bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of the intratumoral heterogeneity of PIK3CA mutant alleles in breast cancer (BC): Implications for the luminal (LUM) phenotype.
Authors: De Mattos-Arruda Leticia , Cortes Javier , Aura Claudia , Oliveira Mafalda , Navarro Alejandro , Caratu Ginevra , Sanchez-Pla Alex , Gregori Josep , Saura Cristina , Tabernero Josep , Seoane Joan , Vivancos Ana 
Published: March 2020

10511 Background: The hyperactivation of the phosphatidylinositol 3-kinase (PI3K) pathway may confer endocrine therapy resistance and is an attractive target for LUM patients (pts). However, PI3KCA mutations could be heterogeneously distributed within the tumor as different genetic clones and this could have therapeutic implications. Our aim was to assess the frequency of PIK3CA mutant alleles in different BC phenotypes. Methods: DNA was obtained from 75 consecutive BC FFPE samples and was profiled with the OncoCarta Panel v1.0 (Sequenom). Frequencies of mutant alleles (% mutant allele, mA) of PIK3CA mutations were extracted from the MassARRAY spectrum data. The viable tumor area (TA) was scored by H&E. Pts were stratified by BC phenotypes: ER+/HER2- (LUM); HER2+ (HER2); triple negative (TN). Results: 25.3% of pts had PIK3CA mutations. The mean PIK3CA mA (p=0.04) and mean TA (p=0.07) differed among phenotypes. LUM tumors demonstrated greater frequencies of PIK3CA mutation (38% vs.15%, p=0.05) and mean PIK3CA mA (31% vs.17%, p=0.01) than non-LUM.There was a significant linear correlation between mA and TAfor LUM tumors (r=0.91); when HER2 and TN tumors were also considered this relation was less pronounced (r=0.66). Overall, LUM pts, median age 55 (42-84), had significantly better clinical outcomes (p=0.00024), whilst analyses of prognosis did not differ among LUM pts (PIK3CA mutant vs. wild-type, p=0.68) nor mutant pts (LUM vs. non-LUM, p=0.36). Outcomes will be presented. To assess the intratumoral heterogeneity of PIK3CA mutations, we determined the mA/TA ratio. The mA/TA ratio should be 0.5 for a homogeneous distribution of the heterozygous PIK3CA mutation. The ratio of LUM patients was close to 0.5, while for non-LUM it was lower, suggesting a non-homogeneous distribution of PIK3CA mutant alleles in non-LUM tumors. Conclusions: Our analysis indicates that LUM tumors tend to be homogeneous regarding PIK3CA mutation as compared to HER2 and TN. This suggests that PIK3CA oncogenic activation could be an early hit for tumor initiation in LUM tumors, which could be more specifically targetable; thus, pts would derive greater benefit from PI3K-inhibitors plus hormonal therapy.
Clinical characteristics and chemotherapy options of triple-negative breast cancer: Role of classical CMF regimen.
