bluuebunny/crossref_metadata_2025_split huggingface dataset:
Frequency of MET amplification determined by comprehensive next-generation sequencing (NGS) in multiple solid tumors and implications for use of MET inhibitors.
Authors: Palma Norma Alonzo , Palmer Gary A. , Ali Siraj M. , Stephens Philip J. , Ross Jeffrey S. , Miller Vincent A. , Lipson Doron 
Published: March 2020

11068 Background: MET expression has been shown to be prognostic and possibly predictive in several tumor types and both small molecule inhibitors of MET kinase as well as monoclonal antibodies are under study as therapies for this subset of patients. However, the methods to assess MET overexpression are not well standardized. In the clinic, NGS is an advanced diagnostic method for identifying known and unknown targeted-therapy options. We therefore sought to explore the ability of NGS to detect high level MET amplifications in a general oncology population. Methods: We review here the results from analysis of 2,221 FFPE tissue samples across a range of tumor types by an NGS assay in a CLIA-certified laboratory (Foundation Medicine). We specifically report base pair substitutions, small insertions/homozygous deletions (indels), high level (> 6 copies/nucleus) amplification (amp) and select rearrangements in 189 genes, including MET. Results: MET was altered in 28/2,223 (1.2%) of patient samples. MET alterations were limited to amplifications (median 15X, range 6X-40X); no base pair substitutions, indels, or rearrangements were found. MET amp was present in 3/48 (6.2%) primary bone sarcomas, 1/20 (5.0%) myogenic sarcomas, 2/58 (3.4%) gastric, 1/38 (2.6%) kidney, 2/78 (2.5%) hepatocellular, 1/41 (2.4%) uterine, 4/188 (2.1%) unknown primary, 2/99 (2.0%) ovarian, 8/386 (2.0%) lung, 3/157 (1.9%) colorectal, and 1/109 (0.9%) pancreatic carcinomas. Conclusions: Use of NGS to characterize MET alterations in a 2,000+ patient population provides evidence for the role of NGS in identifying the future use of MET-targeted therapy in a variety of common and uncommon solid tumors. Clinical follow-up of the subset of cases treated with a MET inhibitor is ongoing.
Prognostic value of microRNAs (miRs) expression in stage I-IIIA lung adenocarcinoma (AC).
Authors: Skrzypski Marcin Tomasz , Goryca Krzysztof , Czapiewski Piotr , Jassem Ewa , Biernat Wojciech , Pawlowski Ryszard , Rzyman Witold , Jassem Jacek 
Published: March 2020

11069 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 samples of early squamous cell lung carcinoma, and the feasibility of their assessment in formalin fixed paraffin embedded (FFPE) samples (Skrzypski et. al. J Clin Oncol 2010;28;15s). In this study, we investigated the expression of 350 microRNAs in operable AC pts. Methods: FFPE tumor samples were obtained from 80 stage I-IIIA pts who underwent curative pulmonary resection, 48% of whom subsequently developed distant metastases. Median follow-up of pts who were disease recurrence-free was 5.8 years (range, 4.0-9.1 years). RNA was isolated from tumor tissue with RecoverAll kit (Ambion). Expression of 350 miRs was analyzed by qRT-PCR (Appliedbiosystems). Raw data were normalized vs. the geometric mean of U6, RNU48 and RNU44 expression. Relative miRs expression was correlated with distant metastases-free survival (MFS) and the mean expression was compared between the groups with and without relapse. Results: Expression of 41 miRs correlated with MFS in Cox regression analysis and 21 of these showed different level in pts with and without relapse in the t-Student test (both at p<0.05 level). The top prognostic miRs included miR-99a* (p=0.006), miR-1255B (p=0.005), miR-1233 (p=0.013) and miR-1303 (p=0.03); all previosly shown to be prognostic in AC or NSCLC. We also found 14 new microRNAs (patent pending) potentially prognostic for relapse in AC. Conclusions: Expression of selected miRs may aid in prediction of distant relapse in AC pts undergoing pulmonary resection.
Clinical and analytical performance of non-small cell lung cancer biomarkers.
Authors: Anderson Steven M. , Cai Li , Tepperberg James H. , Faruki Hawazin 
Published: March 2020

