bluuebunny/crossref_metadata_2025 huggingface dataset:
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.
Nonclinical endpoint assessment utilizing a digital vivarium cloud platform in an ovarian cancer xenograft model.
Authors: Nwagwu Chibueze Dominic , Defensor Erwin , Schaevitz Laura , Carbonell Shawn
Published: May 2019

e14690

Background: Translation of preclinical data is highly dependent on the validity of the metrics for assessing disease progression and endpoint in mouse oncology models. A digital cloud platform would provide an objective and non-invasive technology allowing real-time assessment of several parameters including motion, breathing, and activity. Here, we hypothesize digital metrics can serve to predict endpoint in an ovarian cancer xenograft model with ascites, thereby improving analysis and interpretation of therapeutic efficacy data and improved adherence to the Three Rs. Methods: Six groups of athymic mice were intraperitoneally inoculated with increasing numbers of ES-2 ovarian cancer cells or control and housed in the Vium Digital Vivarium. Leveraging Vium’s readily accessible videographic and electronic records we retrospectively analyzed night time motion data using the ROC curve on GraphPad Prism and R programming. The following parameters were defined: motion loss post induction (MLPI) and motion loss from endpoint (MLFE). These were in turn compared to the conventional parameters (ie, number of tumor nodules, tumor weight, volume of ascites, and clinical signs) in terms of predicting disease and endpoint. Results: MLPI showed significantly high correlation with endpoint when graphed on a linear regression plot (R2= 0.8671; p< 0.0001), while the conventional metrics showed low correlations with endpoint: number of tumor nodules (R2= 0.1334; p= 0.1133); volume of ascites (R2= 0.2524; p= 0.0240); tumor weight (R2= 0.1162; p= 0.1413). We also showed that MLFE was significantly higher than the days from onset of first clinical sign to endpoint. Analysis of additional digital metrics are underway. Conclusions: The results support the improved ability of a digital platform to predict endpoint over conventional metrics, and earlier than manually-recorded clinical signs. These results are important as they not only provide an objective parameter to enhance study interpretation, but they also reduce the time to humane endpoint. Additionally, the continuously recorded digital metrics increase statistical power, which can be leveraged to potentially reduce the number of animals required per study.
Clinical-relevant model of intraductal papillary mucinous neoplasm induced by ARID1A loss.
Authors: Wei Tao , Chen Qi , Liang Tingbo , Bai Xueli
Published: May 2019

e14696

Background: Intraductal papillary mucinous neoplasm (IPMN) constitutes a precursor lesion for malignancy of pancreas. Genes encoding subunits of SWI/SNF chromatin-remodeling complexes like ARID1A are collectively mutated in a significant proportion of patients with pancreatic neoplasm. In the present study, we characterize the role of ARID1A in pancreatic tumorigenesis using genetic engineering mouse models. Methods: Various mouse strains were interbred to obtain pancreas-specific Arid1aflox, KrasLSL-G12D/+; Arid1aflox, KrasLSL-G12D/+; Tgfbr2flox; Arid1aflox, and various littermate control animals. Tissue microarrays were used to determine the expression of ARID1A in human pancreatic ductal adenocarcinoma and IPMN. Results: Arid1a loss in pancreas of mice incurred pancreatic duct dilation and development of cystic lesions. Concomitant Kras mutation and Arid1a inactivation accelerated formation of cystic neoplasm resembling human IPMN. These lesions were reminiscent of specific subtype of IPMN given their morphology and expression pattern of mucin proteins. Histological examination further revealed the step-wise progression of these neoplasm from low-grade to high-grade dysplasia and even invasive carcinoma. TGFBR2 deletion promoted the malignant transformation of IPMN to invasive carcinoma in the background of Kras and Arid1a alterations. Analysis of human tissues consistently showed negative or low expression of ARID1A in over half of IPMN patients. Moreover, patients with pancreatic adenocarcinoma also exhibited downregulated ARID1A expression, and reduced expression correlated with worse prognosis. Conclusions: We have established a preclinical mouse model of pancreatic cystic tumor closely resembling human IPMN. This is helpful for the further understanding of biology of IPMN and highlight therapeutic niches for patient tailored treatment in those with altered SWI/SNF function.
Effect of GPR87 on cell proliferation via KRAS signaling pathway in p53-mutant lung cancer cells.
Authors: Nakano Takayuki , Nakashima Nariyasu , Liu Dage , Zhang Xia , Matsuura Natsumi , Tarumi Shintaro , Chang Sung soo , Go Tetsuhiko , Kakehi Yoshiyuki , Yokomise Hiroyasu
Published: May 2019

