bluuebunny/crossref_metadata_2025_split huggingface dataset:
An analysis of ERBB2 alterations (amplifications and mutations) found by next-generation sequencing (NGS) in 2000+ consecutive solid tumor (ST) patients.
Authors: Palmer Gary A. , Wang Kai , Miller Vincent A. , Yelensky Roman , Stephens Phil , Ross Jeffrey S. , Lipson Doron 
Published: March 2020

11000 Background: Testing for ERBB2 amplification by FISH and IHC is routine in breast and gastro-esophageal cancer. There are 3 approved and multiple targeted therapies in clinical trials that rely on the results of these tests. ERBB2 amplification and activation by mutation/fusion has also been described in a wide variety of other ST. As these alterations are not routinely tested for but may predict response to anti-ERBB2 agents we sought to determine their frequency in an unselected cohort of specimens from advanced ST patients. Methods: We reviewed genomic profiles from the first 2,223 formalin-fixed, paraffin-embedded specimens received and analyzed by our CLIA-certified lab (Foundation Medicine) with our NGS platform. 3,230 exons in 182 cancer-related genes and 14 genes frequently rearranged were assayed for base pair substitutions, small insertions/deletions (indels), amplifications, and rearrangements. Results: 110/2,223 (4.9%) specimens had 116 ERBB2 alterations: 67 (58%) amplifications, 29 (25%) substitutions, 16 (14%) indels, 2 (2%) splice site variants and 2 (2%) translocations, including a potential fusion. Six samples (5%) had multiple alterations, and two had both ERBB2 substitution and amplification. 14 ST types had evidence of ERBB2 alterations including 29% of esophageal, 20% of uterine, 14% of breast, and 12% of stomach carcinomas. 6% of all lung cancer samples had ERBB2 alterations. Amplifications predominated, but lung specimens had predominantly indels. Durable responses exist to anti-ERBB2 agents in STs with activating ERBB2 mutations. Conclusions: Use of a broad NGS panel identifies an unprecedented number of actionable genomic changes including a significant rate of ERBB2 alterations across 14 different solid tumor types. The discovery of unanticipated ERBB2 amplifications and activating mutations in a wide variety of ST highlights the need to study a broad range of genes at a high level of sensitivity and specificity when searching for novel targets of therapy. Widespread use of this approach could provide more treatment options and enable more rapid accrual to ongoing and planned trials of agents targeting pathways under study.
Amplification of the MET receptor to drive resistance to anti-EGFR therapies in colorectal cancer.
Authors: Bardelli Alberto , Corso Simona , Bertotti Andrea , Hobor Sebastijan , Siravegna Giulia , Sartore-Bianchi Andrea , Migliardi Giorgia , Galimi Francesco , Lauricella Calogero , Zanon Carlo , Amatu Alessio , Gambacorta Marcello , Diaz Luis A. , Velculescu Victor E. , Sausen Mark , Comoglio Paolo M. , Trusolino Livio , Di Nicolantonio Federica , Giordano Silvia , Siena Salvatore 
Published: March 2020

11005 Background: The anti EGFR monoclonal antibodies cetuximab and panitumumab are used to treat metastatic colorectal cancer patients but their clinical efficacy is limited by the development of acquired resistance. We recently reported that secondary KRAS mutations are responsible for acquired resistance in approximately 50% of the patients who initially respond to cetuximab or panitumumab (Misale et al., Nature 2012; Diaz et al., Nature 2012). Here we studied the molecular bases of relapse in CRC patients who do not develop KRAS mutations during the course of anti-EGFR therapy. Methods: Next generation sequencing was applied to tumor biopsies to identify genetic alterations associated with relapse to cetuximab and panitumumab in mCRC patients. Detection and quantitation of genetic alterations in circulating tumor DNA was used to monitor the occurrence of KRAS mutations and MET amplification in blood samples. Results: Molecular analyses of tumor biopsies from patients who did not develop KRAS mutations during anti-EGFR therapy revealed high level of amplification of the MET proto-oncogene in 3/5 cases. Quantitative PCR, FISH and IHC analysis confirmed high level of MET amplification in the post-therapy samples but not in the matched pre-treatment tissues. We developed a PCR based assay to detect the presence of the MET amplicon in circulating, cell-free, DNA. We found that MET amplification could be detected in the blood as early as 3 months after initiation of anti EGFR therapy. To functionally evaluate the role of MET amplification on resistance to anti EGFR antibody therapies we exploited patient-derived CRC xenografts (‘xenopatients). We found that (2/2) xenopatients established from MET amplified tumors were completely refractory to cetuximab but showed sensitivity to the Met inhibitor crizotinib. Conclusions: Amplification of the MET proto-oncogene is responsible for acquired acquired resistance to anti-EGFR antibody therapy in a subset of CRCs. The emergence of MET amplification in circulating, cell-free, DNA may be used to select patients most likely to benefit from anti MET therapies.
