bluuebunny/crossref_metadata_2025_split huggingface dataset:
Salivary miRNA-210 involvement in medication-related osteonecrosis of the jaws.
Authors: Picone Antonio , Marcianó Antonia , Dimarco Rosanna , Miano Eleonora , Zacchia Alessandra , Sanò Maria Vita , La Fauci Alessia , Chiarenza Maurizio , Ali Marco , Di Leo Maria Grazia , Aiello Rosa Anna , Taibi Eleonora , Fallica Giuseppa , Caruso Michele 
Published: September 2018

e23052 Background: Improved survival rates from cancer have increased the need to understand the health related problems of cancer treatment. Persistent oral health related problems significantly affect patient's quality of life. Medication-related osteonecrosis of the jaws (MR-ONJ) is an oral complication of antiresorptive medications, denosumab and other medications that target angiogenesis for the management of metastatic bone cancer. The purpose of this pilot study, is to investigate, for the first time, microRNAs expression in MR-ONJ. Recent studies reported the miRNA-210 (a specific angiogenic-related miRNA) demethylation in the Osteonecrosis of the Femoral Head. We hypothesized that MiRNA-210 could also be involved in MR-ONJ development. Primary objective of the study is to investigate the role of miRNA-210 in MR-ONJ pathogenesis. Secondary objective is to investigate the feasibility of salivary miRNAs detection as potential non invasive biomarkers for MR-ONJ. Methods: A case-and-control study has been designed. Inclusion criteria are malignant tumors with ongoing treatment or previous history of anti-resorptive or anti-angiogenic medications. The predictor variable is the presence or absence of MR-ONJ. Oral examination and dental x-ray examinations suggestive of MR-ONJ will be performed. Saliva sample will be collected according to the protocol by Navazesh. The methylation status of miRNA-210 will be investigated using quantitative PCR (Q-PCR). Values will be compared between case and control group. Results: The main expected results are to enroll approximatively twenty patients in case group and sixty patients in control group within a one year recruitment period, validate that saliva is a medium for the identification of biomarkers associated with MR-ONJ and confirm the hypothesis that miRNA-210 is involved in MR-ONJ development. Conclusions: Results acquired within this project would represent a contribute to the understanding of the molecular mechanisms driving to the development of MR-ONJ lesions. MiRNA-210 demethylation could serve as a potential therapeutic target for the treatment of MR-ONJ through stimulation of angiogenesis.
Comparison of BEAMing assays and competitive approaches in the detection of main alteration of RAS in circulating DNA of non small-cell lung cancer (NSCLC) and metastatic colon cancer. Manuscript 2016.
Authors: Garcia Jessica , Forestier Julien , Dusserre Eric , Rodriguez-Lafrasse Claire , Cheynet Valérie , Wozny Anne-Sophie , Ferraro Peyret Carole , Brengel-Pesce Karen , Guillet Marielle , Chauvenet Marion , Brevet Marie , Couraud Sebastien , Walter Thomas , Payen Lea Francoise 
Published: September 2018

e23056 Background: A number of RAS mutations confer resistance to anti-EGFR therapies routinely used in the treatment of colon cancer. The objective of this study was to evaluate the pertinence of analyzing circulating-free plasma DNA (cfDNA) as an indicator of the mutational status of a tumor, in order to use liquid biopsies instead of invasive and painful tumor biopsies during tumor progression. Methods: A cohort of 24 lung and 25 colon cancer patients was constituted in the Hospices Civils of Lyon. Liquid biopsy plasma samples were collected at diagnosis (colon cancer) and during tumor progression (lung cancer) for the purpose of the current study. KRAS and NRAS somatic alterations were quantified using three different technologies: the Droplet Digital polymerase chain reaction (ddPCR) from BioRad, the BEAMing Digital PCR from Sysmex Inostics, and the NGS NextSeq 500 by Illumina with the Accel-Amplicon 56G Oncology Panel from SWIFT BIOSCIENCES. Results: We observed a high level of sensitivity and specificity with the BEAMing technology, which provided us with excellent matches, around 96% and 73%, between solid and liquid biopsies taken at diagnosis (colon cancer) or during tumor progression (lung cancer), respectively. Indeed, when examining cfDNA from patients displaying one of the KRAS or NRAS mutations, 11 of the 13 mutations were confirmed using this technology, whereas only 5-6 matched the initial NGS status, using the two other technologies. The detection threshold was estimated at 1% for samples containing at least 0.8 ngctDNA/µL for the multiplex screening ddPCR from BioRad and for the 56G Oncology Panel from SWIFT BIOSCIENCES. The threshold was lower, at 0.03%, in samples containing only 0.25 ng ctDNA/µL for the BEAMing technology, which includes a PCR pre-amplification step. Conclusions: The advantage of the Illumina NGS technology is the larger coverage of longer gene regions, and thus the detection of more genetic mutations. Finally, the BEAMing technology enabled us to follow the appearance and disappearance of somatic alterations, with a very high level of sensitivity.
Metabolomics signature in serum months to years before thoracic cancer: The HUNT study.
Authors: RÃ¸e Oluf D. , Lagani Vincenzo , Kvitvang Hans Fredrik , Markaki Maria , Tsamardinos Ioannis , Mjelle Robin 
Published: September 2018

