scholarly journals Selecting short length nucleic acids localized in exosomes improves plasma EGFR mutation detection in NSCLC patients

2019 ◽  
Vol 19 (1) ◽  
Author(s):  
Yoonjung Kim ◽  
Saeam Shin ◽  
Boyeon Kim ◽  
Kyung-A Lee
Keyword(s):  
Nucleic Acids ◽  
Mutant Allele ◽  
Mutation Testing ◽  
Short Length ◽  
Lung Cancer Patients ◽  
Dna And Rna ◽  
Detection Assay ◽  
Positive Rate ◽  
The Difference ◽  
Nsclc Patients

Abstract Background Exosomal nucleic acid (exoNA) is a feasible target to improve the sensitivity of EGFR mutation testing in non-small cell lung cancer patients with limited cell-free DNA (cfDNA) mutant copies. However, the type and size of target exoNA related to the sensitivity of EGFR mutation testing has not been explored extensively. Methods The type and size of target exoNA related to the sensitivity of EGFR mutation testing was evaluated using ddPCR. A total of 47 plasma samples was tested using short-length exoTNA (exosomal DNA and RNA) and cfDNA. Results The sensitivity of short-length exoTNA (76.5%) was higher than that of cfDNA (64.7%) for detecting EGFR mutations in NSCLC patients. In EGFR-mutant NSCLC patients with intrathoracic disease (M0/M1a) or cases with low-copy T790M, the positive rate was 63.6% (N = 7/11) and 45.5% (N = 5/11) for short-length exoTNA and cfDNA, respectively. On average, the number absolute mutant copies of short-length exoTNA were 1.5 times higher than that of cfDNA. The mutant allele copies (Ex19del and T790M) in short-length exoTNA were relatively well preserved at 4 weeks after storage. The difference (%) in absolute mutant allele copies (Ex19del) between 0 days and 4 weeks after storage was − 61.0% for cfDNA. Conclusion Target nucleic acids and their size distribution may be critical considerations for selecting an extraction method and a detection assay. A short-length exoTNA (200 bp) contained more detectable tumor-derived nucleic acids than exoDNA (~ 200 bp length or a full-length) or cfDNA. Therefore, a short-length exoTNA as a sensitive biomarker might be useful to detect EGFR mutants for NSCLC patients with low copy number of the mutation target.

Outcomes of non-small cell lung cancer patients with adenocarcinoma histology compared with other histologies: SEER registry data 2004-2008.

2012 ◽  
Vol 30 (15_suppl) ◽  
pp. e17560-e17560 ◽  
Author(s):  
Monika Joshi ◽  
John M. Varlotto ◽  
Suhail M. Ali ◽  
Jennifer Toth ◽  
Michael Reed ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Stage Iv ◽  
P Value ◽  
Seer Database ◽  
Cancer Specific Survival ◽  
Lung Cancers ◽  
Lung Cancer Patients ◽  
Stage Disease ◽  
The Difference ◽  
Nsclc Patients

e17560 Background: For convenience, the majority of lung cancers are commonly lumped together as non-small lung cancer (NSCLC). Patients with adenocarcinoma of the lung have a higher incidence of driver mutation as compared to those with squamous histology. In addition pemetrexed containing regimens have preferential activity in this histology and agents such as bevacizumab are administered to this subgroup only based on toxicity. The currentanalysis was performed to compare outcomes for patients in the SEER database between 2004 and 2008 with adenocarcinoma (Adenoca), squamous cell carcinoma (SCCA) and NSCLC not otherwise specified (NOS). Methods: Data for 161,175 patients was available in SEER database between 2004 and 2008 with 38 different histology ICD codes. 134,947 patients (83.7%) were included in the study. NSCLC NOS (ICD-3 8046) n=36,408, SCCA (ICD-3 8070) n= 36, 454 and Adenoca (ICD-3 8140) n=62,085. Overall survival (OS) and lung cancer specific survival (LCSS) were analyzed using cox proportional Hazard model for the 3 groups. Results: Patients in the three groups were age-matched. Male gender was more common in patients who had SCCA compared to Adenoca (62.6% vs. 49.5%). Percentage of poorly differentiated tumors was higher in patients with SCCA (35.9%) compared to NSCLC NOS (32%) and Adenoca (27.5%). SCCA had fewer stage IV patients at diagnosis (29.5%) vs. 51.4 % for NSCLC NOS and 45% for Adenoca. OS and LCSS are listed in the table below with Hazard ratio (HR) and p value. Total of 23.54% (n=31,768) patients underwent surgical resection. Stage I patients who underwent surgery (n=18,517) also had similar results. Conclusions: NSCLC patients who have adenocarcinoma histology have significantly better overall outcome when compared to other histologies. The difference is more pronounced in an earlier stage disease. [Table: see text]