Early PET/CT scan compared with RECIST to predict long-term outcome of patients with liver metastases from colorectal cancer treated with preoperative chemotherapy plus bevacizumab.
Authors: Piccirillo Maria Carmela , Lastoria Secondo , Nasti Guglielmo , Caraco Corradina , Aloj Luigi , Arrichiello Cecilia , Ottaiano Alessandro , Izzo Francesco , De Lutio Elisabetta , Albino Vittorio , Romano Carmen , Palaia Raffaele , Daniele Gennaro , Di Maio Massimo , Giordano Pasqualina , Signoriello Simona , Delrio Paolo , Iaffaioli Rosario Vincenz , Romano Giovanni , Perrone Francesco 
Published: March 2020

11008 Background: Early changes in tumor metabolism measured with positron-emission-tomography/computerized tomography (PET/CT) could predict the long-term efficacy of treatment better than dimensional RECIST response. Methods: We performed PET/CT before and after 1 cycle of treatment in patients with resectable liver metastases from colorectal cancer, within a phase II trial of preoperative FOLFIRI plus bevacizumab. For each lesion, the maximum SUV (SUVmax) and the total lesion glycolisis (TLG) were determined. For both, based on previous studies, a ≤-50% change from baseline was used as threshold for significant response. Metabolic response was categorized no/yes by using three different methods that enter into the calculation (i) the largest observed value (highest SUVmax/TLG), or (ii) the sum of all the observed values (Total SUVmax/TLG), or (iii) each observed values (SUVmax/TLG-by-lesion). Standard RECIST response was assessed after 3 months of treatment. The association between metabolic and RECIST response was tested with the Mc Nemar’s test and their agreement was expressed as Kappa statistics; the ability to predict progression-free (PFS) and overall (OS) survival was tested with Log-rank test and a multivariable Cox model. Results: 33 patients were analyzed. After treatment, there was a notable decrease of all PET/CT parameters, with a median change of -33.9% for the highest SUVmax, -61.5% for the highest TLG, -34.9% for the total SUVmax, and -65.5% for the total TLG. The association of SUV-based metabolic response (but not the TLG-based) with RECIST was statistically significant. However, the agreement between RECIST and PET/CT responses was consistently small. PFS and OS were significantly longer among PET/CT responding patients, whichever the measure used. On the contrary, no significant outcome difference was evident according to RECIST response. Conclusions: Early PET/CT response was significantly predictive of long-term outcomes during preoperative treatment of patients with liver metastases from colorectal cancer and its predictive ability was higher than that of RECIST response. Clinical trial information: 2006-006572-38.
Olaparib monotherapy in patients with advanced cancer and a germ-line BRCA1/2 mutation: An open-label phase II study.
Authors: Kaufman Bella , Shapira-Frommer Ronnie , Schmutzler Rita K. , Audeh M. William , Friedlander Michael , Balmaña Judith , Mitchell Gillian , Fried Georgeta , Bowen Karin , Fielding Anitra , Domchek Susan M. 