e23059 Background: The Cancer-Biomarkers in HUNTinitiative seeks to identify novel biomarkers for the early cancer diagnosis. For lung cancers and mesothelioma clinically useful early markers are not available. In the prospective HUNT study in Norway, pre-diagnostic samples ranging 0-20 years before diagnosis are available for research purposes. Here we present our first results on high-throughput metabolomics analysis in serum two months to 16 years before diagnosis. Methods: LC-MS untargeted (Amide-) metabolites (n = 1042) were profiled in serum samples from 48 future patients (12 each of adeno-, squamous cell carcinoma, small-cell lung cancer and mesothelioma) and from 48 controls that were cancer-free 5 years after blood sampling. All were active smokers. Metabolic features for (a) each cancer and (b) all cancers pooled together were analyzed with moderated t-test (R limma package). Multivariate analyses included (a) OPLS-DA and (b) signature identification through a data-analysis pipeline that includes feature selection (such as the algorithm in [1]), non-linear modelers (e.g., Random Forests) and Cross-Validation with bootstrapping [2] for optimizing algorithms and providing unbiased performance estimation. The pipeline is implemented in the Just Add Data software (Gnosis Data Analysis). Results: Univariate and OPLS-DA analyses did not identify any association between metabolites and cancer. The non-linear data analysis pipeline identified a signature containing five metabolites able to discriminate between cancer and non-cancer patients, statistically significantly better than random (AUC = 0.667, CI = [0.536, 0.784]). Conclusions: Our results indicate that metabolic profiling in serum may help in identifying subjects who are likely to be diagnosed with lung cancer/mesothelioma in a time period of several years before diagnosis. More data will be presented at the annual meeting. Further validation studies are planned for confirming the replicability of these findings. 1) Lagani V et al., 2016. arXiv:1611.03227 2) Greasidou L, 2017. Bias Correction of the Cross-Validation Performance Estimate and Speed Up of its Execution Time, MSc Thesis, University of Crete
Detecting ultra low-frequency variants and gene fusions in lung cancer patients using an amplicon-based Firefly NGS method.
Authors: Weng Li , Wang Lin , Chen Xiao , Zhang Jacey , Lin Chiahui , Wang Yingyu , Brice Tim , Huang Yi , Wang Hongyan , Tang Paul , Sun Zhaohui Johnny , Zhao Grace Q. , Lou Jiatao , Ying Kang , Faham Malek , Lin Shengrong 
Published: September 2018

e23062 Background: The analysis of EGFR, KRAS, and BRAF mutations and Alk fusion is critical for guiding targeted therapy selection, detecting drug resistance, and monitoring residual disease in patients with NSCLC. Designing next-generation sequencing (NGS) assays for detecting low-frequency variants, however, is an ongoing challenge. The limited availability of cfDNA combined with the breadth of coverage necessary to create meaningful, clinically-actionable results requires a solution with multiplex capacity which, in turn, requires greater technological sensitivity and specificity. Here we aim to develop such a solution: an ultra-accurate NGS technology using concatmer-based error correction with amplicon workflow for fast detection of rare mutations including SNV and fusion. Methods: We developed an amplicon-based panel covering variants of EGFR, BRAF, and KRAS, as well as a panel to detect Alk fusion. CfDNA simulate and cfDNA from healthy individuals were used to test assay sensitivity and specificity. Further validation was performed via a comparative analysis of 64 late-stage lung cancer patients using both Firefly -Comet and ddPCR. Results: Analytical sensitivity of the EGFR-TKI 3-gene panel was 100% detection at an allele frequency of 0.1% for 20ng of cfDNA input. Similarly, analytical sensitivity of the Alk fusion panel was 75% detection at an allele frequency of 0.1% and 100% at an allele frequency of 0.25% for the same input. Among our patient cohort, 5 EGFR variants (19del, T790M, L858R, G719X, L861X) and 2 KRAS variant (G12X) were detected. Firefly-Comet demonstrated strong per-variant detection-rate concordance ( > 99%) compared to ddPCR results. The PPV is 100% and the NPV is 98.7%. Statistical analysis of reported allele frequency concordance between Firefly-Comet and ddPCR reveals R-Sq > 0.9. Conclusions: In summary, we have developed Firefly-Comet, an easy-to-use amplicon-based NGS assay capable of detecting single-digit copies of somatic mutants and gene fusions in cfDNA. The multiplex capacity of Firefly-Comet makes it well-suited for supporting targeted therapy selection, drug resistance detection, and treatment monitoring.
Identification of epitopes of cancer testis antigen cyclin A1 for targeted T-cell therapy of acute myeloid leukemia (AML) and solid tumors.
Authors: Teck Anja-Tatjana , Urban Sabrina , Quass Petra , Nelde Annika , Walz Juliane , Keilholz Ulrich , Ochsenreither Sebastian 
Published: September 2018