e14713

Background: GPR87 is a member of the cell surface molecular G protein-coupled receptors (GPCRs) family and suggested to contribute to the viability of human tumor cells including lung cancer cell. The mechanism of GPR87 in promote cell proliferation is still not yet well understand. p53 was reported to take an important role in keeping cell viability of GPR87-expressing cells. However, most of lung cancer cells possess p53 mutation. In the present study, several reported signal pathway were investigated in lung cancer cells. Methods: Two p53 mutant GPR87-overexpressing lung cancer cell H358 and PC9 lung cancer cell was investigated. An adenoviral vector that encoded a short hairpin siRNA targeting the GPR87 gene (Ad-shGPR87) was constructed. Real-time RT-PCR was performed to evaluate gene expressions and westen blotting analysis for protein expression. MTT assay was used to evaluate the cell viability. Results: Ad-shGPR87 effectively inhibited the GPR87 expression and significantly reduced the percentage of viable cells in GPR87-overexpression H358 and PC9 cell. Regading the signal pathway, there was no p53 expression in H358 cell and no changes in PC9 cell. However, both cells showed a significant decrease in KRAS and c-Myc gene expression 5 days after Ad-shGPR87 transfection. On the other hand, after Ad-shGPR87 transfection, Akt and Cyclin-D1gene expression decrease slightly in H358, but not in the PC9 cell. Conclusions: Theses result show that GPR87 may promoting cell proliferation through several signaling pathways and that the active in p53 mutant cell may linked to KRAS pathway in lung cancer cell.
Targeting EGFR Ex20 mutant lung cancer with the wild type sparing kinase inhibitor PRB001.
Authors: Sos Martin L. , Tumbrink Hannah Lea , Schultz-Fademrecht Carsten , Lategahn Jonas , Keul Marina , Niggenaber Janina , Heimsoeth Alena , Baumann Matthias , Werr Lisa Hanna , Degenhart Carsten , Menninger Sascha , Heuckmann Johannes M , Thomas Roman K. , Rauh Daniel , Klebl Bert
Published: May 2019

e14718

Background: The majority of EGFR mutant tumors can be effectively treated with targeted drugs. Lung adenocarcinoma patients with EGFR Ex20 insertion mutations, however, lack safe and potent treatment options. These genetic alterations share homology with HER2 Ex20 insertion mutations and perturb the ATP binding pocket in a way that limits accessibility through currently available tyrosine kinase inhibitors. Second-generation EGFR inhibitors are partially active in EGFR Ex20 mutant models but their potent activity against wild type (WT) EGFR and the resulting adverse effects largely prohibit the clinical use of these drugs. To address this medical need, we developed PRB001, a novel EGFR kinase inhibitor. Methods: We facilitated protein X-ray crystallography to guide the development of small molecule inhibitors with high potency against EGFR/HER2 Ex20 mutant kinases and low activity against WT EGFR. Iterative compound optimization involved biochemical profiling concerning inhibition and binding kinetics, cellular profiling as well as mouse pharmacokinetic and mouse efficacy studies. Results: PRB001 exhibits potent activity against EGFR/HER2 Ex20 insertion mutations, in genetically engineered Ba/F3 cell line models and patient derived cell lines. At the same time, PRB001 exhibits a 10-100 fold lower activity against WT EGFR in several cellular models. Our data indicate that PRB001 and its derivatives display a therapeutic window for an effective treatment of EGFR Ex20 mutant tumors with a limited toxicity profile. Mouse xenograft experiments support these results, showing that, in contrast to second-generation EGFR inhibitors, PRB001 does not inhibit WT EGFR and does not lead to loss of weight of treated animals at effective doses of 90 mg/kg daily. Conclusions: Our data support the notion that PRB001 effectively kills a wide range of EGFR Ex20 mutant cellular models and together with its safety profile builds a basis for the development of a mutant-selective and clinically effective tyrosine kinase inhibitor.
Urinary excretion of components of the renin-angiotensin-aldosterone system in patients having localized renal cancer.
Authors: Osokin Roman , Kit Oleg Ivanovich , Komarova Ekaterina , Aboyan Igor , Komarova Elizaveta
Published: May 2019