Published: March 2020

11024 Background: The oral PARP inhibitor olaparib has shown antitumor activity as monotherapy in patients (pts) with breast and ovarian cancer with gBRCA1/2 mutations. This multicenter non-comparative study evaluated whether tumors in gBRCA1/2 mutation carriers are responsive to olaparib regardless of tumor type (NCT01078662). Methods: Heavily pretreated pts with advanced cancer refractory to standard therapy (98% of breast cancer pts had ≥3 lines of prior chemotherapy for metastatic disease) and with a gBRCA1/2 mutation, received olaparib 400 mg bid (capsule) until disease progression. Primary objective: tumor response by RECIST 1.1. Secondary objectives: PFS, OS and safety. Results: 298 pts received treatment and were evaluable. Enrollment is complete, 33 pts remain on study. Median duration of treatment in this heavily pretreated population was 5.5 months (range <1–28.5 months). Most common AEs (generally grade 1/2) were fatigue (59%), nausea (59%) and vomiting (37%). Grade ≥3 AEs were reported for 162 pts (54%); most common was anemia (17%). 11 pts (4%) had AEs that led to treatment discontinuation. Conclusions: The observedtumor response rates indicate antitumor activity of olaparib monotherapy in gBRCA mutated pts with advanced cancer refractory to standard therapy. A clinical benefit was seen in prostate and pancreatic cancer and activity in ovarian and breast cancer was confirmed. Prolonged responses to olaparib across all tumor types support the hypothesis that therapy directed against a genetically-defined target has activity regardless of anatomic organ of origin. Olaparib was generally well tolerated with toxicities consistent with prior studies. Clinical trial information: NCT01078662. [Table: see text]
Components of homologous recombination and translesion synthesis (TLS) in pemetrexed/cisplatin-treated non-small-cell lung cancer (NSCLC) patients (p).
Authors: Lopez-Vivanco Guillermo , Marti Thomas , Kotov Ilya N. , Chaib Imane , Ponce-Aix Santiago , García Campelo Rosario , Sanchez Jose Miguel , Artal Angel , Bover Isabel , Taron Miquel , Sanchez-Ronco Maria , Rolfo Christian Diego , Massuti Bartomeu , Stahel Rolf A. , Rosell Rafael ,   Spanish Lung Cancer Group
Published: March 2020

11028 Background: REV3, the catalytic subunit of the TLS polymerase ξ, can continue replication past DNA adducts. Depletion of REV3 sensitizes A549 lung cancer cells to cisplatin. REV3 expression is part of a gene signature that predicted pemetrexed sensitivity in 17 NSCLC cell lines. Homologous recombination and TLS pathways have non-redundant functions in response to cisplatin. We hypothesized that low REV3 mRNA expression – alone or in combination with low expression levels of genes involved in homologous recombination – could correlate with better outcome to cisplatin/pemetrexed in NSCLC. Methods: REV3, BRCA1, RAP80, TS and AEG1 mRNA was examined by quantitative RT-PCR and categorized by terciles. Expression of each gene was correlated with outcome in 47 cisplatin/pemetrexed-treated NSCLC p. Results: 63.8% male; 47% smokers; 80.9% ECOG PS 1; 80.8% adenocarcinoma. Overall response rate was 51%, with no differences according to expression levels of any of the genes. Progression-free survival (PFS) for p with low, intermediate and high BRCA1 levels was 13.4, 5.5 and 3.9 months (m), respectively (P=0.005). Similar differences in PFS were observed according to TS (P=0.003) and AEG1 (P<0.001) expression. Hazard ratio (HR) for PFS for p with high BRCA1 levels was 4 (P=0.002). Overall survival (OS) for p with low, intermediate and high BRCA1 levels was 29.7, 7.4 and 6.3 m, respectively (P=0.05). Similar differences in OS were observed according to TS (P=0.005) and AEG1 (P=0.001) expression.HR for OS for p with high BRCA1 levels was 3.6 (P=0.004). There were no differences in PFS or OS according to REV3 or RAP80 levels. However, the joint effect of BRCA1 and REV3 was significant for predictive modeling. PFS for p with low, intermediate and high levels of both genes was 14.9, 7.2 and 2.8 m, respectively (P=0.001). OS for p with low, intermediate and high levels of both genes was 29.7, 7.8 and 6.3 m, respectively (P=0.04). Conclusions: Low BRCA1 expression predicts longer PFS and OS in pemetrexed/cisplatin-treated NSCLC p. Low TS and AEG1 levels have similar predictive value. Analysis of these genes could be useful for customizing pemetrexed/platinum chemotherapy.
