scholarly journals Performance Evaluation of SHOX2 and RASSF1A Methylation for the Aid in Diagnosis of Lung Cancer Based on the Analysis of FFPE Specimen

2020 ◽  
Vol 10 ◽  
Author(s):  
Juanhong Shi ◽  
Xue Chen ◽  
Long Zhang ◽  
Xia Fang ◽  
Yuting Liu ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Dna Methylation ◽  
Clinical Manifestations ◽  
Accurate Method ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Rassf1a Methylation ◽  
Specificity And Sensitivity ◽  
Test Kit

Emerging molecular diagnostic methods are more sensitive and objective, which can overcome the intrinsic failings of morphological diagnosis. Here, a RT-PCR-based in vitro diagnostic test kit (LungMe®) was developed and characterized to simultaneously quantify the DNA methylation of SHOX2 and RASSF1A in FFPE tissue specimens. The clinical manifestations were evaluated in 251 FFPE samples with specificity and sensitivity of 90.4 and 89.8%, respectively. Furthermore, the quantitative analysis shows that the degree of SHOX2 methylation was correlated with the stages of lung cancer, but not in the case of RASSF1A. Our observation indicated that the DNA methylation of SHOX2 and RASSF1A may play different roles in cancer development. Comparison of the methylation levels of SHOX2 and RASSF1A between cancer and cancer-adjacent specimens (n = 30), showed they have “epigenetic field defect”. As additional clinical validation, the hypermethylation of SHOX2 and RASSF1A was detected not only in surgical operative specimens, but also in histopathological negative puncture biopsies. SHOX2 and RASSF1A methylation detection can be used to increase sensitivity and NPV, which provide us with a more accurate method of differential diagnosis and are likely to be rapidly applied in clinical examinations.

scholarly journals Early diagnostic of lung cancer based on methylation of mononuclear cell fraction: Method development

2020 ◽  
Vol 57 (3) ◽  
pp. 11-16
Author(s):  
T. G. GONCHAROVA ◽  
D. R. KAIDAROVA ◽  
R. E. KADYRBAYEVA ◽  
M. G. ORAZGALIEVA ◽  
D. G. ADILBAY ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Dna Methylation ◽  
Method Development ◽  
Mononuclear Cells ◽  
Malignant Neoplasm ◽  
Diagnostic Methods ◽  
International Agency ◽  
Specificity And Sensitivity ◽  
Blood Mononuclear Cells ◽  
Early Diagnostic

Relevance: According to the International Agency for Research on Cancer (IARС), lung cancer (LC) today ranks first in cancer incidence worldwide [1]. In the Republic of Kazakhstan, about 3800 new cases of LC and more than 2000 deaths from LC are registered each year (one-year mortality exceeds 49.4%) [2]. This supports the relevance of early LC diagnostics. The study of DNA methylation in human peripheral blood mononuclear cells (PBMC) suggests its use as an early diagnostic and prognostic marker for LC before detecting a malignant neoplasm by visual diagnostic methods. The purpose of the study was to find specific diagnostic and prognostic markers by DNA methylation profiling of PBMC in patients with LC. Results: Methylation markers of blood mononuclear fraction were detected in CG islets associated with genes ICAM5, mir138, SYNE1, and KLK4 in 97% of plasma samples from patients with LC and were absent in healthy people. The usability of these markers to differentiate LC from 16 other cancers using NCBI GEO and TCGA methylation data was demonstrated with a specificity level of 0.96 and a sensitivity of 0.84. Conclusion: The specificity and sensitivity of the method of LC early diagnostics and prognosis based on the methylation of blood mononuclear cells (detection of methylation of CG islets associated with the ICAM5, mir138, SYNE1, and KLK4 genes in PBMC) are enough to use it in screening for LC.

scholarly journals Peripheral Blood Based Discrimination of Ulcerative Colitis and Crohn’s Disease from Non-IBD Colitis by Genome-Wide Gene Expression Profiling

