This abstract was not presented at the symposium.
Background Deregulation of the phosphoinositide 3-kinase (PI3K) signaling pathway is essential to malignant cellular processes of breast cancer, including proliferation and drug response. Oncogenic somatic mutations of the PI3K pathway are pervasive in breast cancer. However, identification of impactful mutations and determination of their relevance to major components of this pathway remains difficult. This study was conducted to identify the landscape of somatic mutations in the PI3K pathway in a Chinese population. Notably, we developed a recombination-based mutation barcoding (ReMB) library which enables a high-throughput mutation-phenotype screens for vulnerable mutations that contribute to the cancer development and drug resistance. Methods We collected 149 breast cancer specimens in a Chinese population and performed Ion Torrent Amplicon Sequencing for the key genes in PI3K/AKT pathway: PIK3CA, PIK3R1, AKT1, AKT2, AKT3, PTEN, PDK1 at 1000× coverage. To discriminate between 'driver' and 'passenger' mutations, we developed a recombination-based mutation barcoding (ReMB) library that contained the novel identified mutations and that reported in TCGA and COSMIC databases in PIK3CA and PIK3R1 genes, each mutation tagging with a specific barcode to identify their potential oncogenic and drug-resistant characteristics. The unique barcode representing each mutation was detected using Illumina Miseq sequencing following proliferation and drug response selection (doxorubicin and BKM-120) assays to screen the functional mutations. Results We identified that mutations in PIK3CA (44%), PIK3R1 (17%), AKT3 (15%) and PTEN (12%) were prevalent and diverse in Chinese patients with a high proportion of tumours harboring multiple mutations, especially PIK3CA plus PIK3R1 mutations (9.0%). With ReMB screening, we found 11 non-synonymous impactful mutations in PIK3CA; these included eight proliferation-driving mutations, nine doxorubicin-resistant mutations, and eight BKM120-resistant mutations. The highest-ranking PIK3CA mutations include the deleterious mutations E542K, E545K and H1047R/L as well as mutations of unknown significance, including E39K, N345I, E453K, and G1049R. We also identified six non-synonymous impactful mutations inPIK3R1, including five proliferation-driving mutations, six doxorubicin-resistant mutations, and five BKM120-resistant mutations. The PIK3R1 impactful mutations include E160D, Q329L, N564D and K674R. Most impactful mutations in PIK3CA and PIK3R1 occurred at residues lying at the interfaces between p110α and p85α, or between the functional domains within p110α. These PIK3CA and PIK3R1 impactful mutations exhibit a mutually exclusive pattern, leading to oncogenesis and hyperactivity of PI3K pathway. Additionally, impactful mutations in PIK3CA are tightly associated with hormone receptor positivity. Conclusion This study identified the landscape of somatic mutations in the PI3K pathway in Chinese breast cancer patients. A novel developed ReMB screening platform allows the rapid identification of impactful PIK3CA and PIK3R1 mutations in breast cancer and has important implications for PI3K-targeted therapy. Citation Format: Chen L, Yang L, Hu X, Shao Z. High-throughput barcode screening elucidates the functional characteristics and mutual relevance of PIK3CA and PIK3R1 somatic mutations in Chinese patients with breast cancer [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 P4-04-07.
KEYWORDS spinal diffuse large B-cell lymphoma; Surveillance, Epidemiology, and End Results 2 database; prognostic factors; survival; nomogram. 3 Abstract Background: Spinal diffuse large B-cell lymphoma (DLBCL) is a rare and malignant tumor, while few studies researched the prognostic factors. The prognostic factors which impacts on spinal DLBCL are not clear. Although chemotherapy was recognized as an optimal treatment method, but the curative effect of radiotherapy and surgery were controversial.Methods: The records of patients with spinal DLBCL were selected from the SEER database from 1991 to 2016. The incidence obtained by database was analyzed by Joinpoint Regression Program. The optimal cut-off values of age and year of diagnosis were identified by X-tail program. Univariate and multivariate survival analysis were calculated to identify independent prognostic factors. Prognostic factors were included to predict the survival possibility compared with 5 years of overall (OS) and cancer-specific survival (CSS) via the new nomograms. Results: A total of 917 patients were enrolled. Age, year of diagnosis and chemotherapy were demonstrated as independent prognostic factors for CSS and OS, and primary site was another independent prognostic factor for CSS. However, radiotherapy and surgery might be ineffective in survival. All factors were included to generate the nomograms for CSS and OS. The concordance indices (C-index) for internal validation of OS and CSS prediction were 0.697 (95%CI:
Background The deregulation of the PI3K/AKT signaling pathway is essential to malignant cellular processes of breast cancer, including proliferation, apoptosis, and drug response. Oncogenic activating somatic mutations in the PI3K/AKT pathway are pervasive. However, it remains difficult to discriminate between driver and passenger mutations. This study was conducted to identify the landscape of genetic mutations in the PI3K/AKT pathway using Amplicon Sequencing in a Chinese population. Notably, we developed a Gateway-based mutation barcoding (GaMB) library which enables a high-throughput mutation-phenotype screen for specific vulnerable mutations that contribute to the cancer development and drug resistance. Method We collected 149 breast cancer specimens in a Chinese population and performed Ion Torrent Amplicon Sequencing for the key genes in PI3K/AKT pathway: PIK3CA, PIK3R1, AKT1, AKT2, AKT3, PTEN, PDK1, and the canonical tumor suppressor gene TP53, at 1000× coverage. Next, we established a high-throughput GaMB library that contained all of the PIK3CA mutations, either newly identified in Chinese population or reported in TCGA and COSMIC database, and tagged each mutations with a specific barcode. We then applied this library to functional screening processes using proliferation and drug response selection (doxorubicin or BKM-120) assays through which we screened the functional mutations with specific characteristics. The genomic DNA of the pooled surviving cells from the library, as well as the original cells before the screenings, was extracted and used for PCR amplification of the barcode regions, and then detected using Illumina Miseq sequencing to analyze the functional mutations. We then validated the cellular 2D- & 3D- proliferation abilities and the status of PI3K/AKT pathway activation in presence of identified mutations, respectively. Result Mutations in the PIK3CA (44%), PIK3R1 (37%), AKT3 (15%) and PTEN (12%) genes were the most prevalent. Mutations in PIK3CA were present in 65 samples (43.6%) which is similar to that reported in TCGA database. PIK3R1 (37%) was found significantly mutated, with a novel recurrent mutation, N595S, being identified in 24 patients. Similarly, AKT1 (10.1%), AKT2 (10.1%), and AKT3 (14.8%) mutations were present at a higher frequency in our population than has been reported in the TCGA and COSMIC database. In the PIK3CA-GaMB library, our highest-ranking mutations included the previously validated deleterious mutations H1047R and E545K and several mutations of uncertain significance, including E39K, G1049R, N345I, N345K, M1043V, and H1047T. In the validation assays, we found a high phenotype-consistency of these identified mutations using these functional validation techniques. The breast cancer cells harboring identified mutations exhibit a relatively higher proliferation ability and tolerance to chemotherapy and pathway inhibitors. Conclusion This study identified the landscape of genetic mutations in the PI3K/AKT pathway using Amplicon Sequencing in a Chinese population. A novel developed GaMB screening platform may allow the rapid identification of significant mutations that dominate breast cancer development and drug responses during treatment. Citation Format: Chen L, Yang L, Yao L, Hu X, Shao Z. The mutation detection and a high throughput screening of driver mutations in PI3K/AKT pathway based on next generation sequencing [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr P1-07-13.
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