11070 Background: A variety of biomarkers are currently used to help guide treatment decisions for patients with non-small cell lung cancer (NSCLC). These include mutation analysis for the EGFR and KRAS genes, along with gene rearrangement analysis for the ALK and ROS1 loci. In this study we have evaluated the clinical and analytical performance features of these assays in a series of formalin-fixed paraffin-embedded (FFPE) tissue samples. Methods: FFPE samples submitted for analysis of the EGFR, KRAS, ALK and ROS1 genes were evaluated using molecular and FISH assays. EGFR mutation analysis was performed using Sanger nucleic acid sequencing methods for exons 18-21. KRAS mutations were detected using allele specific PCR or pyrosequencing methods. Rearrangements involving the ALK gene were detected using break-apart FISH probes (Abbott Molecular). Genetic alterations involving the ROS1 gene were determined using FISH probes (Kreatech Diagnostics). Over 6,200 test results for these 4 markers are included in this analysis. Results: Mutations in the EGFR gene were detected in 10.1% of samples evaluated (n=3,872). A slightly higher percentage of samples from female patients (13%) had a detectable mutation compared to samples from males (7%) (chi-square p<0.0001). Deletions in exon 19 (51%) were the most common alterations detected, followed by point mutations in exon 21 (35%). KRAS mutations were detected in approximately 22% of specimens. ALK gene rearrangements were observed in 3.1% of samples (n=1,524). Specimens from individuals <50y of age were more likely to provide a positive result (11%) compared to samples from individuals >50y of age (2.5%) (chi-square p<0.0001). Gene amplification for the ALK gene was a common finding in the NSCLC samples evaluated. ROS1 alterations were detected in 2.8% of the specimens. In this cohort, no specimens were positive for both an EGFR mutation and an ALK gene rearrangement. Conclusions: Biomarker testing is well established in clinical practice for NSCLC, with results from the tests used to guide important therapy decisions. Assays for biomarkers such as EGFR, KRAS, ALK and ROS1 are robust, allowing for the analysis of multiple analytes in FFPE samples, even when the amount of tissue may be limiting.
Prognostic value of waterfall plots with the addition of nontarget lesion data.
Authors: Mietlowski William Leonard , Stein Andrew Marc , Bao Weichao , Waltzman Roger J. , Wood Patricia Ann 
Published: March 2020

11082 Background: In patients with solid tumors, the use of a waterfall plot displaying the best percentage change in sum of the longest diameters of target lesions per patient is a common way to depict anti-tumor activity for cytostatic agents (Booth 2008, Dhani 2009). This representation assumes that the best percentage change represents the maximum anti-tumor activity for each patient. Information about new lesions and/or changes in non-target lesions is not incorporated in the waterfall plot; yet these additional events were found to be significant prognostic factors for overall survival adjusting for change in the target lesions (Litiere 2012, Suzuki 2012). Methods: We analyzed two phase III lung cancer trials of 1st and 2nd line combination chemotherapy ± ASA404 (ATTRACT-1,n=1299, ATTRACT-2, n= 920). For patients whose best response in the target lesions was shrinkage, we calculated how often this best response was synchronously accompanied by non-target disease progression. Results: See Table. Conclusions: There can be substantial tumor shrinkage in target lesions synchronously with progressive disease outside the target lesions. Therefore, graphical displays of anti-tumor activity should consider incorporating new and non-target lesion information, as well as target lesion tumor burden. We propose an extended waterfall plot presenting a more complete assessment of anti-tumor activity by incorporating non-target lesion information. We illustrate its utility in an additional data set, the RECORD-1 phase III renal cell cancer trial. Clinical trial information: NCT00662597. [Table: see text]
Application of next-generation sequencing (NGS) for evaluation of advanced epithelial cancers: A single institution experience.
Authors: Boland Patrick McKay , Skarbnik Alan P. , Cristofanilli Massimo , Alpaugh R. Katherine , Olszanski Anthony J. 
Published: March 2020

