell cycle pathway were associated with impaired disease-free survival (HR 2.6, P = 0.038). Three subgroups based on AR and ERBB2 status were identified, which featured distinct molecular patterns and outcome. Among AR positive SDCa, HRAS mutations were restricted to AR positive tumors without ERBB2 amplification and HRAS mutations featured high co-occurrence with PIK3CA alterations, which seems specific to SDCa. AR negative SDCa were associated with poor disease-free survival in multivariate analysis (HR 4.5, P = 0.010) and none of these tumors exhibited ERBB2 amplification or HRAS mutations. AR and ERBB2 status in SDCa thus classifies tumors with distinct molecular profiles relevant to future targeted therapy. Furthermore, clinical factors such as smoking and molecular features such as MYC amplification may serve as markers of poor prognosis of SDCa.

Deletion of p53 and Hyper-Activation of PIK3CA in Keratin-15+ Stem Cells Lead to the Development of Spontaneous Squamous Cell Carcinoma.

Squamous cell carcinoma (SCC) is the second commonest type of skin cancer, and SCCs make up about 90% of head and neck cancers (HNSCCs). HNSCCs harbor two frequent molecular alterations, namely, gain-of-function alterations of phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha (PIK3CA) and loss-of-function mutations of tumor protein p53 (TP53). However, it remains poorly understood whether HNSCCs harboring different genetic alterations exhibit differential immune tumor microenvironments (TME). It also remains unknown whether PIK3CA hyperactivation and TP53 deletion can lead to SCC development spontaneously. Here, we analyzed the Cancer Genome Atlas (TCGA) datasets of HNSCCs and found that patients with both PIK3CA and TP53 alterations exhibited worse survival, significantly lower CD8 tumor infiltrating lymphocytes (TILs) and higher M0 macrophages than other controls. To better model human tumorigenesis, we deleted TP53 and constitutively activated PIK3CA in mouse keratin-15-expressing stem cells, which leads to the spontaneous development of multilineage tumors including SCCs, termed Keratin-15-p53-PIK3CA (KPPA) tumors. KPPA tumors were heavily infiltrated with myeloid-derived suppressor cells (MDSCs), with a drastically increased ratio of polymorphonuclear-MDSC (PMN-MDSC) versus monocytic-MDSC (M-MDSC). CD8 TILs expressed more PD-1 and reduced their polyfunctionality. Overall, we established a genetic model to mimic human HNSCC pathogenesis, manifested with an immunosuppressive TME, which may help further elucidate immune evasion mechanisms and develop more effective immunotherapies for HNSCCs.

CYLD mutation characterizes a subset of HPV-positive head and neck squamous cell carcinomas with distinctive genomics and frequent cylindroma-like histologic features

Mutations in the tumor suppressor CYLD, known to be causative of cylindromas, were recently described in a subset of high-risk (hr) HPV-positive head and neck squamous cell carcinomas (HNSCC). Pathologic and genetic characterization of these CYLD-mutant carcinomas, however, remains limited. Here, we investigated whether CYLD mutations characterize a histopathologically and genomically distinct subset of hrHPV-positive HNSCC. Comprehensive genomic profiling via hybrid capture-based DNA sequencing was performed on 703 consecutive head and neck carcinomas with hrHPV sequences, identifying 148 unique cases (21%) harboring CYLD mutations. Clinical data, pathology reports, and histopathology were reviewed. CYLD mutations included homozygous deletions (n = 61/148; 41%), truncations (n = 52; 35%), missense (n = 26; 18%) and splice-site (n = 9; 6%) mutations, and in-frame deletion (n = 1; 1%). Among hrHPV-positive HNSCC, the CYLD-mutant cohort showed substantially lower tumor mutational burden than CYLD-wildtype cases (n = 555) (median 2.6 vs. 4.4 mut/Mb, p < 0.00001) and less frequent alterations in PIK3CA (11% vs. 34%, p < 0.0001), KMT2D (1% vs. 16%, p < 0.0001), and FBXW7 (3% vs. 11%, p = 0.0018). Male predominance (94% vs. 87%), median age (58 vs. 60 years), and detection of HPV16 (95% vs. 89%) were similar. On available histopathology, 70% of CYLD-mutant HNSCC (98/141 cases) contained hyalinized material, consistent with basement membrane inclusions, within crowded aggregates of tumor cells. Only 7% of CYLD-wildtype cases demonstrated this distinctive pattern (p < 0.0001). Histopathologic patterns of CYLD-mutant HNSCC lacking basement membrane inclusions included nonkeratinizing (n = 22, 16%), predominantly nonkeratinizing (nonkeratinizing SCC with focal maturation; n = 10, 7%), and keratinizing (n = 11, 8%) patterns. The latter two groups showed significantly higher frequency of PTEN alterations compared with other CYLD-mutant cases (38% [8/21] vs. 7% [8/120], p = 0.0004). Within our cohort of hrHPV-positive HNSCCs, CYLD mutations were frequent (21%) and demonstrated distinctive clinical, histopathologic, and genomic features that may inform future study of prognosis and treatment.