e14725

Background: The aim of the study was exploring the content of components of the renin-angiotensin-aldosterone system (RAAS) in the urine of renal cancer (RC) patients depending on the clinical and morphological characteristics. Methods: In the urine of patients having localized renal cancer Т1N0M0 (the main group, n = 40) the level of angiotensinII (ATII), angiotensin-converting enzymes (ACE and ACE2) was studied by the ELISA with excretable creatinine taken into account in order to eliminate the differences of diuresis. The control group was made up of 35 healthy donors. Results: In patients of the main group, the content of ATP in the urine is 71,5% higher (р = 0,003) than in the healthy donors. In 50% of the patients, the range of fluctuations of ATI in the urine from the lower to the upper quartile amounts to 4,2-9,8 pg/µmol of creatinine against 2,1-5,2 pg/µmol of creatinine in the healthy ones.The level of ACE and ACE2 in the patients as compared to the healthy donors is also 35,4% and 24,5% higher, respectively (at p < 0,05). The proportion of increment ΔATII/ΔACE in the patients amounted to 2,2±0,1as compared to the healthy donors, that of ΔATII/ΔACE2 – to3,2±0,2. Meanwhile, ΔACE/ΔACE2 was 1,6±0,1, which confirms the predominance of the activity of ACE. In patients of the main group, no statistically valid difference of the urinary excretion value of ATII, ACE and ACE2 has been identified between the subgroups depending on the RC stage T1a, Т1bas well as on dimensions of the tumor nodes. However, in case of the RC with G2 tumor differentiation grade as compared to the G1, the content of ATII, ACE and ACE2 in the urine is 3,5; 2,5 and 2,1 times higher, respectively (p < 0,05). Conclusions: In patients having localized renal cancer, increased urinary excretion of components of the renin-angiotensin-aldosterone system has been found. The content of angiotensin II in the urine exceeds the activity of angiotensin-converting enzymes, which may be related to the alternative ways of its formation under tumor growth. The content of the RAAS components in the urine in patients having localized renal cancer does not depend on the stage and dimensions of the tumor but it correlates with the differentiation grade.
ALK resistance mutations (muts) developed in different ALK fusion types.
Authors: Zhao Jun , Liu Caixia , Chen Jianhua , Chen Likun , Ai Xinghao , Fan Zaiwen , Wu Yifen , Chen Rongrong , Xia Xuefeng
Published: May 2019

e14741

Background: Patients (pts) treated with ALK inhibitors (ALKi) inevitably develops resistance. Diverse mutations (muts) confer resistance to ALKis, which may be related to the diverse types of ALK fusion. The objective of this study is to see whether the resistance mechanisms developed during ALKi therapy are ALK fusion types dependent. Methods: The mutation profiles of 38 pts with known ALK fusion partners and positions, who ordered NGS test in our institution after progressed on ≥ 1 ALKis, were analyzed. Results: Resistant muts in ALK kinase domain ( ALK resistant muts) were detected in 53% (20/38) of the resistant pts. 100% (1/1) of the EML4-ALK V5’ variant (V5’), 81% (13/16) of the EML4-ALK V3 variant (V3), 60% (3/5) of the non- EML4-ALK, 23% (3/13) of EML4-ALK V1 variant (V1), and 0% (0/3) of the EML4-ALK V2 variant (V2) had ALK resistant muts. ALK G1202R was detected in 29% of the pts. 100% (1/1) of the V5’, 50% (8/16) of the V3, 20% (1/5, HIP1-ALK) of the non- EML4-ALK, and none of the V1 (0/13) and V2 (0/3) had G1202R. Amplification and gain of function muts in oncogenes and loss of function muts in tumor suppressor gene were detected in 16% (6/38) of the pts, namely 4 V1, 1 V2, and 1 V3. On average, pts treated with 3rd generation ALKis had significantly more muts in ALK (7.5 vs. 3.6, p = 0.0008) and in all targeted regions (9.1 vs. 4.3, p = 0.0005) than pts treated with only 1st and 2nd generation ALKis. Conclusions: The type of resistance mechanisms developed during ALKi therapy may depend on the ALK fusion type of the pt. ALK resistant muts, especially G1202R, developed most frequently in V3/V5’, followed by non- EML4-ALK, and V1/V2, while amplification and grain of function muts in oncogenes and loss of function muts in tumor suppressor genes developed more often in V1/V2 than in V3/V5’. The 3rd generation ALKi may increase the genomic alterations in treated pts.
Differential copy number alteration profiles among gynecological malignancies.
Authors: Romero Ignacio , López-Reig Raquel , Fernandez-Serra Antonio , Garcia-Casado Zaida , Illueca Carmen , Zorrero Cristina , Poveda Andres , Lopez-Guerrero Jose Antonio
Published: May 2019