11092 Background: The use of molecular targeted therapeutic agents may require the application of sophisticated diagnostic technologies for patients’ selection. Next generation DNA sequencing (NGS) has the ability to identify genetic alterations (GA) including mutations, copy number alterations, insertions/deletions, and rearrangements in tumor specimens. We sought to evaluate patients with advanced and refractory epithelial tumors to detect potentially actionable molecular abnormalities. Therapeutic intervention driven by GA findings was determined solely by the patient’s treating physician. Methods: Tumor samples from 77 patients ≥ 18 years old with any solid malignancy were sequenced. NGS of 186 genes was performed by FoundationOne through funding from Foundation Medicine using archival or newly acquired tumor tissue. Results: Seventy-four patients had specimens with adequate material for DNA extraction and analysis. Characteristics: 74% female, median age 55 years (19-82). Tumor sites included inflammatory breast (50%), colon (12%), unknown primary (5%) and other (33%). At least one genetic alteration was seen in 71 (96%) patients. The most common GA included mutations in 65 (60%) samples revealing TP53 (32%), KRAS (10%), PIK3CA (8%), and APC (6%) and amplifications in 38 (35%) samples which included MYC (18%), MCL1 (14%), CCND1 (12%), and ERBB2 (7%). Copy number loss (4%), fusion (1%) and deletions (2%) were also discovered. An actionable GA was seen in 46 of 74 patients successfully tested (62%), with 54% of GAs being amplifications and 43% mutations. Patients had a median of 3 GA (range 0-7). One patient with anal cancer had a concomitant PIK3CA mutation and amplification. NGS in association with immunohistochemistry helped identify site of origin for one patient with an occult primary. Conclusions: NGS identified GAs in the majority of patients with advanced epithelial cancers, including actionable abnormalities in a large fraction of this heterogeneous population. NGS shows promise in the diagnostic evaluation of advanced malignancies. Future studies should include the potential prognostic implications of genomic-driven personalized therapy.
MRI apparent diffusion coefficient in a murine orthotopic glioblastoma model as a clinically translatable early readout of efficacy for AMG 595, an antibody drug conjugate targeting EGFRvIII.
Authors: Yerby Brittany , Estrada Juan , Silva Matthew D. , Hamblett Kevin J. , Coberly Suzanne K. , Hill John S. , Ungersma Sharon E. , Beltran Pedro J. 
Published: March 2020

11095 Background: Epidermal growth factor receptor variant III (EGFRvIII) is a constitutively active mutant of EGFR present in thirty to fifty percent of glioblastoma (GBM) patients. AMG 595, currently in Phase I trials, is composed of a fully human anti-EGFRvIII-specific antibody conjugated to the maytansinoid DM1 via a non-cleavable linker. The MRI apparent diffusion coefficient (MRI ADC) has been shown to correlate with tissue cellularity, and changes in MRI ADC can be an early indicator of therapeutic efficacy. The aim of this work is to evaluate MRI ADC as a clinically translatable early readout of tissue changes due to AMG 595 treatment in a murine orthotopic GBM model. Methods: D317 human GBM cells were intracranially injected into in female CB17 SCID mice at Day 0. Mice were randomized at Day 7, using tumor volumes calculated by MRI, and were treated with vehicle, 6.5, 11, or 22 mg/kg AMG 595 i.v. twice per week, or temozolomide 10 mg/kg p.o. daily five days per week (N=8/group). MRI was repeated at days 14 and 21. Tumor volumes were manually traced on multi-slice T2-weighted RARE images covering the entire tumor volume. The mean MRI apparent diffusion coefficients for each tumor in the vehicle and 22 mg/kg AMG 595-treated groups were calculated from diffusion-weighted spin echo images (b = 100-1200 s/mm2). Results: A dose-dependent effect of AMG 595 on tumor volume was observed at Day 21; growth was inhibited in both the temozolomide and AMG 595-treated groups (22 and 11 mg/kg) relative to vehicle (p<0.0001). At Day 14, this significant treatment effect on tumor volume was not yet detectable. However, mean MRI ADC values were already significantly higher in the AMG 595 (22 mg/kg) treated group than in the vehicle group (23% higher at Day 14, p<0.01 vs vehicle; 32% higher at Day 21, p<0.0001 vs vehicle). The increase in MRI ADC in the AMG 595-treated group preceded observable tumor growth inhibition in the AMG 595-treated animals. Conclusions: Increases in tumor MRI ADC in response to AMG 595 treatment precede measurable inhibition of tumor growth, supporting the use of MRI ADC as a clinically relevant early biomarker for therapeutic efficacy.
Cross-species synthetic lethal interaction screening as a strategy for the identification of novel therapeutic targets in cancer.
Authors: Shen John P. , Srivas Rohith , Bojorquez-Gomez Ana , Licon Katherine , Li Jian Feng , Sobol Robert W. , Ideker Trey 
Published: March 2020

