bluuebunny/crossref_metadata_2025_split huggingface dataset:
Impact of precision medicine on clinical care: A single institution retrospective study.
Authors: Patel Rajvi , Quinn Ryann , Zhu Xinhua 
Published: May 2019

e14601 Background: In Oncology, precision medicine (PM) looks at molecular characteristics of tumors instead of traditional histology to determine treatment strategies. Examples are EGFR, ALK, BRAF, ROS1 and PD-L1 in non-small cell lung cancer, HER2 in breast and gastric cancer, K-RAS, N-RAS in colon cancer, and MMR/MSI in all solid tumors. Genomic testing is commonly done for patients with advanced cancer resistant to standard treatment. FoundationOne-CDx (F1CDx) is expensive but only FDA approved test for somatic genomic profiling of tumors. It is necessary to review an expensive test and its impact on clinical care. At our institution, we have patients who have had F1CDx testing. Our aim was to determine proportion of tumors that have actionable mutation (AM) for which there are currently FDA or non-FDA approved targeted treatment(s) (TT) available, proportion of pts who received TT, and barriers to receiving TT. Methods: Retrospective study of 1000 patients treated at our institution who had F1CDx testing done between September 2012 and July 2018. Variables collected included primary tumor type, F1CDx results, treatments received, and any barriers. Descriptive statistics including frequencies and proportions were utilized. Results: Of 1000 pts, 652 had tumors harboring AM. Of the 652 pts: 42 went on a clinical trial, 165 received standard next line chemotherapy, 135 received TT (38 pts received currently non-FDA approved TT), 144 either went on hospice or died prior to receiving treatment, 142 were lost to follow up, 21 were treated with surgery only, and 3 had issues with insurance approval of TT. Conclusions: Of the 65% of pts with tumors harboring AM, only 20% received TT. 25% of pts received standard next line chemotherapy. Going on hospice and being lost to follow up largely accounted for patients not receiving TT. Therefore, treating physicians should strongly consider pts’ performance status and co-morbidities prior to sending expensive genomic testing as it may have limited impact on clinical outcome. Our next steps to further investigate will be to look at objective response rate, progression free survival, and overall survival in pts who received non-FDA approved TT.
Relationship of MET exon 14 splicing variants and MET exon 14 skipping expression in NSCLC FFPE samples.
Authors: Williamson John B. , Li Xia , Liu Guang , Gu Haigang , Orton Janet , Seidman David , Sundin Tabetha , Salazar Suzanne , Sadis Seth , Lincecum Tommie , Ha Thomas , Chin Christine 
Published: May 2019

e14603 Background: MET is the target of recurrent somatic alterations in approximately 7% of non-small cell lung carcinomas (NSCLC). A key class of therapeutically relevant MET mutations results in aberrant mRNA splicing, deletion of exon 14 from the mRNA transcript (METex14 skipping), and MET overexpression. METex14 skipping assays routinely use next-generation sequencing (NGS). However, because most NGS assays are DNA based, the relationship between METex14 DNA alterations and METex14 skipping mRNA expression is not well understood. Furthermore, because METex14 skipping may have low background levels, setting a threshold for calling METex14 skipping based on RNA levels alone is challenging. To investigate these relationships, we initiated a research study in 3 CLIA/CAP laboratories using an NGS panel (OCAv3, for research use only, not for use in diagnostic procedures) that includes 161 cancer genes and detects METex14 splicing variants and METex14 skipping mRNA isoforms. Methods: OCAv3 libraries were prepared following kit instructions with templating and sequencing performed on the Ion Chef and S5 XL systems. Reads were aligned to hg19 using Torrent Suite Software and variant calling was performed using Ion Reporter software. Two cell lines (HS746T and NCI-H596) known to contain METex14 splice site mutations were used as controls. Results: Of the first 28 NSCLC FFPE specimens selected having a range of METex14 RNA expression, we detected METex14 skipping alterations in 9 cases: 6 cases with variants at exon 14 canonical splice sites and 3 cases of novel deletions in the intron 13 poly-pyrimidine tract. METex14 skipping alterations were exclusive to other oncogenic driver variants but occasionally associated with MDM2 amplification. All cases with splice site variants showed elevated METex14 skipping expression. Cases without splicing variants had no or lower METex14 skipping expression and commonly harbor activating mutations in other oncogenes (6 KRAS, 5 EGFR, 1 ERBB2, 1 MYC and 1 CD74-NRG1 fusion). Conclusions: We demonstrate a framework for interpreting MET alterations that considers both MET splice site variants and METex14 skipping transcript expression in the context of additional oncogenic mutations. An update will be presented as additional cases accrue.
Highly sensitive detection of rare mutant alleles by combining argonaute-based enrichment and XNA-PCR.
Authors: Song Jinzhao , Powell Michael Joseph , Liu Wei , Chen Junman , Bau Haim 
Published: May 2019