Unique Genomic Landscape of High-Grade Neuroendocrine Cervical Carcinoma: Implications for Rethinking Current Treatment Paradigms.

PURPOSEHigh-grade neuroendocrine cervical cancer (HGNECC) is an uncommon malignancy with limited therapeutic options; treatment is patterned after the histologically similar small-cell lung cancer (SCLC). To better understand HGNECC biology, we report its genomic landscape.PATIENTS AND METHODSNinety-seven patients with HGNECC underwent comprehensive genomic profiling (182-315 genes). These results were subsequently compared with a cohort of 1,800 SCLCs.RESULTSThe median age of patients with HGNECC was 40.5 years; 83 patients (85.6%) harbored high-risk human papillomavirus (HPV). Overall, 294 genomic alterations (GAs) were identified (median, 2 GAs/sample; average, 3.0 GAs/sample, range, 0-25 GAs/sample) in 109 distinct genes. The most frequently altered genes were PIK3CA (19.6% of cohort), MYC (15.5%), TP53 (15.5%), and PTEN (14.4%). RB1 GAs occurred in 4% versus 32% of HPV-positive versus HPV-negative tumors (P < .0001). GAs in HGNECC involved the following pathways: PI3K/AKT/mTOR (41.2%); RAS/MEK (11.3%); homologous recombination (9.3%); and ERBB (7.2%). Two tumors (2.1%) had high tumor mutational burden (TMB; both with MSH2 alterations); 16 (16.5%) had intermediate TMB. Seventy-one patients (73%) had ≥ 1 alteration that was theoretically druggable. Comparing HGNECC with SCLC, significant differences in TMB, microsatellite instability, HPV-positive status, and in PIK3CA, MYC, PTEN, TP53, ARID1A, and RB1 alteration rates were found.CONCLUSIONThis large cohort of patients with HGNECC demonstrated a genomic landscape distinct from SCLC, calling into question the biologic and therapeutic relevance of the histologic similarities between the entities. Furthermore, 73% of HGNECC tumors had potentially actionable alterations, suggesting novel treatment strategies for this aggressive malignancy.

Clinical implications of HER2 mRNA expression and intrinsic subtype in refractory HER2-positive metastatic breast cancer treated with pan-HER inhibitor, poziotinib.