2011 ◽  
Vol 30 (1) ◽  
pp. 1-17 ◽  
Author(s):  
Ferenc Sipos ◽  
Orsolya Galamb ◽  
Barnabás Wichmann ◽  
Tibor Krenács ◽  
Kinga Tóth ◽  
...  
Keyword(s):  
Gene Expression ◽  
Ulcerative Colitis ◽  
Crohn’S Disease ◽  
Crohn's Disease ◽  
Peripheral Blood ◽  
Independent Set ◽  
Molecular Diagnostic ◽  
Blood Samples ◽  
Specificity And Sensitivity

A molecular diagnostic assay using easily accessible peripheral blood would greatly assist in the screening and diagnosis of ulcerative colitis (UC) and Crohn’s disease (CD). Transcriptional profiles in blood/biopsy samples from 12 UC (6/12), 9 CD (5/9), 6 non-inflammatory bowel disease (non-IBD) colitis (6/0), and 11 healthy (11/11) patients were assessed by Affymetrix HGU133Plus2.0 microarrays. Prediction analysis of microarrays, discriminant and ROC analyses were performed, the results were validated by RT-PCR and immunohistochemistry using also an independent set of samples (15 blood samples, 45 biopsies). A set of 13 transcripts was differentially expressed in IBD, non-IBD controls and healthy blood samples (100% specificity and sensitivity). Validated difference was found in 16 transcripts between UC, non-IBD and normal blood, and 4 transcripts between CD, non-IBD and normal samples. UC and CD blood cases could be also distinguished by 5 genes with 100% specificity and sensitivity. Some disease associated alterations in blood transcripts were also detected in colonic tissue. IBD subtypes may be discriminated from non-IBD (diverticulitis, infective and ischemic colitis)in vitrofrom peripheral blood by screening for differential gene expression revealed in this study. Transcriptional profile alterations in peripheral blood can be located in diseased colon.

scholarly journals OmniSARS2: A Highly Sensitive and Specific RT-qPCR-Based COVID-19 Diagnostic Method Designed to Withstand SARS-CoV-2 Lineage Evolution

Biomedicines ◽  
2021 ◽  
Vol 9 (10) ◽  
pp. 1314
Author(s):  
Eduarda Carvalho-Correia ◽  
Carla Calçada ◽  
Fernando Branca ◽  
Nuria Estévez-Gómez ◽  
Loretta De Chiara ◽  
...  
Keyword(s):  
Cross Reactivity ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Clinical Samples ◽  
Analytical Sensitivity ◽  
S Gene ◽  
Genomic Knowledge ◽  
Gene Assay ◽  
One Step

Extensive transmission of SARS-CoV-2 during the COVID-19 pandemic allowed the generation of thousands of mutations within its genome. While several of these become rare, others largely increase in prevalence, potentially jeopardizing the sensitivity of PCR-based diagnostics. Taking advantage of SARS-CoV-2 genomic knowledge, we designed a one-step probe-based multiplex RT-qPCR (OmniSARS2) to simultaneously detect short fragments of the SARS-CoV-2 genome in ORF1ab, E gene and S gene. Comparative genomics of the most common SARS-CoV-2 lineages, other human betacoronavirus and alphacoronavirus, was the basis for this design, targeting both highly conserved regions across SARS-CoV-2 lineages and variable or absent in other Coronaviridae viruses. The highest analytical sensitivity of this method for SARS-CoV-2 detection was 94.2 copies/mL at 95% detection probability (~1 copy per total reaction volume) for the S gene assay, matching the most sensitive available methods. In vitro specificity tests, performed using reference strains, showed no cross-reactivity with other human coronavirus or common pathogens. The method was compared with commercially available methods and detected the virus in clinical samples encompassing different SARS-CoV-2 lineages, including B.1, B.1.1, B.1.177 or B.1.1.7 and rarer lineages. OmniSARS2 revealed a sensitive and specific viral detection method that is less likely to be affected by lineage evolution oligonucleotide–sample mismatch, of relevance to ensure the accuracy of COVID-19 molecular diagnostic methods.

scholarly journals The Sulfotransferase SULT1C2 Is Epigenetically Activated and Transcriptionally Induced by Tobacco Exposure and Is Associated with Patient Outcome in Lung Adenocarcinoma