e23080 Background: Cyclin A1 is a promising antigen for T-cell therapy being selectively expressed in ovarian cancer and AML stem cells. For adoptive T-cell therapy, a single epitope has to be selected, which should bind with high affinity to MHC class I and should be adequately processed and presented by malignant cells to trigger full activation of specific T-cells. Methods: Three algorithms were used to predict in silicopeptides of Cyclin A1 with high affinity to HLA A*02:01. Affinities were tested by HLA stabilization assay using TAP-deficient T2 cells. Immunogenicity of peptides was assessed by stimulation of T-cells with peptide pulsed dendritic cells and monocytes. Specificity of T-cells was assessed by intracellular cytokine staining. Specific cell lines were cloned and used in killing assays to demonstrate recognition of endogenous Cyclin A1 in the HLA A*02:01-positive AML line THP-1. Data from immunopeptide analysis based on direct isolation of HLA peptides by affinity chromatography and mass spectometry of 20 primary AML samples were analyzed retrospectively to identify naturally presented epitopes of Cyclin A1. Results: Thirteen peptides nine to eleven amino acids of length were predicted. Ten showed stabilization of HLA A*02:01 on T2 cells. By repetitive stimulation of T-cells of two healthy donors with single peptides, 40 T-cell lines were generated, of which eight were specific for the respective peptides. Five peptides were immunogenic. Against two peptides (Cyclin A1 isoform c, p156-164, p410-420) T-cell lines could be generated from both donors. For T-cell clones against two peptides (p111-120, p289-297), specific lysis of THP-1 was shown indicating adequate processing. Peptide p410-420 was found by mass spectroscopy-based ligandome analysis to be presented by AML blasts in vivo. Conclusions: We identified ten peptides with adequate binding to HLA A*02:01. We describe three new HLA A*02:01–restricted epitopes as targets for T-cell therapy. Epitope p410-420 showed high affinity to HLA A*02:01 and immunogenicity in both donors. It proved to be naturally presented on AML blast, and therefore warrants further development for clinical application.
Human papillomavirus (HPV) induced malignancies and markers of immunogenicity.
Authors: Hashemi Sadraei Nooshin , Koncar Robert , Poorman Kelsey , Bahassi El Mustapha 
Published: September 2018

e23083 Background: Approximately 5% of all cancers result from HPV, commonly leading to head and neck (HN) and anogenital (AG) cancers. Immune therapy is used in many cancers including HN. Positive PDL1 and high tumor mutation load (TML) have been proposed as potential markers of immunogenicity among many tumors, but little is known specifically among HPV driven cancers. Methods: A retrospective analysis of patients with HPV related cancers was performed based on tissue availability. TP53 wild type status was used as a surrogate for HPV positivity. Among oropharynx cases with TP53 wt, p16 testing was performed for confirmation. Next generation Sequencing (NGS Sanger) was used for tumor mutation load (TML) calculation. High TML cut off was defined as ≥17 mutations/megabase based on prior publications. PDL1 status was reported based on IHC ≥5%. A 2-tail Fisher’s exact test was utilized for statistical analysis. Results: A total of 737 patients with HN and AG (cervical, anal, vulvar, penile) squamous cell carcinoma were identified. Of these, 251 had complete 592 gene panel NGS data. HPV + TP53 Wt disease was detected in oropharynx (70%), cervical (88%), and anal (82%) cancer. HPV+ HNSCC had a trend to a higher PDL1 compared to HPV neg (50% vs 31%, p = 0.16) but there were no significant differences among PDL1 between HPV+ and neg patients across the entire combined disease cohorts (41% vs 36%, p = 0.56). TML-high patients showed a trend to increased PDL1 positivity (60% vs 38%, p = 0.09). However, high TML was less common in HPV+ HNSCC vs HPV neg (2.2 vs. % 9.7% p = 0.19). Unlike some other malignancies, high TML was uncommon across HPV+ tumors in general (8%). Conclusions: Despite fewer TML high cases among HPV + patients, there was no difference among PDL1 expression. It is possible that a lower threshold may need to be used when determining TML high vs. low in viral-driven cancers. It is also possible that in view of viral immunogenicity, certain genomic alterations contribute more to higher PDL1 expression rather than the sum of total genomic alterations. We are currently pursuing both lines of investigation. These findings are hypothesis generating for future trial design rather than treatment decision-making, and need to be confirmed in large prospective cohorts.
Comparative characteristics of the genes expression of cancer-testis antigens in tumor and non-tumor breast tissues.
Authors: Mogushkova Khava A. , Vodolazhsky Dmitriy I. , Kutilin Denis S. , Kit Oleg I. 
Published: September 2018

