bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient segmentation assay for MAPK pathway mutations.
Authors: Marton Matthew John , Chang Ken , Galuska Stefan , Samatar Ahmed , Zhang Ling , Weiner Russell 
Published: March 2020

11059 Background: Mutational status of solid tumors is increasingly important for identifying the best treatment options. Tumors harboring activating mutations in RAS and RAF result in constitutive activation of the RAS/MAPK signal transduction pathway and do not respond well to MAPK pathway inhibitors. Scientific attention is mostly focused on the major mutational hotspots in these genes (e.g., KRAS codons 12, 13 and 61, BRAF codon 600). However, there is increasing evidence that other mutations can be tumorigenic. Thus, there is a need for highly sensitive and specific assays to detect these mutations. To address this need, we developed and analytically validated an assay that detects 33 mutations that activate the MAPK pathway. Methods: We constructed a set of multiplexed single nucleotide primer extension (SNPE) assays that detect 33 activating mutations in KRAS, NRAS, or BRAF. The assays were analytically validated using a set of 60 formalin fixed paraffin embedded (FFPE) tissue samples from various tumor types, cell lines, and oligos with specific mutations. Performance was compared to dideoxy sequencing. Discordant calls were resolved with next generation sequencing (NGS). The limit of detection was determined by serial dilution of mutant DNA into wildtype DNA. Results: The developed multiplexed assay requires only 15 ng genomic DNA, relies on established technology, is cost effective, is amenable to high throughput, and can yield a patient eligibility decision in a CLIA lab in 4 days, making it a practical alternative to a NGS-based assay. Since low allele frequency mutations may be critical to patient survival, we devised a replicate strategy to increase the specificity and sensitivity of the assay. We showed that analysis of technical triplicates relative to no replicates increased the sensitivity from 97 to 100% and the specificity from 91 to 100%. Limit of detection varied from 2 -12%, depending on the mutation. Conclusions: We developed a selective and sensitive SNPE assay capable of detecting 33 hotspots in the MAPK pathway. Our approach reduced false positive and false negative calls of low allele frequency samples. The assay has clinical applicability for the selection of patients for early phase clinical studies.
Exploration of a plucked hair gene signature as a potential pharmacodynamic marker for the dual PI3K/mTOR inhibitor VS-5584.
Authors: Weaver David T. , Paterson Daniel , Miele Gino 
Published: March 2020

11064 Background: The PI 3-kinase/mTOR pathway plays a central role in cancer cell proliferation, survival, and cancer stem cell mechanisms. Depending on the mode of pathway activation, different PI3K isoforms and mTOR complexes have been shown to play essential roles in oncogenesis. VS-5584 inhibits PI3K/mTOR signaling with equipotency against all four human Class I PI3K isoforms and the mTOR kinase. VS-5584 has been shown to induce broad and robust antitumor activity with corresponding inhibition of PI3K/mTOR downstream targets in human xenograft models. Considering the inhibitory activity of VS-5584 against multiple targets within the PI3K/mTOR pathway, multiple clinical pharmacodynamic biomarkers need to be assessed. Methods: Due to its vascularization, ease of sampling and epithelial origin, anagen hair represents a practical surrogate tissue for monitoring drug effects in patients. Human anagen hair from volunteer donors were treated ex vivo with VS-5584 and another PI3K/mTOR dual inhibitor, BEZ235. Following 6, or 24 hour exposure to various drug concentrations, RNA was extracted, amplified and analyzed on Affymetrix PrimeView microarrays. Results: Transcriptomic profiles indicated a robust and dose-dependent response to VS-5584. A VS-5584-specific 91 gene signature was identified by 3-way ANOVA, and a Connectivity map evaluation indicated a strong positive correlation with other agents targeting the PI3K/mTOR pathway (wortmannin, LY-294002 and sirolimus). Likewise, VS-5584 exposure ex vivo in human anagen hair follicles resulted in a dose responsive suppression at both 6 and 24 hrs with an alternative PI3K/mTOR dual inhibitor 115 gene signature trained on BEZ235. A seven gene subset was consistently reduced by both VS-5584 and BEZ235 at 6 hrs and 24 hrs. Conclusions: Gene signatures from plucked anagen hair may provide a non-invasive approach to assess pharmacodynamic effects of VS-5584 in cancer patients.