scholarly journals Graphene Oxide: A Smart (Starting) Material for Natural Methylxanthines Adsorption and Detection

Molecules ◽  
2019 ◽  
Vol 24 (23) ◽  
pp. 4247 ◽  
Author(s):  
Rita Petrucci ◽  
Isabella Chiarotto ◽  
Leonardo Mattiello ◽  
Daniele Passeri ◽  
Marco Rossi ◽  
...  
Keyword(s):  
Electrical Conductivity ◽  
Graphene Oxide ◽  
Nucleic Acids ◽  
Reduced Graphene Oxide ◽  
Electrochemical Sensors ◽  
Enzymatic Digestion ◽  
Biologically Active ◽  
Polar Solvents ◽  
Dna And Rna ◽  
Reduced Graphene

Natural methylxanthines, caffeine, theophylline and theobromine, are widespread biologically active alkaloids in human nutrition, found mainly in beverages (coffee, tea, cocoa, energy drinks, etc.). Their detection is thus of extreme importance, and many studies are devoted to this topic. During the last decade, graphene oxide (GO) and reduced graphene oxide (RGO) gained popularity as constituents of sensors (chemical, electrochemical and biosensors) for methylxanthines. The main advantages of GO and RGO with respect to graphene are the easiness and cheapness of synthesis, the notable higher solubility in polar solvents (water, among others), and the higher reactivity towards these targets (mainly due to – interactions); one of the main disadvantages is the lower electrical conductivity, especially when using them in electrochemical sensors. Nonetheless, their use in sensors is becoming more and more common, with the obtainment of very good results in terms of selectivity and sensitivity (up to 5.4 × 10−10 mol L−1 and 1.8 × 10−9 mol L−1 for caffeine and theophylline, respectively). Moreover, the ability of GO to protect DNA and RNA from enzymatic digestion renders it one of the best candidates for biosensors based on these nucleic acids. This is an up-to-date review of the use of GO and RGO in sensors.

scholarly journals Triazole-Modified Nucleic Acids for the Application in Bioorganic and Medicinal Chemistry

Biomedicines ◽  
2021 ◽  
Vol 9 (6) ◽  
pp. 628
Author(s):  
Dagmara Baraniak ◽  
Jerzy Boryski
Keyword(s):  
Nucleic Acids ◽  
State Of The Art ◽  
Modified Oligonucleotides ◽  
Synthetic Genes ◽  
Chemically Modified ◽  
Amide Linkage ◽  
Dna And Rna ◽  
Modified Dna ◽  
Modified Nucleic Acids ◽  
Non Coding Rnas

This review covers studies which exploit triazole-modified nucleic acids in the range of chemistry and biology to medicine. The 1,2,3-triazole unit, which is obtained via click chemistry approach, shows valuable and unique properties. For example, it does not occur in nature, constitutes an additional pharmacophore with attractive properties being resistant to hydrolysis and other reactions at physiological pH, exhibits biological activity (i.e., antibacterial, antitumor, and antiviral), and can be considered as a rigid mimetic of amide linkage. Herein, it is presented a whole area of useful artificial compounds, from the clickable monomers and dimers to modified oligonucleotides, in the field of nucleic acids sciences. Such modifications of internucleotide linkages are designed to increase the hybridization binding affinity toward native DNA or RNA, to enhance resistance to nucleases, and to improve ability to penetrate cell membranes. The insertion of an artificial backbone is used for understanding effects of chemically modified oligonucleotides, and their potential usefulness in therapeutic applications. We describe the state-of-the-art knowledge on their implications for synthetic genes and other large modified DNA and RNA constructs including non-coding RNAs.