e23085 Background: Breast cancer (BC) is the most common cancer among women. The development of immunotherapy which targets cancer-testis antigens (CTA) is needed for the decreasing in breast cancer mortality. Therefore, the aim of this work was the study of specific CTA of breast cancer tissue among CTA-family, role of which has been previously mentioned. Methods: The paired surgical biopsies of tumor and non-tumor breast tissue of 25 patients (50 samples) residing in the South of Russia and treated in Rostov Research Institute of Oncology were included in the present study. Total RNA was extracted from tissue samples by P. Chomczynski and N. Sacchi (2006) method. cDNA library was synthesized using reagent kit "Reverta-L» (Russia, "InterLabService"). Primers were designed using the NCBI GenBank database. The relative expression of 17 genetic loci ( MAGE-A1, MAGE-A2, MAGE-A3, MAGE-A4, MAGE-B1, MAGE-B2, GAGE1, GAGE3, GAGE4, MAGE-C1, BAGE, CTAG-1B, XAGE3, NY -ESO1, SSX2, SYCP1, PRAME1) was determined by Real-Time qPCR (reference gene - GAPDH) using CFX96 thermal cycler (Bio-Rad, USA). Statistical analysis was performed using nonparametric Mann-Whitney U-test. Results: The expression of CTA genes MAGE-A4, MAGE-B1, MAGE-B2 and GAGE3 was found to be significantly (p < 0.05) increased by 1.4; 9.5; 4.0 and 9.8 fold, respectively, in tumor tissue compared with non-tumor breast tissue. The expression of other CTA genes were not differed between tumor and non-tumor samples. Conclusions: Detected increasing of the expression levels of MAGE-A4, MAGE-B1, MAGE-B2 and GAGE3 genes evidences that these CTA may serve as the effective immunotherapeutic targets in breast cancer.
Diagnostic accuracy of molecular tumor profiling in determining the tissue of origin in adult patients with cancer of unknown primary: A meta-analysis.
Authors: Inocencio Rowena Torres , Kesari Kavitha , Smith Susan 
Published: September 2018

e23092 Background: Appropriate cancer treatment requires determination of the primary site of origin. The standard of care for diagnosing Cancer of unknown primary (CUP) based on the 2016 NCCN Guidelines is a comprehensive clinical work-up including biopsy and immunohistochemistry (IHC). However, IHC was able to identify a primary tumor in only 25% of CUP. Molecular tumor profiling (MTP) validation studies demonstrated sensitivities of 74-89% and specificities of 95-99%. Only a few studies with small sample sizes using MTP to diagnose the primary in CUP have been performed yielding variable results. This study aims to evaluate the diagnostic accuracy of MTP in determining the tissue of origin in adult patients with CUP. Methods: Literature search included articles published in any language indexed in MEDLINE and Cochrane. A Google Scholar search and a review of all published articles’ references were performed. Unpublished studies and abstracts from conference proceedings were also reviewed. Studies involving adult patients with CUP who underwent both MTP and clinical evaluation with IHC were identified. Articles were included if they had primary data sufficient to calculate both sensitivity and specificity. Methodological qualities of the included studies were evaluated using the QUADAS-2 tool. Data was analyzed using Review Manager 5.3 and MetaDiSc 1.4. Results: Seven studies with 549 patients were analyzed. MTP was found to have a pooled sensitivity of 89% (95% CI 0.85-0.92)and pooled specificity of 74% (95% CI 0.67-0.80)with pooled positive and negative likelihood ratios of 2.97 (95% CI 1.17-7.63) and 0.20 (95% CI 0.07-0.51), respectively. Area under the curve was measured to be 0.9107. Conclusions: This meta-analysis suggests that MTP could be useful in determining the tissue of origin in adult patients with CUP. With an area under the curve of 0.9107, it is an excellent diagnostic test. The results showed considerable heterogeneity as expected in meta-analyses of diagnostic test accuracy. In this case, it may be due to variability among the MTP assays used which may reflect different cutoffs.
Copy number variation of MDM2 and p53 genes in extracellular DNA as potential marker for lung adenocarcinoma diagnostics.
Authors: Kutilin Denis S. , Enin Yaroslav S. , Vodolazhsky Dmitriy I. , Sustretov Vyacheslav A. , Ayrapetova Tamara G. , Anistratov Pavel A. , Pyltsin Sergey P. , Leyman Igor A. , Chubaryan Anna V. , Bogdanova Olesia A. , Kharin Leonid , Turkin Igor N. , Dyritsky Maxim N. , Kit Oleg I. 
Published: September 2018