We explored clinical implication of intrinsic molecular subtype in human epidermal growth factor receptor 2 (HER2) + metastatic breast cancer (BC) with pan-HER inhibitor from a phase II clinical trial of poziotinib in refractory HER2+BC patients. For this translational research correlated with phase II clinical trial, we performed an nCounter expression assay, using gene panel including 50 genes for PAM50 prediction and targeted deep sequencing. From 106 participants, we obtained 97 tumor tissues and analyzed gene expression in 91 of these samples. Of 91 HER2+BCs, 40 (44.0%) were HER2-enriched (E) intrinsic molecular subtype, 17 (18.7%) of Luminal A, 16 (17.6%) of Basal-like, 14 (15.4%) of Luminal B and 4 (4.4%) of Normal-like. HER2-E subtype was associated with hormone receptor negativity (odds ratio [OR] 2.93; p = 0.019), 3 + of HER2 immunohistochemistry(IHC) (OR 5.64; p = 0.001), high mRNA expression of HER2 (OR 14.43; p = 0.001) and copy number(CN) amplification of HER2 (OR 12.80; p = 0.005). In genetic alterations, alteration was more frequently observed in HER2-E subtype (OR 3.84; p = 0.022) but there was no association between PIK3CA alteration and HER2-E subtype (p = 0.655). In terms of drug efficacy, high mRNA expression of HER2 was the most powerful predictor of poziotinib response (median progression-free survival [PFS): 4.63months [high] vs. 2.56 [low]; p < .001). In a combination prediction model, median PFS of intrinsic subtypes except Her2-E with high HER2 mRNA expression without PIK3CA genetic alteration was 6.83months and that of the remaining group was 1.74months (p < .001). HER2-E subtype was associated with hormone receptor status, HER2 IHC, CN and mRNA expression and TP53 mutation. In survival analysis, the information of level of HER2 mRNA expression, intrinsic molecular subtype and PI3K pathway alteration would be independent predictors to poziotinib treatment. ClinicalTrials.gov identifier: NCT02418689.

Genetic profiling of somatic alterations by Oncomine Focus Assay in Korean patients with advanced gastric cancer.

Gastric cancer is one of the leading causes of cancer-associated death; however, analysis of its molecular and clinical characteristics has been complicated by its histological and etiological heterogeneity. The present study aimed to estimate somatic mutation profiling in gastric cancer. To do so, targeted next-generation sequencing (NGS) was performed with the Oncomine Focus Assay to compare the clinicopathological characteristics with the mutation profiles in 50 patients with advanced gastric cancer (AGC). Among the 35 hotspot genes and 19 genes for copy number variations (CNVs), 18 single nucleotide variants (SNVs) or small insertions and deletions (14 missense and four frameshift mutations), and 10 amplifications were identified. To examine the association between mutation profiles and clinicopathological characteristics, each element of the clinicopathological characteristics was categorized into three groups: No alteration, PI3K catalytic subunit α (PIK3CA) alterations and alterations other than PIK3CA. Fisher's exact test identified no statistical differences between the clinicopathological characteristics, with the exception of the Tumor-Node-Metastasis (TNM) T stage between the three groups. Cases of AGC with somatic alterations but no PIK3CA exhibited a significant difference in the TNM T stage compared with those with no alterations or PIK3CA alterations (P=0.044). In addition, AGC with PIK3CA alterations was categorized by Lauren's classification to the intestinal type only. The distribution of Lauren's classification in AGC with PIK3CA alterations was statistically different compared with AGC with alterations other than PIK3CA (P=0.028), but not compared with AGC with no alterations (P=0.076). In conclusion, the present study demonstrated a molecular profiling approach that identified potential molecular classifications for gastric cancer and suggested a framework for precision medicine in AGC.

Mutational Landscape of Esophageal Squamous Cell Carcinoma in an Indian Cohort.