Differential luminal breast cancer (LBC) reprogramming in response to BIBF1120 (BIBF) or bevacizumab (B).
Authors: Quintela-Fandino Miguel , Navarro Paloma , Mondejar Tamara , Sanchez Jesus , Garcia Elena , Gomez Gonzalo , Gonzalez-Pisano David , Colomer Ramon 
Published: March 2020

11033 Background: FVB MMTV PyMT is a great mouse model for studying LBC due to its stochastic nature, immune system preservation, natural growth kinetics and ER/HER2 status. We approached the transcriptomic (T), proteomic (P), phospho-proteomic (P-P) and metabonomic (M) layers of regulation of the tumor phenotype attempting to unravel mechanisms of resistance to antiangiogenic drugs (ADs) and find new targets. Methods: Treatments started when tumors measured 0,1cm3; with the VEGFR/PDGFR inhibitor BIBF 85mg/kg/day; a murine analog of B 10mg/kg/biweekly; or vehicle (V). Tumors were harvested at time 0, week 1 (T1), or at sacrifice (Tend, 1cm3). Cd31 and pimomidazole measured vascularization and O2. T; P/P-P; and M layers were interrogated with sure print 3G arrays; titanium separation - HPLC fractionation - orbitrap spectrometer run; and GC/MS and LC/MS. Gene ontology pathways were discovered with GSEAS; kinase networks by consensus domain analysis; metabolic pathways rearrangement with in-house built bioinformatic tools. Pairwise comparisons included >15 mice/condition. All results: p or false-discovery ratio<0,05. Results: Total mice in study:2,327. BIBF-treated showed: early (T1 vs. 0) ↓glycolysis (55%) and ↑pyruvate diversion to Krebs mediated by ↓800% phosphorylation of PDH, ↑ ketones uptake and degradation (220%), mediated by 2700% ↑AMPK activity; late (Tend) 900% ↑ lipid uptake and aerobic degradation mediated by >800% ↑ ERK/B-adrenergic/PKA and PPARg (1600%) signaling. All changes supported by GSEAS. Adding blockade of AMPK, ERK, B-adrenergic or PPARg (ShRNAs or compounds) to BIBF yielded at least 50% growth delay (Anova). Tend B-treated tumors showed 210% ↑degradation of tryptophan to immunosuppressive (IS) kynurenine, and >200% ↑ levels of IS/vasodilator prostaglandins. Celecoxib added to B delayed growth 90%. B and V induced similar ↑of hypoxic/necrotic areas (T0-1-end: 5%-15%-52%, Poisson), no change in CD31. BIBF avoided necrosis/hypoxia despite >30% ↓ in CD31. Conclusions: Our strategy identified differential mechanisms of action of ADs in LBC. BIBF induces a switch from Warburg to aerobic metabolism; B reprograms the immune response. Regulators of these processes constitute targets.
Targeted next-generation sequencing (NGS) of circulating tumor cells (CTCs) in hormone-sensitive prostate cancer (HSPC).