2021 ◽  
Vol 19 (1) ◽  
pp. 416
Author(s):  
Candace Johnson ◽  
Daniel J. Mullen ◽  
Suhaida A. Selamat ◽  
Mihaela Campan ◽  
Ite A. Offringa ◽  
...  
Keyword(s):  
Lung Cancer ◽  
Dna Methylation ◽  
Lung Adenocarcinoma ◽  
Binding Site ◽  
Cell Line ◽  
Cigarette Smoke ◽  
Cell Lines ◽  
Normal Lung ◽  
Tobacco Exposure

Lung cancer is the leading cause of cancer-related death. Tobacco exposure is associated with 80–90% of lung cancer cases. The SULT1C2 sulfotransferase modifies xenobiotic compounds to enhance secretion but can also render these compounds carcinogenic. To determine if SULT1C2 contributes to tobacco-related carcinogenesis in the lung, we analyzed the expression and epigenetic state of SULT1C2 in human lung adenocarcinoma (LUAD) samples and in LUAD cell lines exposed to cigarette smoke condensate (CSC). SULT1C2 expression was significantly positively correlated to overall LUAD patient survival in smokers, was elevated in LUAD tumors compared to adjacent non-tumor lung, and was significantly correlated with levels of patient exposure to tobacco smoke. SULT1C2 promoter DNA methylation was inversely correlated with expression in LUAD, and hypomethylation of the SULT1C2 promoter was observed in Asian patients, as compared to Caucasians. In vitro analysis of LUAD cell lines indicates that CSC stimulates expression of SULT1C2 in a dose-dependent and cell-line-specific manner. In vitro methylation of the SULT1C2 promoter significantly decreased transcriptional activity of a reporter plasmid, and SULT1C2 expression was activated by the DNA demethylating agent 5-Aza-2′-deoxycytidine in a cell line in which the SULT1C2 promoter was hypermethylated. An aryl hydrocarbon receptor (AHR) binding site was detected spanning critical methylation sites upstream of SULT1C2. CSC exposure significantly increased AHR binding to this predicted binding site in the SULT1C2 promoter in multiple lung cell lines. Our data suggest that CSC exposure leads to activation of the AHR transcription factor, increased binding to the SULT1C2 promoter, and upregulation of SULT1C2 expression and that this process is inhibited by DNA methylation at the SULT1C2 locus. Additionally, our results suggest that the level of SULT1C2 promoter methylation and gene expression in normal lung varies depending on the race of the patient, which could in part reflect the molecular mechanisms of racial disparities seen in lung cellular responses to cigarette smoke exposure.

scholarly journals DNA methylation markers in lung cancer

2020 ◽  
Vol 21 ◽  
Author(s):  
Yoonki Hong ◽  
Woo Jin Kim
Keyword(s):  
Lung Cancer ◽  
Dna Methylation ◽  
Early Stage ◽  
Lung Cancer Screening ◽  
Dna Demethylation ◽  
Diagnostic Methods ◽  
Common Cancer ◽  
Promoter Dna Methylation ◽  
Potential Alternative ◽  
Promoter Dna

: Lung cancer is the most common cancer and the leading cause of cancer-related morbidity and mortality worldwide. As early symptoms of lung cancer are minimal and non-specific, many patients are diagnosed at an advanced stage. Despite a concerted effort to diagnose lung cancer early, no biomarkers that can be used for lung cancer screening and prognosis prediction have been established so far. As global DNA demethylation and gene-specific promoter DNA methylation are present in lung cancer, DNA methylation biomarkers have become a major area of research as potential alternative diagnostic methods to detect lung cancer at an early stage. This review summarizes the emerging DNA methylation changes in lung cancer tumorigenesis, focusing on biomarkers for early detection and their potential clinical applications in lung cancer.

scholarly journals Fast and Accurate Large-Scale Detection of β-Lactamase Genes Conferring Antibiotic Resistance