e23094 Background: Today, the problem of early diagnostics of lung cancer remains unsolved as every fourth patient diagnosed with the disease already has distant metastases. Studying gene copy number variation (CNV) in extracellular DNA in the blood plasma can become a basis for a new effective and low invasive method for predictive diagnostics and disease prognosis. The purpose of the study was to examine the copy number of the MDM2 and p53 genes in extracellular DNA of patients with metastatic and non-metastatic lung cancer and healthy donors. Methods: The blood samples of 30 patients with lung adenocarcinoma (collected before surgery) and 30 healthy donors (without cancer) were studied. Each sample was centrifuged to obtain blood plasma. DNA was isolated from plasma using a phenol-chloroform extraction method. Detection of relative copy number of the MDM2 and p53 genes (reference gene - GAPDH) was performed by RT-qPCR using CFX96 thermocycler (Bio-Rad, USA). The groups were compared by the Mann-Whitney U- test. Results: Reduction of the p53 gene copy number by 57% (p < 0.05), as well as increasing of the MDM2 gene copy number by 160% (p < 0.05), were found in the extracellular DNA of patients with lung adenocarcinoma compared with healthy donors. As a result, the ratio of copy number of pro-/anti-apoptotic genes p53:MDM2 in extracellular DNA of patients with lung adenocarcinoma (1:23 ratio) was different from that of healthy donors (1:4 ratio). The MDM2 gene copy number in extracellular DNA of patients with metastases exceeded the value in non-metastatic patients two-fold (p < 0.05). The p53 gene copy number in extracellular DNA of patients with metastatic and non-metastatic cancer did not differ significantly. Conclusions: CNV of the p53 and MDM2 genes in extracellular DNA has a high potential for low invasive diagnostics and prognosis of lung adenocarcinoma.
Integrated DNA, RNA and protein analyses for a better treatment of cancer patients.
Authors: Laes Jean-Francois , Cesbron Francois , Ghitti Gregori 
Published: September 2018

e23099 Background: Advances in the molecular profiling of tumours, together with the expanding portfolio of targeted cancer therapies have established the terrain on which personalised cancer treatment can be conducted. This expanding area of precision medicine has the potential to be offered as a routine cancer-diagnostic service. Methods: We evaluated two molecular-profiling approaches : next-generation sequencing (NGS) and a group of several assays, termed Package Plus (PP), which have been primarily designed at identifying specific clinically-relevant alterations including protein expression/activation (by immunohistochemistry), and gene-promoter methylation, gene translocations and microsatellite instability (by PCR). The molecular profiling was conducted as diagnostic service for practising oncologists, who provided formalin-fixed paraffin-embedded tumour samples (for NGS and PP) and blood samples for circulating tumour DNA (for NGS only). A subset of oncologists who received the molecular profiling results and treatment advice was then surveyed to assess whether and how the results affected their treatment plans. Results: 980 samples from 16 different cancer types were received, out of which 914 (93%) were of sufficient quality to be included in this study. Clinically-relevant (actionable) alterations that provided treatment advice were identified for the large majority (841/914; 92%) of patients using the combination of NGS and PP data, but only for a minority of (247/912; 27%) of patients using NGS data alone. Treatment advice was adhered to by the oncologist in the majority (60%) of surveyed cases, and in the cases where the advice was not followed, reasons most often cited were treatment unavailability or cost. Conclusions: Our study demonstrates the utility of a precision-medicine service based on supervised tests (protein and RNA) in combination with NGS (DNA) profiling methods for advising oncologists on appropriate cancer-treatment plans.