e14744

Background: Copy number alterations (CNA) constitutes a genomic hallmark that defines specific outcomes in gynecological neoplasms, as evidenced by the integrated analysis of the high-grade serous ovarian carcinoma (HGSOC) and endometrial carcinomas (EC) performed by the TCGA Consortium. The purpose of this study is to set up an NGS-based technology to obtain CNA profiles on formalin-fixed paraffin-embedded (FFPE) samples with clinical utility. Methods: FFPE blocks from 14 EC and 12 HGSOC were analyzed using a SureSelectXT custom panel plus OneSeq backbone, interrogating 147.000 SNPs (Agilent). CNA groups were defined in EC with a RF algorithm based on genotyping data as previously reported (Romero, ASCO 2018) and in HGSOC Homologous recombination deficiency (HRD) was determined by sequencing a serie of 35 HR genes. saasCNV pipeline was used to perform CNA calling. Results: Ten (38.50 %) of our cases were classified as CN Low (CNL), 8 as CN high (CNH)-RF (30.75 %) and 8 CNH-HRD (30.75 %). CNL profiles from EC and OC are homogenous in terms of genomic stability. CNH-RF and CNH-HRD cases harbor the highest percentage of genomic instability (p = 0.012) with distinct patterns of CNA. CNH-HRD is characterized by a higher ratio of genomic losses (p = 0.023). However, CNH-RF is mainly defined by gains (p = 0.011) (Table). Conclusions: Our NGS-based approach represents a FFPE clinically available procedure to define CNA alterations in gynecological cancer with distinct CNH patterns with prognostic potential.[Table: see text]
A large subtype of squamous cell carcinoma enriched for TrkB-T1 mRNA.
Authors: Zhou Yalu , Schwartz Joel L. , Sinha Saurabh , Shergill Ardaman , Adami Guy
Published: May 2019

e14751

Background: A large subtype of squamous cell carcinoma enriched for TrkB-T1 mRNA. Background The NTRK2 genetic locus encodes neurotrophin membrane receptors that play an important role in normal neural tissue plasticity, growth, and survival. One NTRK2-encoded protein is TrkB-FL, which can regulate multiple pathways relevant to cancer. A second NTRK2 gene mRNA isoform encodes TrkB-T1, a receptor that has a different cytoplasmic domain and is encoded in a mRNA with a unique 3’ terminal exon. Methods: Tumors from The Cancer Genome Atlas (TCGA) and other studies were classified according to the expression of a single form of NTRK2 mRNA that of TrkB-T1. Analysis of differentially expressed genes in TrkB-T1 high expressers was done to determine if tumors enriched for TrkB-T1 were a uniform group independent of anatomic site. Results: The mRNA for TrkB-T1 is the most abundant NTRK2 gene mRNA in all squamous cell carcinomas (SCCs). Comparison of oral SCC (OSCC) high TrkB-T1 RNA expressers to low expressers (n = 284) revealed gene expression differences consistent with the high TrkB-T1 tumors being more neural-like. The upregulated genes in the TrkB-T1 RNA high expressers also showed enrichment of pathways involved in retinol metabolism, hedgehog signaling, and the Nfe2l2 response, among other pathways. An examination of larynx, esophagus, and lung SCCs (n = 100, 100, 540) showed induction of the same pathways among the tumors that expressed high levels of TrkB-T1 mRNA.. Surprisingly, the relationship of high level TrkB-T1 expression to patient outcomes was SCC anatomic site specific. High TrkB-T1 mRNA levels in laryngeal SCC correlated with poor survival, but the opposite was true for lung SCC. This may be because pathways enriched in the TrkB high expressers, like those regulated by Nfe2l2, Pik3ca, and Sox2, are known to have SCC anatomic site-specific effects on progression. Conclusions: High level TrkB-T1 mRNA serves as a marker of a distinct SCC subtype. These tumors share the enrichment of at least 3 pathways relevant to tumor progression, Nfe2l2 response, retinol metabolism, and hedgehog signaling.
Somatic mutations in non-small cell lung cancer and their correlation with overall survival, tumor mutation burden, and programmed-death cell ligand-1 (PD-L1) status.
Authors: Dotson Jennifer , Jamil Muhammad
Published: May 2019