11105 Background: Mutation, deletion, or epigenetic silencing of tumor suppressor genes is a near universal feature of malignant cells. However, therapeutic strategies for restoring the function of mutated or deleted genes have proven difficult. Synthetic lethality, an event in which the simultaneous perturbation of two genes results in cellular death, has been proposed as a method to selectively target cancer cells. Identifying and pharmacologically inhibiting proteins encoded by genes that are synthetic lethal with known tumor suppressor mutations should result in selective toxicity to tumor cells. Methods: To identify candidate target proteins we measured all pair-wise genetic interactions between all known orthologs of human tumor suppressor genes (162 genes) and all orthologs of druggable human proteins (~400 genes) in the model organism S. Cerevisiae. Analysis of the data uncovered 2,087 distinct synthetic lethal interactions between a tumor suppressor and druggable gene. A computational algorithm was then developed to identify those interactions which were likely to be conserved in humans based on conservation of the synthetic lethal relationship in the distant fission yeast S. pombe. Results: Our bioinformatic analysis suggested a high probability of conservation of the synthetic lethal interactions between the yeast RAD51 (ortholog of BRCA1) and RAD57 (ortholog of XRCC3) with HDA1 (a histone deacetylase; HDAC). We confirmed this by treating LN428 cells with stable lentiviral knockdown of BRCA1 or XRCC3 with the HDAC inhibitors vorinostat (SAHA) and entinostat (MS-275). Both the BRCA1 and XRCC3 knockdown cell lines were significantly more sensitive to HDAC inhibition relative to wild-type (non-silencing lentiviral control) cell line (Table). Conclusions: These results demonstrate that high-throughput approaches for screening synthetic lethal interactions in model organisms such as S. cerevisiae and S. pombecan serve as a valuable resource in helping to identify novel therapeutic targets in human cancer. [Table: see text]
Highly active combination of BRD4 antagonist and histone deacetylase inhibitor against human AML.
Authors: Bhalla Kapil N. , Fiskus Warren , Peth Karissa 
Published: March 2020

11107 Background: The bromodomain-containing protein 4 (BRD4) is a member of the BET (bromodomain and extraterminal) protein family, which regulate the assembly of chromatin complexes and transcriptional regulators at the target gene promoters, e.g., of Myc and BCL2. JQ1 competitively binds and inhibits the bromodomains of the BET proteins, including BRD4. Treatment with JQ1 attenuates Myc and BCL2 levels and promotes growth arrest, differentiation and apoptosis of AML cells. Methods: Here, we determined the growth inhibitory, differentiation and apoptotic effects of JQ1 (100 to 500 nM) alone and in combination with low concentrations of the deacetylase inhibitor panobinostat (PS) (5 to 20 nM) (gift from Novartis) in cultured (OCI-AML3, MV4-11 and MOLM13) and primary AML blast progenitor cells. We also determined the in vivo anti-AML activity of JQ1 (50 mg/kg/day IP) and/or PS (5 mg/kg/MWF IP) for 3 weeks against the OCI-AML3 xenograft in the NOD/SCID mice. Results: Treatment with JQ1 decreased the binding of BRD4 at the chromatin associated with Myc and BCL2 promoters (by ChIP-qPCR) and attenuated the mRNA and protein levels of Myc, BCL2 and cyclin D1, while increasing the levels of p21, CEBPα, BIM and cleaved PARP in the cultured and primary AML blasts. This was associated with an increase in the % of G1 phase cells, attenuation of the colony growth, and induction of apoptosis of the cultured (OCI-AML3 >MV4-11 >MOLM13) and primary AML cells. JQ1 treatment also dose-dependently inhibited the viability of CD34+ primary AML progenitor cells (n=10). Gene expression microarray analysis revealed a JQ1 treatment-associated signature of the most up- and down-regulated mRNAs that correlated with its anti-AML effects. Co-treatment with JQ1 and PS synergistically induced apoptosis of AML cells (by isobologram analysis; CI < 1.0). As compared to the mice treated with vehicle alone, or with each agent alone, co-treatment with JQ1 and PS, without inducing toxicity, significantly improved the survival of the OCI-AML3 engrafted NOD/SCID mice (p < 0.01). Conclusions: These pre-clinical findings warrant further in vivo evaluation of the efficacy of the combination of a BRD4 antagonist and PS, and its predictive biomarkers, against human AML.
NGS-based targeted RNA sequencing for expression profiling and relative quantitation of specific gene isoforms and fusions in tumor-specific panels.
Authors: Vansant Gordon , Landers Mark , Vo Lien , Oades Kahuku , Kim Hyunsoo , Lee Jerry , Meredith Rhonda , Lee Byung-In , Monforte Joseph 
Published: March 2020