Association of IGF2 DMR0 hypomethylation in esophageal squamous cell carcinoma with poor prognosis.
Authors: Baba Yoshifumi , Watanabe Masayuki , Murata Asuka , Shigaki Hironobu , Iwagami Shiro , Ishimoto Takatsugu , Baba Hideo 
Published: March 2020

11065 Background: The insulin-like growth factor 2 gene (IGF2) is normally imprinted. Loss of imprinting (LOI) of IGF2 in humans is associated with an increased risk of cancer and is controlled by CpG-rich regions known as differentially methylated regions (DMRs). Specifically, the methylation level at IGF2 DMR0 is correlated with IGF2 LOI and is a suggested surrogate marker for IGF2 LOI. A relationship between IGF2 DMR0 hypomethylation and poor prognosis has been shown in colorectal cancer. However, no study has examined the relationships among the IGF2 DMR0 methylation level, LOI, and clinical outcome in esophageal squamous cell carcinoma (ESCC). Methods: The IGF2 imprinting status was screened using ApaI polymorphism, and IGF2 protein expression was evaluated by immunohistochemistry with 30 ESCC tissue specimens. For survival analysis, IGF2 DMR0 methylation was measured using a bisulfite-pyrosequencing assay with 216 ESCC tissue specimens. The Cox proportional hazards model was used to calculate mortality hazard ratios (HR) adjusted for clinical, epidemiologic, and pathological variables.The term “prognostic marker” is used throughout this article according to the REMARK Guidelines. Results: Twelve (40%) of 30 cases were informative (i.e., heterozygous for ApaI), and 5 (42%) of 12 informative cases displayed IGF2 LOI. IGF2 LOI cases exhibited lower DMR0 methylation levels (mean, 23%) than IGF2 non-LOI cases (37%). The IGF2 DMR0 methylation level was significantly associated with IGF2 protein expression. Among 202 patients eligible for survival analysis, IGF2 DMR0 hypomethylation was significantly associated with higher cancer-specific mortality (log-rank P=0.013; univariate HR=2.03, 95% confidence interval: 1.14–3.58, P=0.017; multivariate HR=2.34, 95% CI: 1.29-4.22, P=0.0054). Conclusions: The IGF2 DMR0 methylation level in ESCC was associated with IGF2 LOI and IGF2 protein expression. In addition, IGF2 DMR0 hypomethylation was associated with a shorter survival time, suggesting its potential role as a prognostic biomarker.
Analysis of the prognostic impact of Treg-related genes in tumor and stroma in resectable NSCLC.