e14752

Background: In recent years, treatments for non-small cell lung cancer (NSCLC) have expanded to include targeted therapies and immune checkpoint inhibitors in addition to traditional treatments. These newer modalities of treatment require testing with next-generation sequencing (NGS) testing, which offers testing for hundreds of somatic mutations, both with known and unknown significance. Tumor mutation burden (TMB), which is the number of mutations per coding sequence, is also reported on NGS. Patients with targetable mutations or a high TMB have been found to have improved survival and higher responses to immunotherapy, respectively. We wanted to investigate whether the total number of mutations (both with known and unknown significance) had any association with PD-L1 status, TMB and overall survival. Methods: This was a single institution, retrospective study of 51 patients with stage I-IV NSCLC. Results: In our study, we found that there was a significant correlation between the number of mutations and TMB in all patients with NSCLC (p = 0.001), including adenocarcinoma (p = 0.005). We found that the number of known mutations, mutations of unknown significance and total overall mutations did not have a significant correlation with survival (p = 0.708, p = 0.808, and p = 0.639, respectively) or PD-L1 status (p = 0.214). In a subset analysis of patients with metastatic NSCLC, there was also no correlation between the total number of mutations and overall survival (p = 0.821). Conclusions: In our study, we determined that there was a positive correlation between TMB and higher number of mutations, though the number of mutations did not correlate with PD-L1 status or overall survival. As TMB is associated with higher immunogenic responses, this data may have future therapeutic implications. Additional investigation of the most frequent mutations is ongoing.
Targeted-sequencing in rare cancers and the impact on patient treatment.
Authors: Okuma Hitomi Sumiyoshi , Kubo Takashi , Ichikawa Hitoshi , Kohno Takashi , Mizuno Takaaki , Kojima Yuki , Sunami Kuniko , Shimomura Akihiko , Iwasa Satoru , Kondo Shunsuke , Fujiwara Yutaka , Yonemori Kan , Tamura Kenji , Yamamoto Noboru
Published: May 2019

e14755

Background: Rare cancers lack standard or investigational therapeutic options. Next-generation sequencing (NGS) has provided new insight into personalized medicine. We sought to catalog genetic alterations detected from tissue NGS in rare cancers and to assess their clinical utility. Methods: This was a single-center series with patients (pts) who had been referred to the National Cancer Center Hospital (Tokyo, Japan). Patients with a metastatic/unresectable disease who underwent comprehensive genomic profiling of their tumor for the purpose of precision treatment were first identified (approved by the NCCH institutional review board). Among them, pts diagnosed as rare cancers, defined as an incidence of < 6/100,000 pts/year, were included in this study. Prospectively consentedpts had tissue NGS testing (NCC Oncopanel) for point mutations, select indels, copy number amplifications, fusions. Alterations were assessed for incidence according to cancer type, functional impact, therapeutic implications. Results: Between July 2013 to April 2016, 289 pts were enrolled. 217 pts with sufficient tissue sample succeeded in sequencing. 78% (169/217) had a least one alteration most likely pathogenic. Most common alterations were TP53, PIK3CA, BRCA2, KRAS, MYC, ERBB2, RB1, CCND1, and ARID1A. 114/289 pts (39%) were classified as rare cancers: gynecological cancers (44 pts), cholangiocarcinoma (20), sarcomas (16), NET (9), thymic carc. (6), mesothelioma (3), CUP (2), urachal carc. (2), GIST (1), thyroid carc. (1), other super-rare cancers (10). 86 pts succeeded in sequencing; 72 % (62/86) had a variant most likely pathogenic. Most common alterations were TP53, KRAS, BRCA2, FBXW7, NF1, PIK3CA, ALK, BRCA1, and CCND1. 23 pts (27%) of rare cancer pts received a targeted drug of which 9 (10%) were “matched” to a detected alteration. Response rate to the “matched” therapy was CR/PR/SD/PD = 0/1/5/3 (ORR 11%). Conclusions: Genomic alterations were equally detected in rare cancers as well as common cancers, however showed different alteration profiles. Rare cancer pts receiving “matched” therapy and the response rate to those remain low, suggesting a need for a more efficient treatment development platform. Clinical trial information: UMIN000011141.
Fruquintinib or regorafenib as the third-line treatments for metastatic colorectal cancer based on CONCUR and FRESCO trials: A cost-effectiveness analysis.
Authors: Li Qiu , Zhang Mengxi
Published: May 2019

