bluuebunny/crossref_metadata_2025_split huggingface dataset:
Molecular sequencing and gene fusion detection in non-small cell lung cancer (NSCLC) patients: Impact of co-existing alterations.
Authors: Martinez de Castro Ana , Remon Jordi , Cedres Perez Susana , Navarro Alejandro , Martinez Marti Alexandre , Pardo Aranda Nuria , Hernando Alberto , Zeron-Medina Jorge , Aguilar-Company Juan , Scheenaard Eulalia , Recasens Sergi , Ruiz-Pace Fiorella , Villacampa Guillermo , Jimenez Jose , Dienstmann Rodrigo , Nuciforo Paolo , Felip Enriqueta , Vivancos Ana 
Published: September 2018

e23103 Background: There is a growing need for accurate molecular diagnostics for proper targeted therapeutics selection in NSCLC patients (pts). We assess whether next generation techniques increase the identification of alterations in a prospective cohort of NSCLC pts, and evaluate prognostic value of different molecular alterations. Methods: Next generation sequencing (Amplicon-seq, 60 genes) and NanoString Gene fusion (20 genes) testing were conducted in NSCLC pts treated in a single center from November 2014 to May 2016. Overall survival (OS) according to the molecular profile was analysed by Kaplan-Meier method and Cox models. Results: Molecular tests were performed in 73advanced NSCLC pts.Median age was 54 year, 50% were women. Histology: 73% adenocarcinoma; 7% squamous, 20% others (Neuroendocrine, NOS). Tests were performed in biopsies from metastatic sites in 55% of pts.These techniques identified molecular alterations in 89% of cases: TP53 mutation (mut) 37/73 (51%); KRASmut 21/73 (29%); EGFRmut 11/73 (15%) ; CDKN2mut 7/73 (9%); BRAFmut (pG469R), ERBB2mut and METexon14mut in (1/73) 1.3%, respectively; ALKfusion (fus) 2/73 (2.7%); ROS1fus 1/73 (1.3%) , and RET fus 3/73 (4%). Concomitant mutations were identified in 32% of pts mainly with TP53 (TP53/EGFR: (5/11) 45% and TP53/KRAS: (7/21) 33%). Matched targeted treatment was offered in 17/73 (23%), mostly tyrosine kinase inhibitors (TKI); anti-EGFR in 11/17 (65%) and ALK/ROS TKI in 3/17 (17.5%). Three pts (17.5%) received anti-MET or anti-HER2 TKI. OS in this whole population treated with target therapies (n = 17) was 45.7 months (m) (CI95% 26.8-NA). The KRASmut group had median OS of 10 m (CI95% 7.5-NA), while the remaining population with wild type (WT) for all driver alterations had median OS of 23 m (CI95% 20-NA), (HR 1.71 for KRASmut vs WT pts, p = 0.18). The presence of coexisting TP53mut did not negatively impact on OS in the cohorts with EGFRmut and KRASmut (p > 0.1) in a multivariate model. Conclusions: Combined next generation techniques for molecular profile in NSCLC pts identifies molecular alterations that have clinically relevant impact in survival. Coexisting TP53mut alteration shows no detrimental effect in OS.
Correlation of low CT attenuation and necrotic features of tumor in contrast-enhanced CT with nivolumab response.
Authors: Ariyasu Ryo , Horiike Atsushi , Koyama Junji , Saiki Masafumi , Sonoda Tomoaki , Takano Natsuki , Kawashima Yosuke , Oguri Tomoyo , Nishikawa Shingo , Kitazono Satoru , Yanagitani Noriko , Ohyanagi Fumiyoshi , Oikado Katsunori , Nishio Makoto 
Published: September 2018