Authors: Usó Marta , Jantus-Lewintre Eloisa , Sirera Rafael , Gallach Sandra , Blasco Ana , Martinez Nieves , Hernando Cristina , Guijarro Ricardo , Camps Carlos 
Published: March 2020

11073 Background: Immunosuppressive regulatory T lymphocytes (Tregs) have been proved to play a critical role in immune tolerance to tumor. In this study we have analyzed the expression of 11 genes related to Tregs in both tumor and stroma samples of resectable NSCLC patients. Methods: Primary tumor tissues of FFPE samples from 125 early-stage NSCLC patients were used in this retrospective study. The most representative areas of tumor cells and tumor stroma of each sample were carefully micro-dissected. RTqPCR using hydrolysis probes (TaqMan, Applied Biosystems) was performed to assess the expression of Treg markers such as: CD127, CD25, FOXP3, CTLA-4, IL-10, TGFB-1, LAG-3, GITR and TNF-a as well as CD4 and CD8. Relative gene expression was assessed using GAPDH and CDKN1B as endogenous controls and results were normalized against a human cDNA (Clontech) as a reference. All statistical analyses were considered significant at p< 0.05. Results: In both tumor and stroma, we found over-expression of CD25 (5.40X and 7.95X, respectively) and down-expression of CD127 (0.28X and 0.37X, respectively). There was a tendency toward higher expression of FOXP3 (1.67X and 2.01X, respectively) and CTLA-4 (1.92X and 1.76X, respectively) as well. Paired Wilcoxon test showed significant gene expression differences between tumor and stroma in FOXP3 (p=0.006), CD25 (p<0.0001), CD4 (p<0.0001), CD8 (p=0.028), IL-10 (p<0.0001) and TGFB-1 (p<0.0001). Kruskal-Wallis test showed that FOXP3 expression was higher in adenocarcinoma than in SCC samples (2.56X vs 1.79X, p=0.002). Survival analyses revealed that patients with a “Treg profile” (↑CD25 and ↓CD127) had a reduced overall survival (OS) (median 29.90 vs 74.33 months, p=0.003). We also found that those patients with higher levels of the ratio FOXP3 stroma/tumor had worse time to progression (TTP) (median 32.50 vs NR, p=0.04). Conclusions: Treg markers in the tumor microenvironment seem to play an important prognostic role in early-stage NSCLC patients. Supported by grants PS09-01149 and RD06/0020/1024 from ISCIII.
Using 124I-PU-H71 PET imaging to predict intratumoral concentration in patients on a phase I trial of PU-H71.
Authors: Gerecitano John F. , Modi Shanu , Gajria Devika , Taldone Tony , Alpaugh Mary , Gomes DaGama Erica , Uddin Mohammad , Chiosis Gabriela , Lewis Jason Stuart , Larson Steven M. , Pillarsetty Naga Vara Kishore , Jhaveri Komal L. , Krichevsky Brian , Chen Mei Hsuan , Dixit Payal , Dunphy Mark 
Published: March 2020

11076 Background: PU-H71 is a Heat Shock Protein 90 inhibitor that can be labeled with 124I without altering its biochemical properties. Intratumoral drug concentration can be calculated based on 124I-PU-H71 (*PU-H71) region of interest analysis and dilution principle. A microdose pilot study has shown uptake of *PU-H71 in a variety of tumors. *PU-H71 PET is currently being used to estimate intratumoral concentrations in subjects on our phase I study. Methods: Patients with previously treated solid tumors or lymphoma are eligible for this phase 1 trial. PU-H71 is given twice-weekly for 2 weeks each 21 days at escalating dose levels. A mix of *PU-H71 and unlabeled PU-H71 is given during cycle 2 followed by serial PET imaging. Patients on the pilot study are administered a microdose of *PU-H71 alone, followed by serial PET scans. Intratumoral PUH-71 concentration is measured directly in optional pre- and post- treatment core needle tumor biopsies (CNB). Results: To date, 13 patients have received PU-H71 on the phase I trial. Of these, 10 have undergone *PU-H71 PET imaging. 4 imaged patients also volunteered for CNBs, with results reported in the table. Of the 10 patients who underwent *PU-H71 imaging in the phase 1 study, 5 also underwent prior *PU-H71 imaging in the microdose pilot. Intratumoral concentrations as calculated in the pilot and phase I studies were in close concordance. Conclusions: *PU-H71 can be used to visualize PU-H71 uptake in a variety of solid tumors and lymphoma, and *PU-H71 PET scans can be used to estimate intratumoral concentrations of PU-H71. Direct intratumoral measurements of PU-H71 correlate reasonably closely with concentrations calculated from *PU-H71 PET imaging. Further refinement of this imaging tool will allow quantitative assessment of PU-H71 uptake in tumors during the ongoing phase I trial. Clinical trial information: NCT01393509. [Table: see text]
Target lesion selection as a source of variability of response classification by RECIST 1.1.