e14605 Background: Characterization of disease-associated, cell-free nucleic acids (liquid biopsy) provides a powerful, minimally-invasive means for early disease detection, genotyping, and personalized therapy. Detection of alleles of clinical interest is often challenged by their low concentration and sequence homology with the much more abundant wildtype nucleic acids. Methods: Argonuate (Ago) from the thermophilic bacterium Thermus thermophilus ( TtAgo) utilizes short DNA guides to specifically cleave complementary DNA and RNA targets. We found that under optimized conditions, TtAgo cleaves DNA and RNA complementary to the guide DNA with high efficiency, but spares nucleic acids with a single nucleotide mismatch at and around its catalytic site with high sensitivity. Based on these findings, we designed a new multiplexed enrichment assay, dubbed NAVIGATER (Nucleic Acid enrichment Via DNA Guided Argonaute from Thermus thermophilus), that utilizes TtAgo, to specifically cleave perfectly complementary DNA and RNA while sparing alleles of interest. Results: NAVIGATER greatly increases the fractions of rare mutant alleles with single nucleotide precision enhancing the sensitivity of downstream detection methods such as XNA-PCR. We demonstrate 60-fold enrichment of KRAS G12D in blood samples from pancreatic cancer patients and over ten-fold improved sensitivity of XNA-PCR, enabling multiplex detection of KRAS and EGFR mutants at 0.01% fractions. Conclusions: NAVIGATER has important advantages over other mutant allele enrichment assays such as the ones based on CRISPR-Cas. It does not require the target to contain a protospacer-adjacent motif; is a true (turnover) catalyst; can cleave both DNA and associated exosomal RNA targets, improving sensitivity; and can operate at elevated temperatures for higher selectivity and compatibility with detection schemes.
Integration of radiomic, genomic and clinical data to support decision making for lung cancer.
Authors: Colin Thierry 
Published: May 2019

e14607 Background: Medical imaging techniques play a central role in the evaluation of lung cancer and proper images analysis is essential for determining the location and stage of tumors, for diagnosis and prognosis assessment, guiding therapeutic decisions and for monitoring tumor response during and after treatment. It also supports interventional radiology acts (i.e. biopsies, thermo-ablations or embolization). Yet, this source of information, which is critical for the decision-making process, is not being used to its full potential. Besides, NGS technics allow the precise characterization of the genomic profile of a tumor by detecting mutations, evaluating the TMB and providing additional information such as the PD-L1 status. Methods: We have used an AI-based strategy to improve the stratification of cohorts of patients suffering from lung cancer. Using an advanced segmentation technology, we were able to quickly and precisely extract 3D Radiomic characteristics from the images. We then combined extracted heterogeneity and texture indicators with the biology information thanks to a machine learning based methodology. Results: We have applied this strategy to stage 4 NSCLC with EGFR mutation treated with TKI and have shown that stratification of the cohort with respect to the OS can be delivered using the base-line CT-scan and the first two exams used for the evaluation of the early response to the treatment. The same strategy was developed for the monitoring of lung metastases in order to help scheduling thermo-ablation by providing a prediction of the growth of the lesion in oligo-metastatic cases. Conclusions: This study paves the way to a near future when Artificial Intelligence will provide precise evaluation of lung tumors and full integration of all the medical information available for each patient to support the decision making within the tumor board.
Antitumor immune response induced by NBTXR3 activated by radiotherapy.
Authors: Thariat Juliette , Laé Marick , Carrère Sebastien , Papai Zsuzsanna , Ducassou Anne , Rochaix Philippe , Sapi Zoltan , Birtwisle-Peyrottes Isabelle , Shen Colette J. , Fernando Nishan H. , Perez Bradford , Seiwert Tanguy Y. , Chateaux Marie-Christine , Marie Sunyach , Agoston Peter , Brisse Hervé , Llacer-Moscardo Carmen , Le Cesne Axel , Bonvalot Sylvie 
Published: May 2019