e23105 Background: Anti-PD1/PD-L1 antibodies, including nivolumab, produce durable responses in non-small cell lung cancer (NSCLC), but the response rate is about 20% in unselected NSCLC. Identifying predictive markers of response is necessary. Although PD-L1 expression may be a potential biomarker, evaluating whole tumors based on a small sample is difficult. Identifying radiographic features of responders can be very useful. We hypothesized that low attenuation on computed tomography (CT), considered to represent necrosis, correlates with nivolumab response. Methods: We retrospectively evaluated contrast-enhanced CT images before treatment and tumor response in 60 patients receiving nivolumab. The largest tumor lesion was characterized in each patient. CT attenuation (CTA) of whole tumor areas was measured; the presence of radiological findings of necrosis (necrotic features), presenting cavitation or ring- or patchy-enhancement in tumors, were assessed. We evaluated the association between CT imaging characteristics and nivolumab response and that between CT imaging characteristics and PD-L1 expression in tumors. Results: Thirty-nine target lesions in lung, 12 in lymph node, and 9 in other organs were chosen. The mean CTA was 58.5 ± 15.3 HU. Necrotic feature were observed in 24 (40%) of 60 lesions.Twenty of 60 lesions (33%) shrank to > 30% with nivolumab treatment. Mean CTA in responding lesions was 48.6 HU, significantly lower than that in nonresponding lesions (63.4 HU) (p < 0.001). The response rate of lesions with/without necrotic features was 45% and 28%, respectively (p = 0.246).Systemic tumor response, assessed by RECIST v1.1, was confirmed in 20 (33%) patients. Mean CTA of target lesions was lower in responders than patients with stable disease or progressive disease (51.4 vs. 62.0 HU, p = 0.011). The systemic response rate of lesions with/without necrotic features was 50% and 25%, respectively (p = 0.081).Mean CTA of target lesions was lower in tumors with high PD-L1 expression than in tumors with low PD-L1 expression (54.8 vs. 64.4 HU, p = 0.045). Conclusions: Low CTA and necrotic features in CT may correlate with nivolumab response. Tumors with low CTA may have high PD-L1 expression.
MET aberrations across multiple tumor types: Results of a molecular screening program (MOSCATO 01).
Authors: El Dakdouki Yolla , Verlingue Loic , Massard Christophe , Rouleau Etienne , Lacroix Ludovic , Auger Nathalie , Scoazec Jean-Yves , Balogh Zsofia , ANGEVIN ERIC , Soria Jean-Charles , Hollebecque Antoine 
Published: September 2018

e23110 Background: MET gene, encoding the tyrosine kinase receptor for HGF, has been shown to have an oncogenic role in several tumors. We report here the frequency, distribution and clinical characteristics of the patients (pts) found to have MET alterations in a molecular screening trial. Methods: InMOSCATO clinical trial, pts with locally advanced or metastatic solid cancers had an on-purpose tumor biopsy to perform a comprehensive molecular characterization. Results: Among the 844 adult pts who had a successful molecular portrait, 29 (3.4%) had MET aberrations distributed as follows: 18 had abnormalities at the genomic analysis level while 11 had exclusively expression of phosporylated-MET by immunohistochemistry (IHC) and/or a positive fluorescence in situ hybridization (FISH). Only one of the 74 pediatric pts included had a missense mutation. According to the primary tumor, MET alterations were found in 13/170 successfully biopsied pts with lung cancer, 8/197 with digestive tumors, 3/158 with genito-urinary tumors, 2/83 with gynecologic tumors, 2/111 with head and neck cancers, 1/135 with breast cancer and 1 pt with pediatric glioblastoma. Pathogenic variants (PV) were detected in 3 pts by targeted Next Generation Sequencing (NGS), 2 of these PV were exon 14 donor splice site mutations detected also by whole-exome sequencing (WES) in 2 lung tumors. Missense mutations were identified in 3 pts by RNA-sequencing and in one patient by WES. 8 pts had MET amplification identified by comparative genomic hybridization array (CGH) in 5 cases, by FISH in one case and by both FISH and CGH in 2 cases. One patient displayed both amplification and a missense mutation. Ten pts received an anti-MET targeted therapy. One had PV on NGS and missense mutation on WES, 3 had amplification on CGH or FISH and 6 positive IHC. One patient displaying MET exon 14 donor splice site mutation was treated with crizotinib achieving a rapid and sustained partial response. The other 9 pts were treated with SAR125844, a selective MET tyrosine kinase inhibitor, in TED11449 trial (NCT01391533). Conclusions: In this analysis, we saw that MET aberrations are rare in various types of advanced cancers. In selected patients, targeting MET is of clinical interest. Clinical trial information: NCT01566019.
Molecular profiling of advanced malignancies: A community oncology network experience.
Authors: Tayshetye Pritam , Monga Dulabh K. , Finley Gene Grant , Vishwanathan Swati , Brem Candice , Silverman Jan F 
Published: September 2018