Authors: Kuhl Christiane K. , Barabasch Alexandra , Dirrichs Tim , Bruners Philipp , Kennes Lieven , Bruemmendorf Tim , Keil Sebastian 
Published: March 2020

11077 Background: Response classification in RECIST is based on manual uni-dimensional quantification of changes of target lesion size. In RECIST 1.1, the maximum number of target lesions was reduced to 5, with a maximum of 2 per organ. We analyzed the importance of different factors (manual vs. automated size measurement, uni- vs. three-dimensional size assessment, and between-reader-variability of target lesion selection) on response categorization. Methods: 41 female patients (58.1±13.2 y) with metastatic breast cancer underwent contrast-enhanced thoraco-abdominal CT for initial staging and first follow-up after systemic chemotherapy. Data were independently and prospectively interpreted by three radiologists. In addition, response was evaluated by a CAD system that allowed automated uni- and three-dimensional assessment of target lesions. Results: Response classification differed between readers in 19/41 patients (46%). In 25/41 patients, readers chose the same target lesions. In 6 of these 25 patients (24%), readers disagreed with regards to response classification. In 16/41 patients, readers chose different target lesions. In 13 of these 16 patients, readers disagreed (81%) (p < 0.001). When dichotomizing response classification according to its therapeutic implication into progressive vs. non-progressive disease, readers disagreed in 11/41 patients (27%). In 9 of these 11 patients, readers had chosen different target lesions. Classification by manual vs. automated uni-dimensional measurement differed in 11/41 of patients (27%). Classification by uni-dimensional vs. volumetric measurements differed in 6/41 of patients (15%). Conclusions: Response classification by RECIST suffers from substantial between-reader variability. Major source of variability is not the manual or uni-dimensional measurement, but the variable choice of target lesions between readers. [Table: see text]
The CAP-IASLC-AMP molecular testing guideline for the selection of lung cancer patients for EGFR and ALK tyrosine kinase inhibitors.
Authors: Ladanyi Marc , Cagle Phil T. , Beasley Mary Beth , Chitale Dhananjay , Dacic Sanja , Giaccone Giuseppe , Jenkins Robert B. , Kwiatkowski David J. , Saldivar Juan-Sebastian , Squire Jeremy , Thunnissen Erik , Lindeman Neal Ian 
Published: March 2020

11085 Background: The College of American Pathologists (CAP), the International Association for the Study of Lung Cancer (IASLC), and the Association for Molecular Pathology (AMP) jointly initiated an effort to establish evidence-based recommendations for the molecular analysis of lung cancers required to guide EGFR- and ALK-directed therapies, addressing which patients and samples should be tested, and when and how testing should be performed. Methods: Three co-chairs without relevant conflicts of interest were selected, one from each of the sponsoring societies: CAP (P.T.C.), IASLC (M.L.), and AMP (N.I.L.). Writing and advisory panels were formed from additional experts from these societies. Unbiased literature searches were performed to capture articles up to February 2012, yielding 1,533 articles whose abstracts were screened to identify 521 pertinent articles that were then reviewed in detail for relevance. Evidence was formally graded for each of the recommendations first formulated by the co-chairs and panel members at a public meeting. Each guideline section was assigned to at least two panelists. Successive drafts were circulated for comments to the writing panel, the advisory panel, the public (online posting), and the three professional societies. Results: We generated 37 guideline items addressing 14 areas of EGFR and ALK testing. The major, evidence-based recommendations are to test for EGFR mutations and ALK fusions in all patients with advanced stage adenocarcinoma, regardless of sex, race, or smoking history, and to prioritize EGFR and ALK testing over other molecular predictive tests. Recommendations and expert consensus opinions were generated for all other key aspects of EGFR and ALK testing in lung cancer related to oncology and pathology practice and technical issues in molecular testing. Conclusions: As scientific discoveries and clinical practice outpace the completion of randomized clinical trials, evidence-based guidelines developed by expert practitioners are vital for communicating emerging clinical standards and thereby improving patient outcomes.