Authors: Liu Stephen V. , Dempsey Paul W. , Strauss William , Xu Yucheng , Xu Tong , Pinski Jacek K. , Dorff Tanya B. , Quinn David I. , Triche Timothy J. , Winer-Jones Jessamine , De Fusco Andre , McMurdie Janine , Goldkorn Amir 
Published: March 2020

11040 Background: Recently a succession of new hormonal therapies has emerged, highlighting the need for biomarkers to guide the management of HSPC. Biomarker development in HSPC has been hampered by the absence of primary tumor tissue in men who undergo radiation or present with metastatic disease. CTCs can address this challenge by providing real-time cancer tissue for biomarker analysis in HSPC. To test this approach we conducted a pilot of CTC capture and targeted NGS in HSPC. Methods: Under IRB approval, blood samples from patients with HSPC were labeled with EpCAM ferrofluid and placed into the LiquidBiopsy platform (Cynvenio Biosystems, Inc.), an immunoaffinity-based microfluidic device tailored to query genomic events. CTCs were identified by CK, CD45 and DAPI expression. A matched WBC pellet served as a control representing germline sequence. Amplicon libraries were generated using Life Technologies AmpliSeq 2.0 and sequenced on an Ion Torrent platform. Somatic single nucleotide variants (SNV) present in CTCs but not in WBC were identified. Results: CTCs were detected in all 8 patients with HSPC (CTC median 64.5, range 17-217). Germline variants were consistently detected in matched CTC and WBC samples. Significant SNVs (occurring in > 1% of DNA in a sample) were found in 4 of 8 CTC samples (range 1-5 SNVs/sample, frequency 1.2%-11.9% with 620X-14,422X coverage). Notably, 3 patients had biochemical recurrence only (no clinical metastases) yet still yielded CTCs associated with SNVs in KIT, APC, RET, SMAD4 and PTEN. One patient who had untreated metastatic disease had the highest number of CTCs which harbored 4 SNVs. Conclusions: This pilot demonstrates the feasibility of using CTCs as real-time disease relevant substrate for NGS to identify personalized genomic targets in HSPC. A high number of CTCs were detectable in all patients and CTC germline variants correlated with matched WBC controls. Encouragingly, even with a relatively narrow, primary tumor-derived AmpliSeq platform, cancer relevant SNVs were detected in half of the patients including those with only biochemical recurrence, making targeted NGS of CTCs a promising approach for biomarker discovery and validation in HSPC.
Persistence of HER2 overexpression on circulating tumor cells in patients after systemic treatment for HER2-positive breast cancer: Follow-up results of the German Success B trial.
Authors: Neugebauer Julia Katharina , Rack Brigitte Kathrin , Jaeger Bernadette Anna Sophia , Andergassen Ulrich , Pestka Aurelia , Fasching Peter A. , Friedl Thomas W. P. , Mouarrawy Doraid , Clemens Michael R. , Ziemendorff Gabriele , Heinrich Georg , von Abel Ekkehard , Schneeweiss Andreas , Beckmann Matthias W. , Pantel Klaus , Janni Wolfgang 
Published: March 2020

11043 Background: The discordance between HER2-expression on circulating tumor cells (CTC) in peripheral blood and the primary tumor has already been shown by our study group for early breast cancer patients with HER2-positive tumors. Here, we compare the results to CTC prevalence and HER2-status of CTC after adjuvant chemotherapy. Methods: The SUCCESS B trial compares FEC-Docetaxel vs. FEC-Docetaxel-Gemcitabine and HER2-targeted therapy as adjuvant treatment for patients with early, HER2-positive, node positive or high risk node negative primary breast cancer. We prospectively analyzed 23ml peripheral blood before and after chemotherapy. CTC and HER2-status were assessed with the CellSearchSystem (Veridex, USA). After immunomagnetic enrichment with an anti-Epcam-antibody, cells were labeled with anti-CK 8/18/19, anti-CD45 antibodies as well as a fluorescein conjugate antibody for HER2-phenotyping. Cutoff for CTC positivity was ≥ 1 CTC. HER-positivity of CTC was assigned if at least one CTC showed strong HER2 staining (3+). Results: CTCs and their HER2-status both before and after chemotherapy were available for 392 patients. In 179 (45.7%) patients no CTC were detected before and after chemotherapy. CTC status changed from positive before to negative after chemotherapy in 104 (26.5%) patients and from negative before to positive after chemotherapy in 69 (17.6%) patients, while 40 (10.2%) patients had a consistently positive CTC status. Patients were significantly more likely to change their CTC status from positive to negative than from negative to positive (p = 0.01). Of the 40 patients with CTC both before and after chemotherapy, 14 (35%) patients had HER2-positive CTC before and after therapy, and 9 (22%) patients had HER2-negative CTC at both time points. 7 (18%) patients had HER2-positive CTC before but not after chemotherapy, while 10 (25%) patients showed the reverse pattern (p = 0.63). Conclusions: Cytotoxic treatment does not seem to influence the HER2-status on CTC. Follow-up data within the Success B trial will analyze the relevance of the HER2-expression of CTC to predict the efficacy of targeted treatment.
