Comparison of Bisulfite Pyrosequencing and Methylation-Specific qPCR for Methylation Assessment

Different methodological approaches are available to assess DNA methylation biomarkers. In this study, we evaluated two sodium bisulfite conversion-dependent methods, namely pyrosequencing and methylation-specific qPCR (MS-qPCR), with the aim of measuring the closeness of agreement of methylation values between these two methods and its effect when setting a cut-off. Methylation of tumor suppressor gene p16/INK4A was evaluated in 80 lung cancer patients from which cytological lymph node samples were obtained. Cluster analyses were used to establish methylated and unmethylated groups for each method. Agreement and concordance between pyrosequencing and MS-qPCR was evaluated with Pearson's correlation, Bland-Altman, Cohen's kappa index and ROC curve analyses. Based on these analyses, cut-offs were derived for MS-qPCR. An acceptable correlation (Pearson's R2 = 0.738) was found between pyrosequencing (PYRmean) and MS-qPCR (NMP; normalized methylation percentage), providing similar clinical results when categorizing data as binary using cluster analysis. Compared to pyrosequencing, MS-qPCR tended to underestimate methylation for values between 0 and 15%, while for methylation >30% overestimation was observed. The estimated cut-off for MS-qPCR data based on cluster analysis, kappa-index agreement and ROC curve analysis were much lower than that derived from pyrosequencing. In conclusion, our results indicate that independently of the approach used for estimating the cut-off, the methylation percentage obtained through MS-qPCR is lower than that calculated for pyrosequencing. These differences in data and therefore in the cut-off should be examined when using methylation biomarkers in the clinical practice

Predictive value of a series of inflammatory markers in COPD for lung cancer diagnosis: a case-control study

Background: There is a relationship between Chronic Obstructive Pulmonary Disease (COPD) and the development of lung cancer (LC). The aim of this study is to analyse several blood markers and compare their concentrations in patients with only COPD and LC + COPD. Methods: Case-control study with cases presenting combined LC and COPD and two control groups (patients presenting only COPD and patients presenting only LC). We also included LC patients with descriptive purposes. In both groups, peripheral blood analyses of TNF-α, IL-6, IL-8, total leukocyte, lymphocyte and neutrophil counts, neutrophil-to-lymphocyte ratio, total platelet count, mean platelet volume, platelet-to-lymphocyte ratio, alpha 1-antitripsin (A1AT), IgE, C-reactive protein, fibrinogen, cholesterol and bilirubin were performed. We developed univariate and multivariate analyses of these markers, as well as a risk score variable, and we evaluated its performance through ROC curves. Results: We included 280 patients, 109 cases (LC + COPD), 83 controls (COPD) and 88 LC without COPD. No differences were observed in the distribution by sex, age, BMI, smoking, occupational exposure, lung function, GOLD stage or comorbidity. Patients with LC + COPD had significantly higher levels of neutrophils [OR 1.00 (95%CI 1.00–1.00), p = 0.03] and A1AT [OR 1.02 (95%CI 1.01–1.03), p = 0.003] and lower cholesterol levels [OR 0.98 (95%CI 0.97–0.99), p = 0.009] than COPD controls. We developed a risk score variable combining neutrophils, A1AT and cholesterol, achieving a sensitivity of 80%, a negative predictive value of 90.7% and an area under the curve of 0.78 (95%CI 0.71–0.86). Conclusions: COPD patients who also have LC have higher levels of neutrophils and A1AT and lower of cholesterol. These parameters could be potentially predicting biomarkers of LC in COPD patients.This work was supported by the project 110/2016 of the Spanish Society of Respiratory Pathology (SEPAR)S

In the search of early stages biomarkers for non small cell lung cancer

Comunicaciones a congreso

Usefulness of carotid ultrasonography in the diagnosis of coronary artery disease in patients undergoing exercise echocardiography