Authors: Hur Min Hee , Kang Tae Ho , Im Ra Joo , Kim Se Won , Yoon Chan Seok , Ko Seung Sang , Lee Haekyung , Lee Ji Hyun , Kang Sung-Soo 
Published: March 2020

1053 Background: Triple-negative breast cancer is a high risk breast cancer that lacks the benefit of specific targeted therapy. We investigated the clinicopathologic characteristics between triple-negative breast cancers (TNBC) and non-TNBC. And we also analyzed the effect of chemotherapy options such as classical CMF regimen, anthracycline-based, or taxane-based chemotherapy. Methods: A total of 826 invasive breast cancer patients were evaluated from March 2003 to December 2008. We investigated them retrospectively, who had the median follow-up for 88 months. We examined the differences between TNBC compared with non-TNBC in relation to the clinicopathologic parameters, chemotherapy regimen, overall survival (OS). Results: 156 (18.9%) cases among 826 patients were triple negative breast cancers. There were significantly positive associations with younger age (below 35 years), large tumor (>2cm), high stage, poorly differentiated nuclear grade, poorly histologic grade in TNBC. Positive lymph node, lymphovascular invasion were not significantly different between TNBC and non- TNBC. A total of 677 patients were treated with chemotherapy. In TNBC patients, 142 (93.4%) patients were treated with chemotherapy more than in 535 (61.4%) of non- TNBC patients. The chemotherapy in TNBC patients was composed of classical CMF (47.9%), anthracycline-based regimen (25.4%), taxane-based regimen (26.8%). 19 cases (12%) of TNBC experienced locoregional or systemic metastases. 48 (7.2%) patients of non- TNBC did local or systemic metastases. Patients with TNBC had worse 5-year OS than with non-TNT (95.7% vs 98.6%, p=0.01). Interestingly, patients treated with CMF regimen were better 5-year OS than with anthracycline-based, or taxane-based regimen in TNBC (100% vs 96.9% vs 89.2%, p=0.001). There was no survival difference among chemotherapy regimens in non-TNBC patients. Conclusions: Patients with TNBC have poor prognosis compared with non-TNBC. Classical CMF regimen for TNBC patients may be more effective than anthracycline-based or taxane-based regimens.
Profiling of circulating tumor cells isolated from 105 metastatic gastric cancer patients revealed HER2 overexpression/activation for potential use in clinical setting.
Authors: Hazra Saswati , Lee Jeeyun , Kim Phillip Sangwook , Kim Kyoung-Mee , Liu Limin , Webster Edvelyn , Fithian Andrew , Singh Sharat , Kang WonKi 
Published: March 2020

10535 Background: Gastric cancer (GCA) is the second leading cause of cancer mortality in the world. Survival of patients with advanced GCA treated with chemotherapy remains low. New targeted therapies are urgently needed. There is mounting evidence of the role of HER2 overexpression in patients with GCA, and it has been highly correlated to poor outcomes with more aggressive disease. The ability to accurately determine HER2 status by testing circulating tumor cells (CTCs) may improve patient treatment by allowing ongoing assessment of HER2 status during treatment and/or identifying additional patients who could potentially benefit from HER2- targeted therapy. Methods: The Collaborative Enzyme Enhanced Reactive-immunoassay (CEER) was utilized to determine the expression and activation (phosphorylation) levels of HER2 in CTCs isolated from blood specimens obtained from 105 metastatic GCA patients. Results: Utilizing the CEER platform, the levels of HER2 expression and phosphorylation were determined for CTCs isolated from metastatic GCA patients. Evaluable CTCs were found in 33% (35/105) of enrolled patients. Out of 35 patients, 7 patients (20%) have high HER2 over expression, 6 patients (17%) have moderate HER2 expression and 11 patients (31%) have HER2 activation (phospho positive) with no HER2 over-expression. Conclusions: When CTCs were present, the CEER assay identified varying levels of HER2 involvements in 68% of metastatic GCA patients. HER2 positive CTCs could serve as a prognostic and/or predictive marker in patients with advanced GCA and CTC-HER2 profile shifts can be utilized to monitor the treatment efficacy.
Biomarkers of response to Akt inhibitor MK-2206 in breast cancer.