Tumor, skin, and plasma concentrations of protein kinase inhibitors (PKIs) in patients with advanced cancer.
Authors: Labots Mariette , Neerincx Maarten , Van der Mijn Johannes C. , Dekker Henk , Honeywell Richard , Rovithi Maria , Gotink Kristy , Voebel-De Jong Margreet , Van der Peet Donald L. , Meijerink Martijn R. , Meijer Gerrit A. , Jiménez Connie R. , Peters Godefridus J , Verheul Henk M.W. 
Published: March 2020

11087 Background: PKIs are selective for target receptors at low concentrations, but they act promiscuously at higher concentrations (PMID 18183025). This lack of selectivity may be relevant for their antitumor activity and for the development of PKI treatment selection tools. To obtain more insight in their clinical mechanism of action, we designed a pilot study to determine PKI tumor, skin and plasma concentrations in patients (pts) after 2 weeks of treatment. Results are related to cell line sensitivity data. Methods: Prior to standard palliative systemic treatment, pts were allocated to standard-dose PKI treatment (N=5 per PKI) for 10-14 days. Plasma, tumor and skin biopsies were collected within 24 hours of last dose. Sample PKI concentrations were determined by liquid chromatography – tandem mass spectrometry (LC-MS/MS); tissue concentrations in pg/mg were converted to molarity for comparison with preclinical sensitivity data (PMID 21980135). Concentrations of sunitinib (SUN), sorafenib (SOR), erlotinib (ERL), dasatinib (DAS) and everolimus (EVE) that inhibit 50% of cell proliferation (IC50) were determined by MTT assay in 1 RCC (786-O) and 8 CRC cell lines (HCT 116, HT-29, RKO, SW480, SW1398, DLD-1, COLO 205, CaCo-2). Results: Since August 2011 samples were obtained from 27 pts; 5 received SUN, 4 SOR, 4 ERL, 5 DAS and 5 EVE. After 12 ± 1 days of treatment, median tumor concentration (TC) was 9.0 µM (2.3-50.0) (range) for SUN, 8.5 µM (3.7-22.0) for SOR, 5.3 µM (0.9-10.8) for ERL and 2.1 µM (0.2-64.0) for DAS. EVE was measurable in 2 of 5 tumors: 3.5 µM (3.4-3.6). On average, PKI skin concentrations were 2.4-fold lower than TCs. SOR and ERL plasma concentrations (PCs) were in the range of TCs while SUN and DAS PCs were at least 14-fold lower than in tumors. Mean IC50 of the cell line panel was 1.3 µM (0.8-1.4) for SUN, 2.2 µM (1.4-3) for SOR, 8.2 µM (4-11.5) for ERL, 0.06 µM (0.02-1.8) for DAS and 1.2 µM (0.05-11) for EVE. Conclusions: PKI tumor concentrations may vary considerably from plasma concentrations, but are in the IC50 range of cancer cells in vitro. These results are indicative for the inhibitory concentrations of PKIs in patient tumors and should be considered for the development of individualized treatment strategies. Clinical trial information: NCT01636908.
Objective measurement of breast density, a marker of breast cancer risk, using fully automated radiation- and compression-free MRI.