Esophageal squamous cell carcinoma (ESCC) is the most common histological subtype of esophageal cancer in India. Cigarette smoking and chewing tobacco are known risk factors associated with ESCC. However, genomic alterations associated with ESCC in India are not well-characterized. In this study, we carried out exome sequencing to characterize the mutational landscape of ESCC tumors from subjects with a varied history of tobacco usage. Whole exome sequence analysis of ESCC from an Indian cohort revealed several genes that were mutated or had copy number changes. ESCC from tobacco chewers had a higher frequency of C:G > A:T transversions and 2-fold enrichment for mutation signature 4 compared to smokers and non-users of tobacco. Genes, such as TP53, CSMD3, SYNE1, PIK3CA, and NOTCH1 were found to be frequently mutated in Indian cohort. Mutually exclusive mutation patterns were observed in PIK3CA–NOTCH1, DNAH5–ZFHX4, MUC16–FAT1, and ZFHX4–NOTCH1 gene pairs. Recurrent amplifications were observed in 3q22-3q29, 11q13.3-q13.4, 7q22.1-q31.1, and 8q24 regions. Approximately 53% of tumors had genomic alterations in PIK3CA making this pathway a promising candidate for targeted therapy. In conclusion, we observe enrichment of mutation signature 4 in ESCC tumors from patients with a history of tobacco chewing. This is likely due to direct exposure of esophagus to tobacco carcinogens when it is chewed and swallowed. Genomic alterations were frequently observed in PIK3CA-AKT pathway members independent of the history of tobacco usage. PIK3CA pathway can be potentially targeted in ESCC which currently has no effective targeted therapeutic options.

Clinical implications of prospective genomic profiling of metastatic breast cancer patients

BackgroundMetastatic breast cancer remains incurable. Next-generation sequencing (NGS) offers the ability to identify actionable genomic alterations in tumours which may then be matched with targeted therapies, but the implementation and utility of this approach is not well defined for patients with metastatic breast cancer.MethodsWe recruited patients with advanced breast cancer of any subtype for prospective targeted NGS of their most recent tumour samples, using a panel of 108 breast cancer-specific genes. Genes were classified as actionable or non-actionable using the European Society of Medical Oncology Scale for Clinical Actionability of Molecular Targets (ESCAT) guidelines.ResultsBetween February 2014 and May 2019, 322 patients were enrolled onto the study, with 72% (n = 234) of patients successfully sequenced (n = 357 samples). The majority (74%, n = 171) of sequenced patients were found to carry a potentially actionable alteration, the most common being a PIK3CA mutation. Forty-three percent (n = 74) of patients with actionable alterations were referred for a clinical trial or referred for confirmatory germline testing or had a change in therapy outside of clinical trials. We found alterations in AKT1, BRCA2, CHEK2, ESR1, FGFR1, KMT2C, NCOR1, PIK3CA and TSC2 to be significantly enriched in our metastatic population compared with primary breast cancers. Concordance between primary and metastatic samples for key driver genes (TP53, ERBB2 amplification) was > 75%. Additionally, we found that patients with a higher number of mutations had a significantly worse overall survival.ConclusionGenomic profiling of patients with metastatic breast cancer can have clinical implications and should be considered in all suitable patients.

Abstract 1427: Co-alteration of the nucleosome remodeler, ARID1A with the PI3K-pathway genes: A signaling opportunity in ovarian cancers