Authors: Sangai Takafumi , Akcakanat Argun , Chen Huiqin , Tarco Emily , Wu Yun , Do Kim-Anh , Miller Todd W , Arteaga Carlos L. , Mills Gordon B. , Gonzalez-Angulo Ana M. , Meric-Bernstam Funda 
Published: March 2020

1054 Background: Akt significantly contributes to cancer pathogenesis. PTEN, a negative regulator of PI3K/Akt signaling, is mutated or decreased, and PIK3CA is frequently mutated in multiple cancer lineages. We hypothesized that MK-2206, an allosteric Akt inhibitor, would inhibit Akt signaling thus blocking cancer cell growth, and PTEN and/or PIK3CA mutations may confer MK-2206 sensitivity in breast cancer. Methods: After determining sensitivity to MK-2206 in16 cell lines, the effect on Akt signaling was tested by reverse-phase protein array analysis and western blotting. The effect to cell cycle progression and cell death were analyzed by flow cytometry. Using RNA knockdown technique, the effect of PTEN, PIK3CA and Akt on MK2206 sensitivity was tested. Anti-tumor effect in vivo with or without paclitaxel was tested using PTEN-mutant ZR75-1 breast cancer xenografts. Results: MK-2206 inhibited Akt signaling and cell cycle progression, and increased apoptosis in a dose-dependent manner in breast cancer cell lines. Cell lines with PTEN or PIK3CA mutations were more sensitive to MK-2206 (P=0.0337), however, a number of lines with PTEN/PIK3CA mutations were MK-2206-resistant. Small interfering RNA (siRNA) knockdown of PTEN in breast cancer cells increased Akt phosphorylation concordant with increased MK-2206 sensitivity. Stable transfection of PIK3CA E545K or H1047R mutant plasmids into normal-like MCF10A breast cells enhanced MK-2206 sensitivity. Cell lines that were less sensitive to MK-2206 had lower ratios of Akt1/Akt2 and had less growth inhibition with Akt siRNA knockdown. In ZR75-1 xenografts, MK-2206 treatment inhibited Akt signaling, cell proliferation, and tumor growth. In vitro, MK-2206 showed a synergistic interaction with paclitaxel in MK-2206-sensitive cell lines, and this combination had significantly greater antitumor efficacy than either agent alone in vivo. Conclusions: MK-2206 has antitumor activity alone and in combination with chemotherapy. This activity may be greater in tumors with PTEN loss or PIK3CA mutation, providing a strategy for patient enrichment in clinical trials. However, not all tumors with PIK3CA/PTEN aberrations are MK-2206-sensitive, emphasizing the need for additional markers of response.
Use of next-generation sequencing (NGS) to detect high frequency of targetable alterations in primary and metastatic breast cancer (MBC).
Authors: Pusztai Lajos , Yelensky Roman , Wang Bailiang , Avritscher Rony , Symmans William Fraser , Lipson Doron , Palmer Gary A. , Moulder Stacy L. , Stephens Philip , Wu Yun , Cronin Maureen T. 
Published: March 2020

10559 Background: The aim of this study was to assess the frequency of genomic alterations in breast cancer potentially treatable with approved targeted agents or investigational drugs in clinical trials. NGS was performed in a CLIA setting (Foundation Medicine). Methods: DNA was extracted from needle biopsies of 33 pre-therapy primary and 17 MBCs (mean age 52 yrs; 58% ER+, 20% HER2+, 30% triple negative) obtained prospectively for biomarker discovery and preserved in RNAlater. Patients with MBC received an average of 7 drugs (range 5-17) including adjuvant therapy before biopsy for this research; 13 biopsies were from soft tissues, 3 from liver and 1 from bone. Sequencing was targeted to 3230 exons in 182 cancer-related genes and 37 introns in 14 genes often rearranged in cancer. Average median depth was >1200x. Results: All biopsies yielded sufficient DNA. NGS revealed a total of 117 known driver mutations across 36 genes (per-tumor average=2.5, range 1-6), including 37 base substitutions (32%), 28 indels (24%), 42 amplifications (36%) and 10 homozygous deletions (9%). NGS identified HER2 gene amplification in 6/7 cases scored HER2+ by FISH. The average number of functionally important alterations was surprisingly similar, 2.3 in primaries vs 2.8 in heavily treated MBCs (p=0.32). Remarkably, 25/33 (76%) of primary and 14/17 (82%) of MBCs had at least 1 genomic alteration targetable with an FDA approved drug or novel agent in clinical trials. These included: ERBB2 alterations (n=9), PIK3CA mutations (n=8), NF1 mutations (n=4, candidate for PI3K/MEK inhibitors), AKT1-3 mutations (n=5, PI3K inhibitors), BRCA1/2, (n=6, PARP inhibitors), and CCND2 (n=3)/CDKN2A (n=3) mutations (CDK inhibitors). Numerous other alterations with less apparent therapeutic implications were also observed. Conclusions: Comprehensive NGS profiling in breast cancer needle biopsies showed high frequency of genomic alterations linked to a clinical treatment option or clinical trials of targeted therapies. These results demonstrate it is feasible to use NGS to guide targeted therapy. Prospective testing of the diagnostic/predictive value of this patient selection approach is currently under way.