e15011

Background: Survival benefit of regorafenib and fruquintinib as third-line agents have been respectively demonstrated in patients with treatment-refractory metastatic colorectal cancer. This study tries to explore the cost-effectiveness of the two agents. Methods: A Markov model was performed based on two phase 3 trials, FRESCO and CONCUR. Health outcomes were measured with quality-adjusted life-years (QALYs). The key outcome was incremental cost-effectiveness ratio (ICER). Probabilistic sensitivity and one-way sensitivity analysis were performed to estimate the impact of essential variables on the results of the analysis. Results: No statistical differences were observed in the baseline patient characteristics, except that the CONCUR trial enrolled older patients and higher ratios of prior use of VEGF or EGFR antibodies in comparison with the FRESCO trial.Treatment with fruquintinib was estimated to cost $25,550.15 with an effectiveness gain of 0.54 QALYs, whereas regorafenib resulted in 0.53 QALY at a mean cost of $29,681.52, yielding ICER of $-413,137.00 per QALY. By using treble the Chinese Gross Domestic Product per Capita as willingness-to-pay threshold, the probability for fruquintinib being cost-effective was higher than regorafenib in the probabilistic sensitivity analysis. Conclusions: Fruquintinib provides a more cost-effective option for metastatic colorectal patients compared with regorafenib in the third line treatment.[Table: see text]
Toxicity syndromes, patient-related clinical indicator of toxicity burden induced by intensive triplet chemotherapy-based regimens in metastatic gastrointestinal cancers.
Authors: Bruera Gemma , Mastropietro Stefania , Dari Salisburgo Luigia , Cosenza Pierluigi , Ricevuto Enrico
Published: May 2019

e15013

Background: Cancer treatments induce symptoms and signs superimposing on clinical and cancer-related status of individual patient, defining heterogenous toxicity syndromes (TS). We reviewed intensive first line triplet chemotherapy-based regimens developed in fit metastatic gastro-intestinal cancers (mGI), based on FIr/FOx schedule including fluorouracil and weekly alternating irinotecan and oxaliplatin. Methods: Metastatic colorectal (mCRC), pancreatic ductal adenocarcinoma (mPDAC), gastric carcinoma (mGC) patients were enrolled by careful decision-making in real life phase II studies: FIr-B/FOx, adding bevacizumab (BEV), in overall, and FIr-C/FOx-C, adding cetuximab (CET), in KRAS/NRAS wild-type mCRC, respectively; FIr/FOx in mPDAC; FD/FOx, adding docetaxel (D), in mGC. Toxicity, and individual limiting toxicity syndromes (LTS), classified as limiting toxicity alone (LTS-single site, LTS-ss) or associated to other limiting or G2 toxicities (LTS-multiple sites, LTS-ms) were evaluated and compared by chi-square test. Results: FIr-B/FOx and FIr-C/FOx-C in mCRC, FIr/FOx in mPDAC, FD/FOx in mGC, respectively reported activity, efficacy and limiting toxicities similar to other triplet chemotherapy-based regimens. Reported LTS: FIr-B/FOx in mCRC 44%, LTS-ms 24% and LTS-ss 20%, in young elderly (yE) 46%, LTS-ms significantly increased vs LTS-ss; FIr-C/FOx-C in KRAS/NRAS wild-type mCRC 65.5%, significantly increased LTS-ms vs LTS-ss, in yE 83%; FIr/FOx in mPDAC 27.5%, mostly LTS-ms, in yE 38.4% all LTS-ms; FD/FOx in mGC 30%, all LTS-ms, in yE 25%. Conclusions: LTS meet the need of an innovative clinical parameter of patient-related toxicity burden, indicating global and individual tolerability, including differential spectrum and intensities of TS related to cancer treatment and according to clinical status of the individual patient. LTS integrated with conventional toxicity evaluation may help properly select patients fit for intensive medical treatments in mGI cancers.
HD204: Analytical biocomparability and clinical trial I progression of bevacizumab.
Authors: hii Jocelyn , Pivot Xavier , Park Lisa Soyeon , Kim Michael , Feyaerts Peggy , Chan Kuo Wei , Lee Jeong-Hyeon , Ang Felicia , Demarchi Martin , Coliat Pierre , Barthelemy Philippe , Ben Abdelghani Meher
Published: May 2019