scholarly journals Characterization of nucleic acids from extracellular vesicle-enriched human sweat

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Geneviève Bart ◽  
Daniel Fischer ◽  
Anatoliy Samoylenko ◽  
Artem Zhyvolozhnyi ◽  
Pavlo Stehantsev ◽  
...  
Keyword(s):  
Nucleic Acids ◽  
Human Genome ◽  
Body Fluids ◽  
Lower Percentage ◽  
Rna Seq ◽  
Protein Coding ◽  
Human Sweat ◽  
Dna And Rna ◽  
Ribonucleoprotein Complexes ◽  
Eccrine Glands

Abstract Background The human sweat is a mixture of secretions from three types of glands: eccrine, apocrine, and sebaceous. Eccrine glands open directly on the skin surface and produce high amounts of water-based fluid in response to heat, emotion, and physical activity, whereas the other glands produce oily fluids and waxy sebum. While most body fluids have been shown to contain nucleic acids, both as ribonucleoprotein complexes and associated with extracellular vesicles (EVs), these have not been investigated in sweat. In this study we aimed to explore and characterize the nucleic acids associated with sweat particles. Results We used next generation sequencing (NGS) to characterize DNA and RNA in pooled and individual samples of EV-enriched sweat collected from volunteers performing rigorous exercise. In all sequenced samples, we identified DNA originating from all human chromosomes, but only the mitochondrial chromosome was highly represented with 100% coverage. Most of the DNA mapped to unannotated regions of the human genome with some regions highly represented in all samples. Approximately 5 % of the reads were found to map to other genomes: including bacteria (83%), archaea (3%), and virus (13%), identified bacteria species were consistent with those commonly colonizing the human upper body and arm skin. Small RNA-seq from EV-enriched pooled sweat RNA resulted in 74% of the trimmed reads mapped to the human genome, with 29% corresponding to unannotated regions. Over 70% of the RNA reads mapping to an annotated region were tRNA, while misc. RNA (18,5%), protein coding RNA (5%) and miRNA (1,85%) were much less represented. RNA-seq from individually processed EV-enriched sweat collection generally resulted in fewer percentage of reads mapping to the human genome (7–45%), with 50–60% of those reads mapping to unannotated region of the genome and 30–55% being tRNAs, and lower percentage of reads being rRNA, LincRNA, misc. RNA, and protein coding RNA. Conclusions Our data demonstrates that sweat, as all other body fluids, contains a wealth of nucleic acids, including DNA and RNA of human and microbial origin, opening a possibility to investigate sweat as a source for biomarkers for specific health parameters.

scholarly journals Evaluation of Different Treatment Strategies Between Right-sided and Left-sided Pneumonectomy for Stage I-IIIA Non-small Cell Lung Cancer Patients

2020 ◽  
Author(s):  
Bo Jia ◽  
Qiwen Zheng ◽  
Jianjie Li ◽  
Jun Zhao ◽  
Meina Wu ◽  
...  
Keyword(s):  
Adjuvant Therapy ◽  
Treatment Strategies ◽  
The United States ◽  
Stage I ◽  
Cancer Specific Survival ◽  
Lung Cancer Patients ◽  
Propensity Score Matching Analysis ◽  
Appropriate Treatment ◽  
Iiia Nsclc ◽  
Nsclc Patients