e14609 Background: Radiotherapy (RT) can prime an anti-tumor immune response. Unfortunately, this response rarely generates total tumor destruction and abscopal effect. When activated by RT, intratumorally (IT) administered hafnium oxide nanoparticles (NBTXR3) locally increase radiation dose deposit and tumor cell death compared to RT alone. We hypothesized that NBTXR3 + RT could enhance the anti-tumor immune response, both in mice and humans. Methods: Murine CT26 cells were injected in both flanks of immunocompetent mice. When tumor volume reached 50-120mm3, NBTXR3 (or vehicle) was injected IT in right flank tumors only, then irradiated (3x4Gy). Mice were sacrificed when tumors reached 800mm3. Alternatively, tumors were collected 3 days after last RT fraction and immune cell infiltrates analyzed by immunohistochemistry (IHC). Patients (pts) with locally advanced Soft Tissue Sarcoma (STS) (NCT02379845) received NBTXR3 + RT or RT alone. Pre- and post-treatment (biopsy and resection, respectively) tumor tissues from pts were analyzed by IHC and Digital Pathology for immune biomarkers ( > 16 pts per arm). Results: In mice, IHC analyses showed an increase of CD8+ T cells infiltrates in both flanks of mice treated with NBTXR3+RT, while this was not observed in animals treated with RT alone. Furthermore, ICH analysis of post- vs pre-treatment samples from STS pts showed a marked increase of CD8+ and PD1 biomarkers for pts treated with NBTXR3 + RT, while no differences were seen for pts treated with RT alone. Conclusions: NBTXR3 + RT markedly changes the tumor immune profile in a similar manner in mice and pts with STS. We hypothesize that this adaptive immune response could help convert a local tumor microenvironment to a “hot” phenotype and thus improve the efficacy of immune checkpoint inhibitors. These results led us to investigate the safety and systemic effect of NBTXR3 activated by stereotactic ablative RT (SABR) in combination with anti-PD-1 antibody in pts with locoregionally recurrent or metastatic (to lung or liver) Head and Neck squamous cell carcinoma HNSCC, as well as in metastatic non-small cell lung cancer (NSCLC) and liver metastasis patients [NCT03589339].
Effect of PGK1 on radiosensitivity through regulation of CIN and CFL1 in human glioma cells.
Authors: Liu Hongyi , Liu Yuchi , Xiao Hong , Zhao Mengjie , Xiao Yong 
Published: May 2019

e14631 Background: Phosphoglycerate kinase 1 (PGK1) has been detected overexpressed in many malignancies and usually correlated with increased tumorigenesis and poor survival. Our previous study revealed that PGK1 significantly up-regulated and positively correlated with cofilin-1 (CFL1) expression in radioresistant astrocytomas samples. However, the further mechanism remains unknown. Methods: In the present study, functional interactions among PGK1, chronophin (CIN) and CFL1 were analyzed by co-immunoprecipitation and immunofluorescence experiments. Transfection of shRNA and pcDNA3.1-plasmid were respectively utilized to silence and overexpress PGK1 or CIN in both normal glioma cells (U251 and U373) and estabilshed radioresistant (RR-U251 and RR-U373) cells. The effect of PGK1 on CIN and CFL1 expression levels was investigated with Western-blot method; while the effect of PGK1 or CIN on radiosensitivity of glioma cells was evaluated using cell viability, migration and invasion assays after irradiation. Results: Cell proliferation, migration and invasion abilities significantly increased in RR-U251 and RR-U373 cells compared with those of normal cells, indicating the successful establishment of RR-glioma cell models. Laser confocal experiment in vitro showed the colocalization of PGK1 and CIN. Meanwhile, PGK1 specifically and directly combined with CIN, while did not interplay with CFL1. Elevated PGK1 expression level was observed in radioresistant cells compared with that of normal cells. The western blot analysis showed that CFL1 and CIN levels were positively correlated with the PGK1 expression in both normal and radioresistant cells. The proliferation, migration and invasion capabilities significantly decreased in PGK1-silenced and CIN-silenced glioma cells, indicating the improvement of the radiosensitivity of radioresistant cells. Conclusions: Our research implied the effect of CIN-mediated PGK1 regulation on CFL1 level, thereby altering the migration and invasion abilities in nomal and notably radioresistant glioma cells. These findings clarify a novel underlying mechanism of radioresistance in glioma cells and provide valid basis for further explorations concerning radiotherapy.
AcornFusion: A novel tool to detect gene fusion events in DNA-Seq data.
Authors: Yao Lifang , Wang Haijun , Zhang Yanrui , Wang Wenping , Dong Yongfang , Wang Wang , Wang Huina , Guo Jing , Lou Feng , Cao Shanbo , Wei Shumei 
Published: May 2019