2015 ◽  
Vol 59 (10) ◽  
pp. 5967-5975 ◽  
Author(s):  
Jae Jin Lee ◽  
Jung Hun Lee ◽  
Dae Beom Kwon ◽  
Jeong Ho Jeon ◽  
Kwang Seung Park ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Pathogenic Bacteria ◽  
Large Scale ◽  
Diagnostic Methods ◽  
Control Measures ◽  
Clinical Isolates ◽  
Molecular Diagnostic ◽  
Resistant Bacteria ◽  
Specificity And Sensitivity ◽  
Almost All

ABSTRACTFast detection of β-lactamase (bla) genes allows improved surveillance studies and infection control measures, which can minimize the spread of antibiotic resistance. Although several molecular diagnostic methods have been developed to detect limitedblagene types, these methods have significant limitations, such as their failure to detect almost all clinically availableblagenes. We developed a fast and accurate molecular method to overcome these limitations using 62 primer pairs, which were designed through elaborate optimization processes. To verify the ability of this large-scalebladetection method (large-scaleblaFinder), assays were performed on previously reported bacterial control isolates/strains. To confirm the applicability of thelarge-scaleblaFinder, the assays were performed on unreported clinical isolates. With perfect specificity and sensitivity in 189 control isolates/strains and 403 clinical isolates, thelarge-scaleblaFinder detected almost all clinically availableblagenes. Notably, thelarge-scaleblaFinder detected 24 additional unreportedblagenes in the isolates/strains that were previously studied, suggesting that previous methods detecting only limited types ofblagenes can miss unexpectedblagenes existing in pathogenic bacteria, and our method has the ability to detect almost allblagenes existing in a clinical isolate. The ability oflarge-scaleblaFinder to detectblagenes on a large scale enables prompt application to the detection of almost allblagenes present in bacterial pathogens. The widespread use of thelarge-scaleblaFinder in the future will provide an important aid for monitoring the emergence and dissemination ofblagenes and minimizing the spread of resistant bacteria.

scholarly journals Laboratory diagnostics of tomato spotted wilt virus by PCR

2021 ◽  
Author(s):  
O.N. Morozova ◽  
D. D. Zvyagintseva ◽  
O.O. Beloshapkina
Keyword(s):  
Self Assembly ◽  
Tomato Spotted Wilt Virus ◽  
Test System ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Laboratory Diagnostics ◽  
Tomato Spotted Wilt ◽  
Specificity And Sensitivity ◽  
Wide Range ◽  
Wilt Virus

AbstractTomato spotted wilt virus is a widespread and harmful virus. It affects a wide range of host plants. The outward signs of TSWV lesions are different on different cultures. For the early diagnosis of TSWV, molecular diagnostic methods such as PCR must be used. In the course of this work, primers were developed for the diagnosis of tomato bronzing virus by real-time PCR and classical PCR. We also compared the specificity and sensitivity of various test systems for the diagnosis of tomato bronzing virus. In the course of this comparison, it was found that the self-assembly test system and the Syntol test system can be recommended for laboratory diagnostics of tomato spotted wilt virus.

scholarly journals Hypermethylation involved in DNA profiles of lung cancer specific tumour suppressor genes and epigenetic modification caused by an ultra-highly diluted homeopathic drug, Condurango 30C, in vitro and in vivo

2021 ◽  
Vol 13 (47) ◽  
pp. 99-99
Author(s):  
Anisur Rahman Khuda-Bukhsh ◽  
Sourav Sidkar
Keyword(s):  
Lung Cancer ◽  
Dna Methylation ◽  
Epigenetic Modification ◽  
Tumour Suppressor ◽  
Tumour Suppressor Genes ◽  
Dna Hypermethylation ◽  
Suppressor Genes ◽  
Homeopathic Drug