e23111 Background: Many genomic alterations have been identified that are critical to the malignant phenotype. Some of these, termed “driver mutations”, are critical for tumor proliferation and progression. The landscape of targeted therapy has expanded as well. Next-generation sequencing (NGS) of tumors reveals cancer-related genomic alterations and provides therapeutic recommendations for specific targeted therapy. We analyzed our experience with FoundationOne, a validated NGS genomic profile in a community oncology network. Methods: NGS results from May 2014 to September 2016 from a community oncology network in Western Pennsylvania were analyzed. Medical records were reviewed for primary site, stage, biopsy site, timing of testing, prior treatment, FDA-approved therapy in patient’s and other tumor types and potential clinical trials based upon mutations detected. Endpoints determined were percentage of patients with targetable mutations and those in whom treatment decisions were made based on NGS results. Results: 157 NGS results were available for analysis. 38.2% cases were tested early in the disease course (at diagnosis, during or shortly after first-line treatment) and 61.8% at progression. FDA-approved targeted agent for a specific mutation was found in 14% of the primary tumor type and 19.8% of other tumor types. Clinical trials were available for 93% cases. The NGS results were utilized in treatment decisions in 28 patients of which, 9 were tested early and 19 at disease progression. Of the 28, 11 were initiated on a targeted agent. Median duration of targeted therapy was 2.6 months. 9 patients were on appropriate targeted agent prior to testing. 8 patients were unable to start the targeted agent because of insurance denial, clinical deterioration or patient preference. Conclusions: NGS is a valuable tool for personalizing cancer care. From our experience, the actual number of patients starting a targeted agent based on NGS results is low. It nevertheless can provide additional treatment options and facilitate clinical trial enrollment. Optimal timing of testing (early vs late), financial implications of testing and using targeted therapy and survival benefit of targeted therapy need further studies.
Accurate and precise targeted NGS with BRCA MASTR Plus Dx for BRCA1 and BRCA2 mutation detection in formalin-fixed paraffin-embedded tumor tissue-derived DNA.
Authors: Boulet Gaelle , Van Barel Djana , Rotthier Annelies , Goossens Dirk , Del-Favero Jurgen 
Published: September 2018

e23116 Background: Targeted next-generation sequencing (NGS) has tremendous potential in clinical diagnostics as it allows oncogenetic profiling to steer therapy. Inhibitors of poly-(ADP-ribose) polymerase (PARPi) have emerged as a new class of targeted anti-cancer drugs, specifically for tumors showing homologous recombination repair deficiency, including BRCA1- and BRCA2-mutated ovarian and breast cancers. This multicentre study evaluated the performance of BRCA Tumor MASTR Plus Dx* (Multiplicom) to routinely diagnose somatic and germline BRCA mutations in formalin-fixed paraffin-embedded (FFPE) tumor tissue-derived DNA. Methods: Three genetic centres participated in this performance evaluation study (PES) to detect single nucleotide variants (SNV) and small indels in the BRCA genes at a variant allele frequency down to 5%. The sample population comprised 54 FFPE-derived DNA extracts from 51 clinical and 3 reference samples. DNA extracts were subjected to quality control using Multiplicom’s QC plex assay. The clinical samples were characterized using an independent targeted NGS method and Integrative Genomics Viewer (IGV) analysis of the mapped raw reads. SNV calling was performed using third-party bioinformatics platforms in the BRCA coding regions +/- 2 intronic bp. Results: BRCA MASTR Plus Dx*showed a uniformity of 93.9%, i.e. the percentage of amplicons with at least 0.2x the mean amplicon coverage, and a target specificity of 99.1%. The limit of detection (LOD) proved to be as low as 1%. The diagnostic accuracy was ≥ 99.99% [95% CI ≥ 99.98%] (100% sensitivity [95% CI ≥ 99.02%] and ≥ 99.99% specificity [95% CI ≥ 99.98%]). Both repeatability and reproducibility were ≥ 99.99% [95% CI ≥ 99.98%]. Lot equivalence was 100% [95% CI ≥ 99.99%]. Conclusions: This multicentre study demonstrated that BRCA MASTR Plus Dx* can be routinely applied as an accurate and precise method with an LOD of 1%. The assay can be used to direct patients with somatic or germline BRCA mutations to PARPi therapy. Currently, a PES for BRCA MASTR Plus Dx* and Multiplicom’s MASTR Reporter software is ongoing. *Products described above are CE-IVD and not available for sale in the US
Assessment of the clinical utility of chip-based digital PCR for HER2 assessment in formalin fixed paraffin-embedded breast carcinoma tissue.
Authors: Shah Parth , Murarka Shiva , Sands Jacob , Mehta Bhavna , Joshi Anupam , Patel Khushbu , Parmar Vipal 
Published: September 2018