e14650 Background: Gene fusions, resulting from chromosomal breakage and rearrangement, play a critical role during oncogenesis. Recently, a growing number of gene fusions are being considered as important therapeutic targets in oncology, for instance, Anaplastic lymphoma receptor tyrosine kinase (ALK) fusion, which confer exquisite sensitivity to ALK tyrosine kinase inhibitors (TKIs). However, available methods are inadequate for unbiased identification of potentially targetable fusions. Hence, we developed a novel fusion gene analyzing method named AcornFusion by DNA-seq data. Methods: The method is purely based on the mapping results of soft-clipped reads and the distribution of the positions where the candidate breakpoints locate, which is significantly different from the traditional methods with assembly of short reads and efficient way to do the detection. 309 patients with advanced non-small cell lung cancer (NSCLC) were enrolled. Formalin-fixed, paraffin embedded (FFPE) samples were used to DNA extracting and analyzed by AcornFusion method. Immunohistochemistry (IHC) and Reverse transcriptase polymerase chain reaction (RT-PCR) platform were also applied. Results: Of 309 pts, 17 patients were identified as fusion-positive cases by AcornFusion. 15 patients were EML4-ALK fusion positive and 1 patient was HIP-ALK fusion positive, which were all confirmed by IHC. 1 patient was ROS1 rearrangement positive, which was validated by Reverse transcriptase polymerase chain reaction (RT-PCR) method. Conclusions: With this advantage of high consistency with IHC and RT-PCR, AcornFusion can be a useful tool for investigating gene fusion events in clinical settings.
A comparative analysis of RNA sequencing methods with ribosome RNA depletion for degraded and low-input total RNA from formalin-fixed and paraffin-embedded samples.
Authors: Lin Xiaojing , Qiu Lihong , Song Xue , Hou Junyan , Chen Weizhi , Zhao Jun 
Published: May 2019

e14654 Background: Formalin-fixed and paraffin-embedded (FFPE) blocks held in clinical laboratories are an invaluable resource for clinical research, especially in the era of personalized medicine. With the development of massive parallel sequencing, RNA expression profiles have become an important source of new biomarkers with potential values in cancer metastasis and disease prognosis. Standard practice in tissue fixing and paraffin-embedding has little impact on the expression analysis of RNA samples, which makes archived FFPE samples valuable and retrospective studies feasible. But it is still difficult for some FFPE samples which have low quality or low amount of RNA to be used in the RNA expression study. Methods: We compared four FFPE RNA library preparation kits (KAPA, TaKaRa, QIAGEN and Vazyme) based on two principles of rRNA depletion, with total RNA from FFPE samples and paired FF samples using two bioinformatics analysis methods. Furthermore, we tried to construct RNA libraries with the two kits allowing for degraded low-input RNA using clinical FFPE samples of different quality. HISAT was used to analyze the data of all the libraries. Results: Our results demonstrated that high concordance in transcript quantifications were shown between FF and FFPE samples using the same kit and more transcripts could be obtained by rRNA depletion after reverse transcript reaction. The gene expression profiling using the TaKaRa kit showed a difference with other kits, which may be due to the different principle of rRNA depletion or the amount of input total RNA. For seriously degraded RNA from FFPE samples, libraries could be constructed with as low as 50 ng of total RNA, although there was higher residual rRNA and lower unique mapping ratio in the libraries. Conclusions: These results indicated that most of clinical FFPE samples could be used in the RNA profiling study. The method of RNA library construction with rRNA depletion can be used for clinical FFPE samples. For degraded and low-input RNA samples, it is still possible to obtain repeatable RNA expression profiling but with a low unique mapping ratio and high residual rRNA.
Utilizing data from patient-derived xenograft mouse models of human tumors to inform clinical decision making in Molecular Tumor Boards (MTB) deliberations.
Authors: Rueter Jens , Airhart Susan D. , Bult Carol J. , Jocoy Emily , Draheim Kyle , Cheng Mingshan , Antov Andrey , Hesse Andrew , Reddi Honey , Haslem Derrick S. , Rhodes Terence Duane , Nadauld Lincoln 
Published: May 2019