Abstract BackgroundThis study aimed to assess the different survival outcome of stage I-IIIA NSCLC patients who received right-sided and left-sided pneumonectomy, and to further develop the most appropriate treatment strategies. MethodsWe accessed data from the Surveillance, Epidemiology, and End Results database in the United States for the present study. An innovative propensity score matching analysis was used to minimize the variance between groups.ResultsFor 2,683 patients who received pneumonectomy, cancer-specific survival (HR=0.863, 95%CI: 0.771 to 0.965, P=0.010) and overall survival (OS) (HR=0.875, 95%CI: 0.793 to 0.967, P=0.008) were significantly superior of left-sided pneumonectomy compared with right-sided pneumonectomy. Cancer-specific survival (HR=0.847, 95%CI: 0.745 to 0.963, P=0.011) and OS (HR=0.858, 95%CI: 0.768 to 0.959, P=0.007) were also significantly longer with left-sided over opposite-sided pneumonectomy after matching analysis for 2,050 patients. Adjuvant therapy could significantly prolong cancer-specific survival (67 versus 51 months, HR=1.314, 95%CI: 1.093 to 1.579, P=0.004) and OS (46 versus 30 months, HR=1.458, 95%CI: 1.239 to 1.715, P<0.001) among left-sided pneumonectomy patients after matching procedure. While adjuvant therapy did not increase cancer-specific survival for right-sided pneumonectomy patients (46 versus 42 months, HR=1.112, 95%CI: 0.933 to 1.325, P=0.236). Subgroup analysis showed that adjuvant chemotherapy could significantly improve cancer-specific survival and OS for all pneumonectomy patients. But radiotherapy was associated with worse survival for patients with right-sided pneumonectomy. ConclusionsPneumonectomy side could be deemed as an important factor when physicians choosing the most optimal treatment strategies.

scholarly journals Acquiring Sentiment from Twitter using Supervised Learning and Lexicon-based Techniques

2016 ◽  
Vol 15 (1) ◽  
pp. 63-80
Author(s):  
Jitrlada ROJRATANAVIJIT ◽  
Preecha VICHITTHAMAROS ◽  
Sukanya PHONGSUPHAP
Keyword(s):  
Supervised Learning ◽  
Mixed Method ◽  
Short Length ◽  
Writing Systems ◽  
Learning Techniques ◽  
Average Accuracy ◽  
The Difference ◽  
Tweet Classification ◽  
Source Of Information ◽  
Processing Steps

The emergence of Twitter in Thailand has given millions of users a platform to express and share their opinions about products and services, among other subjects, and so Twitter is considered to be a rich source of information for companies to understand their customers by extracting and analyzing sentiment from Tweets. This offers companies a fast and effective way to monitor public opinions on their brands, products, services, etc. However, sentiment analysis performed on Thai Tweets has challenges brought about by language-related issues, such as the difference in writing systems between Thai and English, short-length messages, slang words, and word usage variation. This research paper focuses on Tweet classification and on solving data sparsity issues. We propose a mixed method of supervised learning techniques and lexicon-based techniques to filter Thai opinions and to then classify them into positive, negative, or neutral sentiments. The proposed method includes a number of pre-processing steps before the text is fed to the classifier. Experimental results showed that the proposed method overcame previous limitations from other studies and was very effective in most cases. The average accuracy was 84.80 %, with 82.42 % precision, 83.88 % recall, and 82.97 % F-measure.

scholarly journals Circulating nucleic acids in blood as biomarkers

2009 ◽  
Vol 16 (1) ◽  
Author(s):  
Reidun Øvstebø ◽  
Peter Kierulf ◽  
Kari Bente Foss Haug
Keyword(s):  
Gene Expression ◽  
Nucleic Acids ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Global Gene Expression ◽  
Short Review ◽  
Drug Susceptibility ◽  
Nucleotide Polymorphisms ◽  
Cytochrom P450 ◽  
Dna And Rna