Background and objectives: DNA hyper-methylation is an important aspect involved in carcinogenesis and cancer progression, which affects mainly CpG islands of DNA and causes inactivation of tumour suppressor genes. Therefore DNA hypermethylation status of the genomic DNA in both the transformed cancerous cell lines and in carcinogen-induced lung cancer was ascertained by analysis of expressions of certain major lung cancer specific tumour suppressor genes. The other objective was to examine if ultra highly diluted homeopathic drug, Condurango 30C, had ability to modulate DNA methylation. Methods: DNA methylation activity, if any, has been ascertained in H460-NSCLC cells in vitro and in BaP-induced lung cancer of rats in vivo, in respect of tumour suppressor genes like p15, p16, p18 and p53 by using PCR-SSCP analyses. The ability of modulation of DNA methylation, if any, by Condurango 30C was also verified against placebo control in a blinded manner. Results: Condurango 30C-treated DNA showed significant decrease in band-intensity of p15 and p53 genes especially in methylated condition, in vitro, at the IC50 dose (2.43µl/100µl). SSCP analysis of p15 and p53 genes in Condurango 30C-treated DNA also supported ability of Condurango 30C to modulate methylation state, in vitro. Inhibition of p15 hypermethylation was observed after post cancer treatment of rat with Condurango 30C. SSCP results gave a better indication of differences in band-position and single strand separation of p15 and p53 in Condurango 30C treated samples. Conclusion: Condurango 30C could trigger epigenetic modification in lung cancer via modulation of DNA hypermethylation but placebos could not.

scholarly journals Development of NCOVID-19 Colloidal Gold Immunochromatographic Test Strip

2021 ◽  
Vol 10 (1) ◽  
pp. 1
Author(s):  
Wenyi Liu ◽  
Zhaohua Li
Keyword(s):  
Colloidal Gold ◽  
Low Cost ◽  
Virus Detection ◽  
High Specificity ◽  
Accurate Method ◽  
Rapid Screening ◽  
Nucleic Acid Detection ◽  
Specificity And Sensitivity ◽  
Control Serum

<div><p>Purpose: To establish a fast, simple and accurate method and immunoassay test card for the detection of new coronavirus (nCOVID-19) antigen. Methods: In this study, colloidal gold immunochromatography technology was used to detect nCOVID-19 virus antigens through the sandwich method. At the same time, the preparation plan of colloidal gold was improved, and the application of rapid immune-diagnosis technology in other fields was developed. In this study, purified recombinant nCOVID-19 nucleocapsid protein is used as the antigen to prepare murine monoclonal antibodies. The BN02 antibody produced by the mouse is used as the detection antibody to couple with colloidal gold, forming a gold-labeled complex probe. BN9m1 is used as the coating antibody for the C-line, and ProA is used for the T-line. The polymerization of colloidal gold particles enables us to detect the new coronavirus antigen’s appearance. Thus an in vitro rapid detection kit for virus detection can be made. Results: The positive detection rate of the antigen quality control serum with this colloidal gold reagent was 100%. The specificity was 100%, and the sensitivity was 1ng/ml.  Conclusion: The nCOVID-19 antigen detection reagent (colloidal gold method) developed in this research has high specificity and sensitivity, and can be used in conjunction with nucleic acid detection. As a means of detecting nCOVID-19, it can achieve qualitative and rapid screening of samples with advantage such as accuracy, repeatability, and low cost.</p></div>

Improving the quality of bacteriological studies for infections caused by carbapenem resistant Klebsiella pneumoniae using molecular diagnostic methods

2020 ◽  
pp. 6-17
Author(s):  
A. Chizhikova ◽  
E. Lisitsyna
Keyword(s):  
Klebsiella Pneumoniae ◽  
Pathogenic Bacteria ◽  
Test System ◽  
Ease Of Use ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Fast Analysis ◽  
Carbapenem Resistant ◽  
Specificity And Sensitivity

The resistance of gram-negative pathogenic bacteria to antibiotics of the β-lactam group — carbapenems — is associated with the ability of bacteria to produce carbapenemases. The relevant task is to determine carbapenem-resistant microorganisms to control the spread of resistant strains and conduct effective pharmacotherapy. The results of the development of molecular diagnostic methods, including use of polymerase chain reaction (PCR), for the detection of carbapenem resistant Klebsiella pneumoniae bacteria are presented. A multiplex PCR test system was developed for detecting carbapenem-resistant K. pneumoniae producing KPC and OXA 48-like carbapenemases. The test system is characterized by high specificity and sensitivity, ease of use, fast analysis time (up to 3 hours). Its introduction into clinical and diagnostic practice is promising in terms of improving the quality of bacteriological studies.

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