Authors: Wengert Georg , Helbich Thomas , Polanec Stephan , Dubsky Peter Christian , Bago-Horvath Zsuzsanna , Bartsch Rupert , Vogl Wolf-Dieter , Curda Michael , Pinker-Domenig Katja 
Published: March 2020

11088 Background: Women may have contraindications to mammography (MG) or simply refuse the test due to subjective reservations usually concerning compression and/or radiation. Other than the detection of suspicious findings these women do not have standardized information concerning their breast density (BD), one of the strongest independent predictors of breast cancer (BC) risk. We developed a fully-automated quantitative magnetic resonance imaging (MRI) based BD measurement system, provided correlation to MG BD estimation and compared BD in BC patients and age-matched healthy controls. Methods: In this IRB-approved prospective study 35 healthy women and 19 BC patients age-matched to one of the healthy controls were included. BD for healthy women and BC patients was assessed using a) subjective qualitative radiologist´s review allocating 1 of 4 ACR BIRADS BD categories, b) Cumulus, a MG based semi-automatic method and c) a radiation- and compression-free MRI measurements system, which automatically calculates volume of breast (cm3), % of fatty tissue and % of glandular tissue. Descriptive statistics were used to define the typical range of quantitative MRI BD readings corresponding to the qualitative four ACR BIRADS BD categories. Áppropriate statistical tests were used to compare mean values of method b) and c) and BD readings of cancers and controls. Results: % MRI BD correlated well with % MG BD (r = 0.83; P < 0.0001). MRI BD measurements ranged from 1.7% to 61.9% (mean 29.05%). MG BD measurements ranged from 5.42% to 74.33% (mean 40.23%). Equivalent values were found with MRI BD readings of 0-7.2%, 7.3-26%, 26.1-39.6% and >39.7% respectively for each of the four ACR BIRADS BD categories. Mean BD (%) was higher in BC patients than in healthy controls: 24% (SD 16.9%) vs. 18.4% (16.6). Conclusions: MRI BD measurement strongly correlates with MG based BD readings. The data suggest that objective, radiation- and compression-free MRI BD measurement is a convenient alternative to MG for assessment of BD. MRI BD measurement confirms higher breast density in BC patients compared to healthy women. The data is entirely consistent with the fact that BD is a strong independent risk factor for BC.
Thymidylate synthase expression as predictive biomarker of pemetrexed sensitivity in advanced cancer patients.
Authors: Rojo Federico , Domine Manuel , Zazo Sandra , Chamizo Cristina , Serrano Gloria , Carames Cristina , Perez-Gonzalez Nuria , Hernandez Tatiana , Auz Carmen Laura , Carvajal Nerea , Moreno Irene , Martin-Valades Jose Ignacio , Izarzugaza Yann , Lendinez Alberto , Martinez-Ammoros Brezo , Arranz Juan Luis , Madoz Juan , Leon Ana , Lobo Francisco , Garcia-Foncillas Jesus 
Published: March 2020

11089 Background: Although a high level of thymidylate synthase (TS) expression in malignant tumours has been suggested to be related to a reduced sensitivity to the antifolate drug pemetrexed, no direct evidence for such an association has been demonstrated in routine clinical samples from patients treated with this drug. The purpose of this study was to evaluate the impact of quantitative TS expression in tumor cells as predictor of the efficacy in patients with advanced non-small cell lung cancer, small cell lung cancer (SCLC) and mesothelioma treated with pemetrexed in our institution. Methods: 54 patients were included in this study: 40 stage IV NSCLC (26 adenocarcinomas, 11 large cell, and 3 squamous cell carcinoma), 3 SCLC and 11 mesothelioma. 21 patients received platins-pemetrexed as first line NSCLC, 20 pemetrexed in monotherapy as second and further lines and 3 carboplatin-pemetrexed fo extensive disease SCLC. Total RNA was isolated by RNeasy FFPE procedure (Qiagen). The expression of TS was analyzed by RT-qPCR using appropriate mRNA specific primers and probes in LightCycler 480II platform at 45 cycles. TS levels was calibrated to expression in normal tissue. Results: From 54 cases, TS expression data were available in 32 cases, detecting overexpression in 23 (71.8%) and low expression in 9 (28.2%) patients. The response rate for patients with low TS expression was 0.63 compared with 0.15 in patients with overexpression (p=0.015). A significant benefit in time to progression was observed in patients with low expression (median TTP 12 vs. 2 months respectively, p= 0.002), whereas did not impact on overall survival (median OS 20 vs. 19 months respectively, p= 0.595). Conclusions: TS overexpression in tumor cells correlated with a reduced response to pemetrexed-containing chemotherapy and might be used as a predictive biomarker in advanced lung and mesothelioma cancer patients.