The role and significance of FoxM1 in invasive breast cancer.
Authors: Yom Cha Kyong , Lee Kyung-Min , Han Wonshik , Kim Sung-Won , Moon Hyeong-Gon , Shin Hee-Chul , Kang Eunyoung , Noh Dong-Young 
Published: March 2020

1056 Background: The Forkhead Box protein M1 (FoxM1) is known to regulate a variety of biologic processes in mammalian cells including cell growth and survival, angiogenesis, DNA damage response, chemotherapeutic drug resistance, and cancer cell migration and invasion. We evaluate the role and significance of Fox M1 in primary breast cancer in vitro and analyzed the relation with FoxM1 expression and clinicopathologic features. Methods: Immunohistochemical staining was used for evaluation of cytoplasmic expression of FoxM1 with TMA of invasive breast cancer. In various breast cancer cell lines, we evaluated FoxM1 expression and treated docetaxel/cisplatin in combination with Siomycin A (FoxM1 inhibitor) for BT20 cell line. Results: From Nov 1995 to Jul 2007, in 84 patients with stage 1-3 invasive breast cancer, FoxM1 expression was noted in 58.7%. Median follow-up duration was 85.1 months. Lymphovascular invasion was positively correlated with FoxM1 expression (p=0.040). In multivariate analysis, FoxM1 expression (p=0.005), HR negativity (p=0.002), high histologic grade (p=0.023), hign nuclear grade (p=0.045), lymphovascular invasiveness (p=0.017), and stage 3 cancer (p=0.015) matched poor disease-free survival. In vitro study, FoxM1 was expressed BT474, JIMT-1, BT20, HCC-1937, and MDA-MB-231 cell lines. The inhibition of FoxM1 had synergistic effect on cisplatin treatment, not docetaxel in BT20 cell. Conclusions: FoxM1 expression was noted in triple negative breast cancer cell lines and its inhibition had synergistically cytotoxic effect on BT20 cell line in combination with cisplatin. Although the further in vivo and clinical study should be needed to draw the solid conclusions, FoxM1 could be both a promising target of treatment for triple negative breast cancer and a independent prognostic factor.
Independent validation of prognostic value of 22 micrornas (miRs) in stage I-II squamous cell lung cancer (SqCLC).