Characterization and identification of specific EGFR mutations in circulating tumor cells (CTCs) isolated from non-small cell lung cancer patients using antibody independent method, ApoStream.
Authors: Tran Hai T. , Melnikova Vladislava O. , Tsao Anne S. , Fossella Frank V. , Johnson Faye M. , Papadimitrakopoulou Vassiliki , Garza Miguel , Neal Chris , Hasegawa Dave , Kruempel Amy , Wu Grant , Richardson Katherine , Lewis Marcia E. , Legendre Benjamin Jr , Anderes Kenna Lynn , Davis Darren W. , Heymach John 
Published: March 2020

11044 Background: A variety of methods for isolation of CTCs of epithelial origin are available; most employ antibodies to epithelial cell adhesion molecule (EpCAM). Using classic phenotypic definition, a CTC is nucleated, cytokeratin CK(+), CD45(-) cell. However, some CTCs may elude capture as they originate from primary tumor cells which have undergone epithelial-mesenchymal transition (EMT). We report here the use of ApoStream, a novel dielectrophoresis field-flow-assisted, antibody-free method to isolate CTCs from blood. Methods: Blood was collected from consented NSCLC patients and processed using ApoStrea. For CTC enumeration comparison, CellSearch FDA-approved kit was used. Isolated cells were evaluated with multiplexed immunofluorescent assay and laser scanning cytometry analysis were applied to identify multiple combinations of positive and/or negative staining for CK/CD45/DAPI and EpCam. To determine specific EGFR mutations from captured CTCs, samples were analyzed using Improved and Complete Enrichment with CO-amplification at Lower Denaturation temperature (ICE COLD-PCR). Results: Blood samples from 32 NSCLC patients and 3 healthy volunteers were processed. ApoStream isolated 0 to 65 CK(+)/CD45(-) CTCs(n=32) and CellSearch isolated 0 to 13 EpCAM(+)/CK(+)/CD45(-) CTCs(n=7). Additionally, ApoStream™ recovered 37-3536 CK(-)/CD45(-) and 4-10702 CK(+)/CD45(+) cells. EpCAM expression was detected in 7-100% of CK(+)/CD45(-) and 0-5% of CK(-)/CD45(-) cells, and 18-100% of CK(+)/CD45(+) cells. EGFR mutations [exon 19 deletion and exon 21 L858R] were determined and found to be concordant when compared to tumor tissue analysis by Sanger sequencing. Conclusions: The ApoStream platform enriched EpCAM(+) and EpCAM(-) CTCs from the blood of NSCLC patients demonstrating utility in recovering cancer cells with multiple phenotypes. From recovered CTCs, detection of EGFR mutations was possible indicating the clinical relevance and potential utility of CTCs as an alternative to tissue biopsy. Complete mutation analysis will be presented.