e23120 Background: 15%-25% of breast cancer neoplasms exhibit Human epidermal growth factor receptor-2(HER2) amplification, as the driver mutation.Techniques to identify HER2 amplification include Immunohistochemistry (IHC) and Fluorescence in situ Hybridization (FISH). Digital PCR (dPCR) has been increasingly explored in determining HER2 status in cases of indeterminate results on IHC, mainly in archived samples. In this study, we aim to demonstrate the clinical utility of the Quantstudio 3D Digital PCR system to evaluate HER2 levels from Formalin Fixed Paraffin Embedded (FFPE) tissue with RNaseP as a control target. Methods: 61 tissue samples were analyzed by IHC and dPCR in parallel in a double blinded manner. IHC equivocal samples were reflexed to FISH and compared to the results obtained from dPCR. Samples suboptimal for IHC or FISH were satisfactorily processed by dPCR. dPCR results were analyzed on the Thermofisher Cloud platform. The general turnaround time(TAT) was about 2 and 3 days for IHC and FISH respectively with that of dPCR being 24 hours. Results: All 9 IHC positive and 35 negative samples had similar results on dPCR using an amplification ratio threshold for a positive result of 1.8. Of 17 IHC-equivocal samples, 5 resulted as positive, 10 negative and 2 as equivocal by dPCR. There was 100% concordance between the dPCR and FISH results. Two IHC equivocal samples that were unanalyzable by FISH were negative on dPCR Conclusions: Our results demonstrate that the chip based dPCR was non-inferior for HER2 detection in FFPE samples in a clinical setting. Superior TAT's and objective results were obtained compared to more subjective techniques like FISH and IHC even with low sample input. dPCR requires controls but no standards for calibration as it gives absolute copy numbers. Further study is needed to understand dPCR interpretation in cases of chromosomal aneuploidy. [Table: see text]
Effect of MCAM on the aggressive phenotype in human prostate cancer.
Authors: Kruithof-de Julio Marianna , Zoni Eugenio , Astrologo Letizia , Melsen Janine , Klima Irena , Grosjean Joel , Van der Pluijm Gabri , Thalmann George N. 
Published: September 2018

e23135 Background: Prostate Cancer (PCa) is the most common cancer in males and the second leading cause of death from cancer in men. Understanding the factors that regulate homing and survival of metastatic cancer cells in the bone is important for the identification of new therapeutic targets. High MCAM expression has been detected in the stroma of lytic and blastic lesions in preclinical models of PCa bone metastasis. The objective of this study is to characterize the role of MCAM in the maintenance of the aggressive phenotype in human PCa. Methods: We knocked and down MCAM in the lytic PC-3M-Pro4Luc2_dTomato and in the blastic C4-2B_dTomato PCa cell lines. Validation was done at both protein and RNA level. We performed functional assays such as migration and proliferation. RT-qPCR was used to test MCAM knockdown on EMT markers. The effect of the knockdown on the maintenance of cancer stem/progenitor-like cells was measured by ALDEFLUOR. Results: MCAM knockdown reduced proliferation in PC-3M-Pro4Luc2_dTomato PCa cells and resulted in increased E-Cadherin expression. Metastatic human PCa cells target the hematopoietic stem cell (HSC) niche in the bone marrow at the level of an “endosteal/osteoblast” niche and a “vascular/perivascular” niche. We set-up an in vitro model of “osteoblast niche” to study the prostate cancer cells upon co-culture with osteoblasts and to determine the effects on cancer stem/progenitor-like markers. We found that MCAM is required for the osteoblast-mediated induction of ALDH activity on PCa cells and MCAM knockdown prevented the increase in the size of the ALDHhigh subpopulation in PC-3M-Pro4Luc2_dTomato, mediated by human osteoblasts. Additionally, MCAM knockdown in PCa cells co-culture with osteoblast, prevented the induction of MCAM expression by osteoblasts. Finally, MCAM is significantly increased in the ALDHhigh cells and identifies a new subset of ALDHhigh / MCAMhigh cells which could be depleted upon MCAM knockdown. Conclusions: We detected a new subset of ALDHhigh/MCAMhigh cells and demonstrated the MCAM influences the maintenance of an aggressive-mesenchymal phenotype in human PCa. Therefore, MCAM represent an interesting target molecule to modulate the behavior of aggressive PCa cells.
Integrated genomics-based discovery of new druggable kinases as a therapeutic target and cancer biomarker for lung cancer.
Authors: Daigo Yataro , Takano Atsushi , Nakamura Yusuke 
Published: September 2018