Authors: Skrzypski Marcin Tomasz , Czapiewski Piotr , Biernat Wojciech , Goryca Krzysztof , Wyrwicz Lucjan , Jassem Ewa , Pawlowski Ryszard , Rzyman Witold , Jassem Jacek 
Published: March 2020

10561 Background: About 50% of NSCLC patients (pts) will develop distant metastases following pulmonary resection. Currently, apart from clinical stage at diagnosis, there are no reliable factors to select high risk pts for adjuvant chemotherapy. We previously demonstrated prognostic value of 22 miRs in frozen tissue samples of early stage SqCLC, and the feasibility of their expression assessment in formalin fixed paraffin embedded (FFPE) samples (Skrzypski et. al. J Clin Oncol 2010;28;15s). In this study, we validated the prognostic value of these miRs in an independent cohort of early SqCLC pts. Methods: FFPE tumor samples were obtained from 132 stage I-II SqCLC pts who underwent radical pulmonary resection, 42% of whom developed distant metastases. Median follow-up of pts who did not develop metastases was 5.6 years (range, 4.1-10.0 years). miRs were isolated from tumor tissue with RecoverAll kit (Ambion). Expression of 22 miRs previously found to be related to the risk of metastases was analyzed by RT-PCR assay (Appliedbiosystems). Raw data were normalized vs. the expression of U6. Individual miRs and the risk score comprising 5 most predictive miRs were correlated with distant metastases-free survival (MFS). Results: Eight miRs were significantly relatedtoMFS. MiR-192 was significantly correlated with MFS (p=0,0007; p=0,02 after correction for multiple comparisons). The 5-miR risk score was an independent prognostic factor (p=1.70E-06) in a multivariate analysis comprising stage (p=1,10E-03) and histological grade (p=0,46). Using the median of the risk score as a cut-off value, the median MFS was 1.73 years in the high risk group, and not reached in the low risk group (HR=2.11). The sensitivity and specificity of the risk score to predict the occurrence of distant metastases were 66% and 64%, respectively. Conclusions: Risk score based on expression of 5 miRs is a strong and independent predictor of distant relapse in operable early SqCLC.
Comparative analysis of myeloid-derived suppressor cell (MDSC) subsets in patients with gastrointestinal (GI) malignancies.
Authors: Duffy Austin G. , Zhao Fei , Fioraventi Suzanne , Greten Tim 
Published: March 2020

10566 Background: Immunotherapy represents a potential new treatment option for patients with cancer. Myeloid derived suppressor cells (MDSCs) constitute a heterogenous cell population, which inhibit the host anti-tumor immune response, limiting the effectiveness of both immune and non-immune treatments. MDSC are known to be increased in patients with GI cancer. Characterization of MDSC in humans has been difficult with heterogeneous phenotype classification. Differences in processing are also potentially important. The aim of this study was to perform a comparative analysis of MDSC subsets in patients with GI cancer. Methods: Fluorescence activated cell sorting (FACS) analysis was performed on PBMC and whole blood (WB) from healthy adults (N=44) and patients with GI cancer (N=41). MDSC subsets were enumerated using the following antibodies: anti-CD14; anti-CD15; anti-HLA-DR; anti-CD33; anti-CD11b; 7-AAD. Suppressor function of MDSC subsets was tested using FACS sorted MDSC subpopulations co-cultured with CD3/CD28-stimulated autologous effector cells. Proliferation and IFN-g were measured. Results: The frequencies of Monocytic (Def: CD14+, HLA-DR -/low) and Granulocytic (Def: CD15+,CD14-CD33+CD11b+) MDSC are shown in the table below. Monocytic MDSC were increased in the blood of patients (vs control; P<.0001) and frozen (vs fresh PBMC; P<.05). While CD15+ cells were increased in cancer patients we did not find an increase in granulocytic MDSC. Functional studies will also be presented. Conclusions: Monocytic MDSC are more frequent in patients with advanced GI cancer compared to healthy volunteers. An increase in this population was also found in WB and frozen PBMC compared to fresh PBMC reflecting the need for homogenous preparation in studies evaluating this population in humans. While CD15+CD14- cells were also increased in cancer patients we did not find an increase in CD14-CD15+CD33+CD11b+ cells. [Table: see text]
Retrospective analysis of gene expression profiling and TTF-1 staining in cancer of unknown primary (CUP).