<p>This short review on a rapidly expanding domain in biomarkers focuses on the value of markers derived from either circulating intracellular DNA and RNA (leukocytes) or from free DNA and RNA in plasma or serum. In circulating intracellular DNA biomarkers, importance has been pointed to reside in the ever increasing number of SNPs directly related to disease such as hemochromatosis or associated with genetic make up that leads to different drug-susceptibility. Quantitative gene expression profiling, increasingly using global expression platforms, is gaining momentum in various disease states such as cancer, inflammation, cardiovascular disease and diabetes. Circulating free nucleic acids in plasma or serum gain in importance as biomarkers particularly in cancer and foeto-maternal understanding. The surprising recent findings of circulating free mRNA carries the potential of examining normal and diseased plasma for global gene expression profiling – opening avenues to new biomarkers. When appropriate, this review gives reference to methodological considerations and refers the readers to important literature in the fields</p><p>I denne korte oversiktsartikkelen redegjøres det for et biomarkørfelt som utvikler seg hurtig. Gjennom en blodprøve kan man få kjennskap til forandringer i sirkulerende leucocytter, intracellulære nukleinsyrer (DNA og RNA) og fritt DNA og RNA fra plasma eller serum. Single Nucleotide Polymorphisms (SNPs) i DNA har allerede bekreftet sine muligheter som biomarkører (f.eks. Hemokromatose, Faktor V Leiden, Cytochrom P450 (CYP’er)). Stadig flere SNP’er vinner innpass i klinisk sammenheng. Siden sirkulerende hvite blodlegemer kan sies kontinuerlig å overvåke kroppens organer og vev, og dette avspeiles i disse blodcellers genekspresjon (RNA), knyttes det i dag forventninger til sykdomsspesifikke genekspresjonsprofiler. Både ved visse kreftformer, betennelsestilstander og hjertekar-sykdom viser hvite blodlegemer mer eller mindre tydelig sykdomsspesifikke genekspresjonsprofiler. Denne type sykdomsspesifikke genekspresjonsmarkører vil bli økende viktig fremover. Ved slike markører vil man kunne ha nytte av kvantitativ måling av enkeltmarkører, og også globale genekspresjonsprofiler på mikroarray-plattformer. Sirkulerende fritt DNA og kanskje særlig RNA i plasma åpner for nye sykdomsmarkører i første rekke ved forskjellige kreftformer og ved foeto-maternelle problemstillinger. Oversikten gir også en henvisning til metodologiske referanser i disse feltene.</p>

Circulating cell-free nucleic acids and platelets as a liquid biopsy in the provision of personalized therapy for lung cancer patients

Lung Cancer ◽  
2017 ◽  
Vol 107 ◽  
pp. 100-107 ◽  
Author(s):  
L. Sorber ◽  
K. Zwaenepoel ◽  
V. Deschoolmeester ◽  
P.E.Y. Van Schil ◽  
J. Van Meerbeeck ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Nucleic Acids ◽  
Cancer Patients ◽  
Liquid Biopsy ◽  
Personalized Therapy ◽  
Lung Cancer Patients

The bovine sex-determining region Y (Sry) gene and its mRNA transcript are present in Y sperm but not X sperm of bulls

2018 ◽  
Vol 68 (3) ◽  
pp. 321-332 ◽  
Author(s):  
Chun-Mei Han ◽  
Rong Chen ◽  
Tao Li ◽  
Xiao-Li Chen ◽  
Yong-Fu Zheng ◽  
...  
Keyword(s):  
Cellular Localization ◽  
Fish Analysis ◽  
Mrna Transcript ◽  
Rt Pcr ◽  
Sry Gene ◽  
Chain Reaction ◽  
Dna And Rna ◽  
Positive Rate ◽  
Polymerase Chain

AbstractThe aims of this study were to establish whether the sex-determining region Y gene and its mRNA transcript are present in the Y sperm and X sperm of bulls and, if present, determine their cellular localization. Semen was collected from three bulls and sorted by flow cytometry into X- and Y-chromosome populations. Reverse transcription-polymerase chain reaction (RT-PCR) was used to determineSrymRNA expression in X sperm and Y sperm. The presence and localization ofSryDNA and RNA were investigated by fluorescence in situ hybridization (FISH). RT-PCR detected a singleSrytranscript of 142 bp in Y sperm but not in X sperm. In Y sperm, the FISH-positive rates forSryDNA andSryRNA did not differ significantly from the re-analyzed Y sperm purity. In further experiments, there were no significant differences between the FISH-positive rate forSryRNA and the re-analyzed Y sperm purity for X-sorted, Y-sorted, or unsorted sperm. In conclusion, FISH analysis revealed thatSrytranscripts are present at the edges of the sperm heads of Y sperm but are absent from X sperm.

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