e23144 Background: Since the number of lung cancer patients responding well to current standard therapies is still small, further development of new anti-cancer agents with minimum risk of adverse effect and highly sensitive cancer biomarkers is eagerly awaited. Methods: We have been developing new molecular therapies targeting oncoproteins with their biomarkers; i) To identify up-regulated genes in 120 lung cancers by the gene expression microarray representing 27,648 genes, ii) To verify the candidate genes for their low expression in 23 normal tissues, iii) To validate the clinicopathological significance of their protein expression by tissue microarray covering 407 non-small cell lung cancers (NSCLCs), iv) To verify whether they are essential for the growth/invasion of cancer cells by siRNA and antibody assays, and v) To measure their serum protein levels by ELISA in 343 lung cancer patients. Results: We identified 50 druggable oncoproteins and selected a LSERT (lung cancer-specific receptor tyrosine kinase). Strong LSERT protein expression was associated with poor prognosis for NSCLC patients (P < 0.0001; N = 407) as confirmed by multivariate analysis. We established an ELISA to measure serum LSERT (a cleaved form of its extracellular domain) and found that the proportion of serum LSERT-positive cases was 149 (56.4%) of 264 NSCLC and 35 (44.3%) of 79 SCLC patients, while only 6 (4.7%) of 127 healthy volunteers were falsely diagnosed. A combined ELISA for both LSERT and CEA classified 77.2% of the NSCLC patients as positive, and the use of both LSERT and ProGRP increased sensitivity in the detection of SCLCs up to 77.5%, while the false positive rate was 7 - 8%. Oncogenic LSERT activity was suppressed by treatment of lung cancer cells with anti-LSERT antibody or siRNA. Induction of LSERT increased the cellular growth and invasion by directly phosphorylating oncogenic driver kinase proteins for lung cancer and enhancing their downstream signaling of MAPK, AKT, and STAT3. Conclusions: Integrated cancer genomics might facilitate the development of diagnostic and prognostic biomarkers as well as therapeutic targets for small molecules, monoclonal antibodies, nucleic acid drugs, and cancer vaccines.
In vitro functional analysis of HER2 variants in lung cancers to evaluate their oncogenic activity and predict clinical response to HER2 targeted therapies.
Authors: Offin Michael , Olah Zachary T. , Sabari Joshua K. , Tandon Nidhi , Feldman Daniel , Abou-Alfa Ghassan K. , Lok Benjamin H. , Burck Nitza , Tarcic Gabi , Miron Ben , Arcila Maria E. , Kris Mark G. , Rudin Charles M. , Li Bob T. 
Published: September 2018

e23150 Background: HER2 variants are implicated as oncogenic drivers in a variety of cancers. However, not all HER2 variants found on next-generation sequencing (NGS) have been studied, raising the question if these variants of unknown significance (VUS) are oncogenic. This study explores the use of an in-vitro functional assay on HER2 and other variants found on NGS in patients (pts) with lung cancer, and its predictive value for response to HER2 targeted therapy. Methods: Pts with lung cancer at Memorial Sloan Kettering identified to have a HER2 variant by NGS on MSK IMPACT are eligible. NGS data on HER2 variants and co-mutations were analyzed. Functional status was determined by the NovellusDx FACT platform. Mutations were synthesized and transfected into HeLa cells with a fluorescently tagged signaling pathway reporter (MAPK, NFKB, JAK-STAT). Fluorescent microscopy quantified the translocation of reporters to the nucleus, inferring gain of function. Afatinib was added and its effect on pathway activation analyzed. Functional information was correlated with clinical outcomes. Results: As of 2/1/17, 13 pts were included, 9 unique HER2 variants analyzed. Known activating HER2 mutations analyzed (exon 20 insertions (A775_G776insYVMA, G778_P780insGSP, G776delinsVC), point mutations (V659E, L755P, S301F)) showed in vitro gain of function. HER2 VUS analyzed included D277Y showed no gain of function; exon 16 splice variant c.1889 showed gain of function. Afatinib was added to 4 cell lines with gain of function variants (G778_P780insGSP, V659E, L755P, exon 16 splice variant c.1889) all had inhibited pathway activation suggesting in vitro sensitivity to afatinib. Clinically, no response was seen in 2 pts treated with afatinib but more pts are planned to be treated. Objective responses to ado-trastuzumab emtansine (NCT02675829) were seen in 5 pts, all of which had HER2 variants with gain of function. Conclusions: In vitro functional analysis of HER2 variants based on NGS reports is feasible, and has the potential to identify novel actionable oncogenic drivers from VUS. Its predictive value for clinical response to targeted therapy requires further study.