11108 Background: Gene expression signatures have become a useful tool for the identification of tumor subtypes and response to specific therapies. Expression of tumor, metastatic and macrophage specific transcripts utilizing alternative promoters and transcriptional start sites can further characterize these tumors . NGS is a powerful tool for gene expression analysis, however larger sample input requirements (>100ng) and excessive sequencing depth requirements (30-40M tags/sample) to detect the expression of rare isoforms or fusions in tumor samples are prohibitive for clinical assay development. We describe the development of a targeted RNA sequencing assay for the relative quantitation of specific gene expression signatures, known splice variants and gene fusions from less than 100 ng of starting material in a single tube universal amplification format. Methods: Primers for 52 genes, isoforms and gene fusion products were designed using the universal amplification strategy. 10 ng of RNA from 5 matched tumor/adjacent normal breast cancer tumor pairs were assayed. Libraries were prepared for sequencing by emPCR and sequenced on Ion Torrent PGM. Data were aligned via TMAP. Relative expression was determined vs. housekeeping genes or wild type transcripts. Results: All gene targets were detected at significant levels in at least one tumor sample. Robust expression profiling (5 log dynamic range) was obtained from FFPE macrodissected tumor and normal samples with as little as 200K reads/sample. Immune specific transcripts demonstrated differential expression (CCL3, AIF, FCGR3A and CSF1) across patients and matched pairs as well as an upregulation of CXCL12, indicative of tumor associated macrophages. Conclusions: Targeted RNAseq demonstrates detection and quantitation of relative expression levels of not only tumor subclass specific gene expression signatures, but immune cell specific transcripts from 10ng of FFPE derived total RNA derived from macrodissected tumor samples. The lower input requirements, quicker turnaround time and incredible sensitivity of targeted RNAseq make this assay a useful tool for clinical assay development.
Randomized study of capecitabine versus S-1 in women with metastatic or recurrent breast cancer: Japan Breast Cancer Research Network (JBCRN) 05 trial.
Authors: Yamamoto Daigo , Iwase Satoru , Yamamoto Chizuko , Tsubota Yu , Yamaguchi Takuhiro 
Published: March 2020

1111 Background: Capecitabine and S-1 are orally administered fluorinated pyrimidines with high-level activity against metastatic breast carcinoma (MBC). Methods: This randomized multicenter phase II study was conducted to investigate the activity and safety of two oral fluoropyrimidines, capecitabine and S-1, in breast cancer patients. Patients with MBC were randomly assigned to receive capecitabine at 1,657 mg/m2two times daily on days 1–21 every 4 weeks, or S-1 at 40–60 mg two times daily according to the body surface area on days 1–28 every 6 weeks. Results: One hundred and forty-two patients were enrolled, and 136 patients were randomized to capecitabine (N=71) or S-1 (N=65). The median progression-free survival, the primary end-point, was 1.4 years for capecitabine and 1.3 years for S-1, with a hazard ratio (S-1/ capecitabine) of 0.85 (95%CI: 0.52-1.38) (log-rank p = 0.5). The confirmed ORR for both populations was 24.0% for capecitabine and 23.1% for S-1(p = 0.938). The median OS was 3.5 years for capecitabine and 2.7 years for S-1; the hazard ratio (S-1/ capecitabine) was 1.32 (95% CI: 0.7–2.48) (p = 0.39). Further, the most common treatment-related adverse events were grade 1/2 in intensity. However, there were more adverse events, thrombocytopenia (p = 0.040, S-1: 9.2%, capecitabine: 1.4%), and nausea (p = 0.079, S-1: 26.2%, capecitabine: 14.1%) in the S-1 group. Hand–foot syndrome occurred in the S-1 and capecitabine groups (p = 0.029, S-1: 10.8%, capecitabine: 25.4%). Conclusions: The results of the current study demonstrate that S-1 or capecitabine is an effective and well-tolerated treatment in patients with MBC. In addition, they are convenient and orally administered drugs, which makes them attractive agents for use in outpatient treatment. Clinical trial information: NCT 00438100.