Abstract Objectives: We present mutations in the ARID1A gene and its co-occurrence with alterations of gene(s) of the PI3K pathway (GOP) in our clinical cohort of ovarian carcinomas (OC). We interrogated the signaling opportunity of the co-occurrence in tumorigenic transformation of OC. Methods: A comprehensive genomic-profiling (FoundationOne) was performed in 90 samples from patients admitted to the Avera Center Institute, USA. The mechanistic study included epithelial endometrioid adenoC cell line A2780 and A2780Cis. CRISPR-Cas9 edited OVCAR3 cell line was used for an ARID1A-incompetent model. Algorithmically chosen drugs, single or in combination were tested for their effect on cell cycle, proliferation, apoptosis, 3D growth, and cellular signals. Results: We recorded 87% metastatic and 11% adjuvant tumors with a predominant histological type of high grade serous (58%). A total of approximately 318 alterations in 100 genes was observed. Alterations (point mutation, frameshifts, and splice site) in the ARID1A was found in 8 patients whose tumors are predominantly clear cell carcinomas (6 out of 8). Interestingly none had alteration in germline BRCA1/2. All frameshift mutations were found in the adjuvant category while alterations in the metastatic category were more diverse. Alteration of GOP included PIK3CA, PIK3R1, AKT2, PTEN, AKT1, AKT3, MDM4, PIK3C2B, PIK3CB, TSC1, STK11, PPP2R1A, and FBXW7 with the most number of alterations in PIK3CA, PIK3R1, AKT2, PTEN genes. A heatmap showed that all patients with ARID1A alterations had alterations in at least one GOP. Treatment with PI3K inhibitor, copanlisib dose-dependently induced apoptosis both as a single agent and in combination with BMN673 in OC cells. Conclusion: OC expressing alteration of ARID1A frequently exhibit a co-alteration in at least one GOP, and the co-alteration provide a unique signaling opportunity to test rational combination of pathway-targeted drugs in OC. Our study provides an insight into the mechanism of how a loss of a tumor suppressor gene, ARID1A co-operates with gain of function mutation(s) of an oncogenic pathway, the PI3K pathway. Background: Nucleosome remodelers controls transcription of genes in human health and sickness by dynamic remodeling of human chromatin in a spatiotemporal manner. ARID1A, a core component of the mammalian SWI/SNF nucleosome remodeler complex, which interacts with DNA in a sequence-nonspecific way to regulate cellular processes, including proliferation and differentiation and hence reported to be involved in tumorigenesis (PMID: 25387058). The mutational (inactivating) status of ARID1A in a broad spectrum of gynecological neoplasms (PMID: 22009941) predominantly ovarian and endometrial cancers established its role as an epigenetic tumor suppressor (PMID: 23208470). The mechanistic study included OC cell line A2780 (epithelial), established from an untreated patient with ovarian endometroid adenocarcinoma and an isogenic cis-platin resistant cell line, A2780Cis. The results were being interrogated in the light of tumor cell signaling. Citation Format: Nandini Dey, Jennifer C. Aske, Ethan Thompson, Luis Rojas-Espaillat, David Starks, Pradip De. Co-alteration of the nucleosome remodeler, ARID1A with the PI3K-pathway genes: A signaling opportunity in ovarian cancers [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 1427.

Abstract 785: Genomic markers of response to monotherapy abemaciclib in the nextMONARCH 1 study

Abstract Background: Clinical data characterizing the genomic markers of response to single agent CDK4 &amp; 6 inhibitors are lacking. Abemaciclib is the only CDK4 &amp; 6 inhibitor indicated as monotherapy for HR+, HER2- advanced breast cancer (ABC) following progression on endocrine therapy (ET) and prior chemotherapy (CT) in the metastatic setting. We explored the genomic alterations detected in baseline circulating tumor DNA (ctDNA) from patients (pts) treated with abemaciclib monotherapy in the nextMONARCH 1 study. Methods: nextMONARCH 1 (NCT02747004) was a Phase 2 study evaluating abemaciclib or abemaciclib + tamoxifen in women with HR+, HER2- ABC who had progressed on or after prior ET and had previously received CT. Pts (n=234) were randomized to abemaciclib 150 mg Q12H + daily tamoxifen 20mg (n=78), abemaciclib 150 mg Q12H (n=79), or abemaciclib 200 mg Q12H + prophylactic loperamide (n=77). Available baseline plasma samples for pts in the abemaciclib monotherapy arms (n=146; 94%) were analyzed by the Guardant360 next-generation sequencing (NGS)-based assay to identify potential tumor-related (i.e., somatic) genomic alterations including point mutations (SNV), indels, amplifications, and fusions in over 70 cancer-related genes. Results: The majority of pts (91%) receiving abemaciclib monotherapy had at least one genomic alteration detected in baseline ctDNA. The intent to treat population and the translational research population had similar treatment benefit (7.4 mos [95% confidence interval, CI: 5.5, 9.1] versus 7.4 mos [CI: 5.5, 9.1], p=0.945). The most frequently altered genes detected in baseline ctDNA included: ESR1 (41%), PIK3CA (35%), TP53 (29%), FGFR1 (23%), GATA3 (20%), and MYC (20%). Overall, pts with any detectable ctDNA genomic alterations generally had a shorter median progression-free survival (mPFS) compared to pts without any detectable genomic alterations (6.8 mos [CI: 5.2, 9.0] versus 12.0 mos [CI: 5.4, 23.9], p=0.099). In particular, genomic alterations in PIK3CA, TP53, FGFR1, MYC, NF1, EGFR, ERBB2, or CCNE1 were associated with a significantly shorter mPFS in this heavily pretreated pt population. Pts with detected alterations in RB1 or ESR1 trended towards a shorter mPFS, while pts with detected alterations in GATA3 trended towards a longer mPFS. Conclusions: To our knowledge, this is the first exploratory study to evaluate the genomic markers of response to monotherapy CDK4 &amp; 6 inhibitor in a heavily pretreated pt population with HR+, HER2- ABC. These results provide insight into the genomic landscape of ABC and, if validated, could inform further trials of CDK4 &amp; 6 inhibitors. Citation Format: Erika P. Hamilton, Javier Cortes, Guy Jerusalem, Peter A. Kaufman, Ozgur Ozyilkan, Roberto Hegg, Lacey M. Litchfield, Hong Wang, Hillary T. Graham, Sameera R. Wijayawardana, Valerie M. Jansen, Miguel Martin. Genomic markers of response to monotherapy abemaciclib in the nextMONARCH 1 study [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 785.