e14660 Background: Molecular Tumor Boards (MTB) are often the critical decision-making step in identifying genome-guided treatments for patients with difficult-to-treat cancers, e.g. BRAF mutated metastatic colon cancers. A common challenge for MTBs is prioritizing between two or more actionable variants in a tumor. A potential solution to this challenge is to incorporate drug response in Patient-derived xenografts (PDX) models into MTB deliberations. The goal of this study was to evaluate the feasibility of using PDX models to elucidate drug-effectiveness in BRAF-mutated cancer as an example of a common clinical scenario. Methods: We selected BRAF-mutated PDX models from the JAX PDX resource based on the presence of an activating BRAF mutation and a second actionable variant from the JAX Cancer Treatment Profile (CTP). Somatic mutation data from PDX tumors were presented to members of the Intermountain MTB. PDX models were then treated with drugs recommended by the MTB; outcomes based on tumor growth inhibition (TGI) were shared with the MTB. Results: Gene/variant targets, associated drugs for the 2nd mutation and responses are described in the table. The MTB members determined that PDX data presented in TGI format is helpful in MTB deliberations. Activity of BRAF-targeted therapy was expected while the low activity of olaparib in the BRCA1-mutated colon cancer model was unexpected. The MTB then discussed molecular mechanisms that contributed to these outcomes. Conclusions: The pilot study demonstrated that utilizing PDX drug response data as an additional molecular annotation for MTB deliberations is feasible. Future studies will further optimize this process. [Table: see text]
Differentiated pharmacokinetic and pharmacodynamic properties of a highly selective MET kinase inhibitor, OMO-1: Implications for efficacy and safety.
Authors: Perera Timothy Pietro Suren , Libouban Marion , Jansen Ellen , Tjwa Marc , Ciamporcero Eric , Meulemans Ann , Van der Aa Annegret , Clack Glen , Lolkema Martijn P. 
Published: May 2019

e14674 Background: The MET kinase is an established therapeutic target in a range of cancer indications, being a primary oncogenic and therapy resistance driver. Methods: OMO-1 is a highly potent, selective oral inhibitor of MET kinase and Organic Cation Transporter 2 (OCT2) that is currently being explored in a Phase I/II study (NCT03138083). Results: Pre-clinical data for OMO-1 indicates that anti-tumor efficacy against MET driven tumor models does not require 24/7 exposure in the plasma. PK/PD assessments indicate that OMO-1 efficacy is AUC driven. Exposures above a trough concentration of ~600ng/ml for a period of 6-8hr and an AUC of 3000ng.h/ml result in complete target inhibition sufficient to induce regression or stasis of MET driven in-vivo models. Dosing of OMO-1 at 12.5mg/kg BD 4hr apart, or split over 4 doses 2hr apart, with a dosing-free period of 18-20hr was sufficient to obtain the effects preclinically. The ongoing Phase I/II study in patients with solid tumours utilised learnings from the pre-clinical and FIH study (NCT01964872) where ascending single doses and multiple doses were evaluated. The selected starting dose for the patient study (100mg BD, 4 hr apart) achieved exposures above the predicted MBAD. Paired tumor biopsies were obtained from a higher dose level (200mg BD). A MET exon 14 skipping mutation NSCLC patient at this dosed demonstrated near-complete inhibition of phospho MET accompanied by signs of clinical benefit and lesion shrinkage, thereby matching the preclinical data. Certain ‘class effect’ adverse events, such as edema, were not observed. Conclusions: OMO-1 is an oral, potent MET TKI with a novel dosing regime, identified during preclinical optimization (BD 4hr apart), that demonstrates encouraging signs of clinical activity without certain ‘class-specific’ adverse events. Further evaluation of this differentiated and efficacious agent is warranted and ongoing.