e15014

Background: Prestige Biopharma Pte Ltd is developing HD204, a biosimilar of the EU-approved and US-licensed Bevacizumab (Avastin) that is approved treatment for a variety of tumour types. Bevacizumab is a recombinant humanized monoclonal antibody (IgG1) that binds to soluble vascular endothelial growth factor (VEGF), thus prevent interaction with VEGF receptors. Due to heterogeneity nature of antibody drug, extensive characterization of antibody from physicochemical and biological properties using multiple bioanalytical assays is required. The development of HD204 from analytical biocomparability to clinical trial I are demonstrated. Methods: Analytical biocomparability in physiocochemical and biological properties of HD204 was compared to Avastin sourced from EU and US using multiple bioanalytical assays as below. Clinical phase I (SAMSON), a randomized, double-blind, single dose and 3-way parallel group was initiated recently to compare pharmacokinetic and to evaluate the safety, tolerability and immunogenicity of HD204, EU-Avastin and US-Avastin. Approximately 120 healthy human subjects (assigned to 3 treatment group) was administered with a single intravenous infusion of 1 mg/kg of either HD204, EU- and US-Avastin. Results: HD204 shows equivalent in physicochemical and biological properties compared to EU- and US-Herceptin. For phase I study, patient recruitment was completed with treatment for come patients initiated but still ongoing. Conclusions: HD204 was shown to be equivalent in all parameters in the analytical biocomparability testing. Clinical Phase 1 trial (SAMSON) is ongoing on and key data from SAMSON trial will be reported in ASCO meeting. [Table: see text]
A phase II study of apatinib combined with S-1 in previously treated refractory metastatic colorectal cancer.
Authors: Li Ning , Deng Wenying , Zhang Guifang , Guo Yanwei , Ma Yijie , Wu Qiong , Yang Xinyi , Luo Suxia
Published: May 2019

e15016

Background: Although regorafenib and fruquintinib have been recommended as the third-line treatment for patients with refractory metastatic colorectal cancer (mCRC), the median survival time of mCRC is still only for 4-8 months and the low response rate and unpleasant side effects limit their use in Chinese patients. Apatinib, an oral VEGFR-2 inhibitor, has been approved as a third line treatment in metastatic gastric cancer. In addition, apatinib has demonstrated good safety, tolerability, and efficacy in the treatment of advanced solid tumors. The aim of this study was to assess the efficacy and safety of apatinib combined with S-1 in the treatment of refractory mCRC. Methods: In this prospective, open-label, single-arm, multicenter, phase II study, patients after failure of second-line chemotherapy were enrolled and took apatinib (250mg, daily) combined with S-1 (standard dose). The primary endpoint was progression free survival (PFS) and the second endpoint was response rate and overall survival time. Results: From December 2017, 22 patients (14 male) with a median age of 56y (range: 34-71 y) were enrolled and eligible for evaluation of the PFS, response rate and safety. The median PFS was 105d (95% CI: 79.01-130.98). two patients (9%) achieved partial response, 15 (68.18%) achieved stable disease, and 5 (22.72%) were progressive disease. The objective response rate and the disease control rate were 9% and 77.27%, respectively. Median overall survival was not reached. The common adverse effects were abnormal liver function (7/22; 31.81%), leukopenia (5/22; 22.72%) and thrombocytopenia (4/22; 18.18%). The incidence for grade 3-4 side effect was very low. One patient experienced grade 3 proteinuria and there were no toxic deaths. Conclusions: This preliminary result indicated that apatinib combined with S-1 may extend the PFS in mCRC, with well-tolerated toxicities, making it a promising therapeutic target for mCRC treatment. Clinical trial information: NCT03397199 .