Abstract NG16: Double PIK3CA mutations in cis increase oncogenicity and sensitivity to PI3Kα inhibitors

Abstract NG16: Double <i>PIK3CA</i> mutations in <i>cis</i> increase oncogenicity and sensitivity to PI3Kα inhibitors

Corrigendum to 'clinical and genetic landscape of treatment naive cervical cancer: Alterations in PIK3CA and in epigenetic modulators associated with sub-optimal outcome'.

The authors wish to clarify that the authors Aljosa Mandic, Katarina Koprivsek, and Goran Malenkovic are also affiliated with Faculty of Medicine Novi Sad, University of Novi Sad, Serbia, as well as Gynecologic Oncology Department Clinic for Operative Oncology, Institute of Oncology of Vojvodina, Serbia.

Real world data analysis of next generation sequencing and protein expression in metastatic breast cancer patients

Next generation sequencing (NGS) together with protein expression analysis is back bone of molecularly targeted therapy in precision medicine. Our retrospective study shows our experience with NGS of 324 genes in combination with protein expression in patients with advanced breast cancer (aBC). The primary purpose was to analyze the prevalence of individual genetic alterations combined with protein expression to define potential targets for an individualized therapy. Between April 2018 and September 2019, 41 patients with aBC were offered a NGS test. The test was used to detect clinically relevant genomic alterations and to support further targeted therapy decisions. Hormone receptors, ERBB2 of tumors and PD-L1 was stained by immunohistochemistry. The data was recorded up to September 2019. After prior consent 41 results were available for further analysis. The most common BC subtypes were triple-negative (n = 16), HR+/ERBB2− (n = 15), and ERBB2+ (n = 9), with one missing data of the primary tumor. 27 patients had more than one genetic alteration. The most common alterations were PIK3CA (n = 14) and ERBB2 alterations (n = 11). Followed by ESR1 (n = 10), FGFR1 (n = 7) and PTEN (n = 7). 68% of the alterations were clinically relevant (tier I and II of ESCAT classification). The most common treatment recommendation was ERBB2-directed therapy (single or double blockade, trastuzumab emtansine and lapatinib) followed by alpelisib in combination with fulvestrant. Comprehensive genomic profiling combined with protein expression analysis in aBC allowed a guided personalized therapy for half of our patients. So far there are no well-defined tools allowing interpretations of genomic alterations detected by NGS in combination with protein expression and other factors.