Authors: Chiang Wendy M. , Strauss Gary M. , Nystrom J. Scott 
Published: March 2020

10579 Background: CUP involves extensive use of immunohistochemical (IHC) stains because no individual marker is highly both site specific or sensitive. IHC algorithms lack standardization and may even eliminate actual primary sites. Extensive validation studies with gene expression profiling (GEP) has shown it be a new diagnostic technique that further contributes tumor site location in CUP. Thyroid transcription factor-1 (TTF-1) IHC stain is commonly used to identify the pulmonary origin of CUP (particularly adenocarcinoma) and is often used to exclude lung primary in CUP patients. This study evaluates the utility of TTF-1 staining in lung primaries (specifically non-small cell lung carcinoma - NSCLC) of CUP to GEP testing. Methods: This retrospective study contains data obtained from a registry of physicians who received the GEP-based Tissue of Origin (TOO) test (Pathwork Diagnostic, Sunnyvale, CA) between 07/2009 and 12/2009 on CUP cases. Sixty-six physicians contributed 111 TOO test cases. Only cases that had TTF-1 done were included for analysis and these were compared to TOO NSCLC results. Results: Out of 111 cases, there were 73 analyzable TTF-1 results with 12 cases of NSCLC and 61 cases of non-NSCLC by TOO (see TABLE). Assuming that the results of TOO testing accurately indicated the true primary site, the sensitivity and specificity of TTF-1 was 50% and 90%, respectively. The false negative rate was 50%, indicating that half of the identified NSCLC cases in this series had negative TTF-1. On the other hand, 10% of the 61 cases with primaries other than NSCLC (none of whom had thyroid cancer), had positive TTF-1. The “false positive” TTF-1 cases comprised 4 ovarian, 1 breast and 1 colorectal as the site of origin. Conclusions: TTF-1 has limited utility in identifying NSCLC in the setting of CUP. Half of NSCLCs identified by TOO testing had negative TTF-1, and 10% of non-lung primaries were TTF-1 positive. Negative TTF-1 should not be used to exclude NSCLC in the workup of CUP. [Table: see text]
Next-generation sequencing mutational analysis of triple-negative breast cancer patients from matched FFPE and fresh frozen samples.
Authors: Landers Mark , Meredith Rhonda , Lee Jerry , Wang Yipeng , Lee Byung-In , Monforte Joseph 
Published: March 2020

1058 Background: TNBC is an aggressive subtype of breast cancer accounting for 10-15% of all cases. TNBC tumors (ER-/PR-/HER-) are more common in patients with BRCA mutations. BRCA mutations leading to homologous DNA repair deficient tumors enhance the efficacy of chemotherapy and PARP inhibitors. BRCA mutations have been identified in 20% of patients without family history. Identification of germline and somatic BRCA mutations in unselected patients could increase the number of patients who benefit from these therapies. Determining BRCA mutational status from FFPE and fresh frozen specimens may enable clinical studies in these patient populations.We describe the development of an NGS BRCA mutational assay compatible with FFPE and fresh frozen samples using tumor/adjacent normal matched tissues. Methods: Matched samples were purchased from Cureline. gDNA was isolated by lysis/column purification (Qiagen) and enriched for BRCA exons/flanking regions (Halogenomics Selector). Fragment libraries were constructed (Ion Torrent frag express) and prepared for sequencing by emPCR (Ion Torrent Template Xpress). Libraries were sequenced for 65 cycles (Ion Torrent PGM) yielding 2-4M reads/sample. Variants were called from tMAP aligned reads by GATK and VarScan. Overlapped exonic variants were filtered by p-value (<0.0001) from VarScan. Results: In the first patient set normalized average depth of BRCA exon coverage was 64X and 72X per 150K reads in FFPE and fresh frozen tissues respectively covering 95-100% of target. hg19 alignment rates varied between 97-99% across all samples. Similar numbers of variants were called in both FFPE (12) vs. fresh frozen (13) with a corresponding mean duplicate removed depth of coverage of 23.3X and 42.4X at the called positions. 10/13 calls in fresh frozen overlapped with those in FFPE. A tumor specific somatic frameshift insertion in BRCA2 was detected in both FFPE and fresh frozen tissues. Conclusions: Results indicate that NGS mediated BRCA mutational analysis demonstrates equivalent utility in both FFPE and fresh frozen tumor samples although more sequencing reads are required to produce equivalent depth of coverage starting from FFPE samples.