[Abstract] Background. Relationship between carotid and coronary artery disease (CAD) in patients undergoing invasive and non-invasive test is unclear. The aim of the study is to evaluate whether carotid disease is associated with CAD in patients submitted to exercise echocardiography (EE) and if it improves the EE ability to predict CAD. Methods. We retrospectively studied 156 subjects without previous vascular disease who underwent EE, carotid ultrasonography and coronary angiography between 2002 and 2013. Positive EE was defined as exercise induced wall motion abnormalities, carotid disease according to Manheim and American Society of Echocardiography Consensus and significant CAD as stenosis ≥50%. Results. Eighty-nine (57.1%) subjects had significant CAD. Factors associated with CAD in multivariate analysis were fasting plasma glucose (odds ratio [OR] 1.02, p = 0.031), pre-test probability of CAD > 65% (OR 3.71, p < 0.001), positive EE (OR 10.51, p < 0.001) and carotid plaque (CP) presence (OR 2.95, p = 0.013). There was neither statistical significant difference in area under the curve after addition of CP to EE results (0.77 versus 0.81, p = 0.525) nor sensitivity, specificity, predictive values or efficiency. CP presence reclassified as very high-risk according to Systematic COronary Risk Evaluation 13 patients (34.2%) with negative EE and 22 (33.3%) without CAD. Conclusion. CP is associated with CAD in patients undergoing EE, however its addition to EE does not improve CAD prediction, probably due to insufficient statistical power. CP reclassified one third of patients to very high-risk category despite negative EE or CAD absence, these subjects benefit from aggressive primary prevention interventions.Fundación Ramón Domínguez para la Investigación, el Desarrollo y la Innovación biosanitaria; ECOE

Validity and reliability of transbronchial needle aspiration for diagnosing mediastinal adenopathies

<p>Abstract</p> <p>Background</p> <p>The aim is to assess the validity and reliability of transbronchial needle aspiration (TBNA) of mediastinal and hilar adenopathies and to evaluate factors predictive of TBNA outcome.</p> <p>Methods</p> <p>We performed an analysis of prospectively collected data of patients (n = 580) who underwent TBNA (n = 685) from January 1998 to December 2007 in our center. Validity and reliability were evaluated for the overall sample and according to specific pathology. Factors predicting the successful acquisition of diagnostic samples were analyzed by multivariate analysis.</p> <p>Results</p> <p>Overall sensitivity, specificity, accuracy, and positive and negative predictive (NPV) values for TBNA were 68%, 100%, 68.8%, 100%, and 10%, respectively. The most sensitive and accurate TBNAs were obtained for patients with small cell lung carcinoma and the worst results were for patients with lymphomas. NPV were similar for all pathologies. The most predictive factors of outcome were adenopathy size and the presence of indirect signs at the puncture site.</p> <p>Conclusion</p> <p>The sensitivity and accuracy of TBNA are high in small cell lung cancer, followed by other types of carcinoma, sarcoidosis, and tuberculosis, and low for lymphoproliferative diseases. The NPV of TBNA for all individual pathologies is low. The size of the adenopathy and the presence of indirect signs at the puncture site predict the achievement of diagnostic samples.</p

Genetic analyses of aplastic anemia and idiopathic pulmonary fibrosis patients with short telomeres, possible implication of DNA-repair genes

Background: Telomeres are nucleoprotein structures present at the terminal region of the chromosomes. Mutations in genes coding for proteins involved in telomere maintenance are causative of a number of disorders known as telomeropathies. The genetic origin of these diseases is heterogeneous and has not been determined for a significant proportion of patients. Methods: This article describes the genetic characterization of a cohort of patients. Telomere length was determined by Southern blot and quantitative PCR. Nucleotide variants were analyzed either by high-resolution melting analysis and Sanger sequencing of selected exons or by massive sequencing of a panel of genes. Results: Forty-seven patients with telomere length below the 10% of normal population, affected with three telomeropathies: dyskeratosis congenita (4), aplastic anemia (22) or pulmonary fibrosis (21) were analyzed. Eighteen of these patients presented known pathogenic or novel possibly pathogenic variants in the telomere-related genes TERT, TERC, RTEL1, CTC1 and ACD. In addition, the analyses of a panel of 188 genes related to haematological disorders indicated that a relevant proportion of the patients (up to 35%) presented rare variants in genes related to DNA repair or in genes coding for proteins involved in the resolution of complex DNA structures, that participate in telomere replication. Mutations in some of these genes are causative of several syndromes previously associated to telomere shortening

Long COVID in hospitalized and non-hospitalized patients in a large cohort in Northwest Spain, a prospective cohort study

Survivors to COVID-19 have described long-term symptoms after acute disease. These signs constitute a heterogeneous group named long COVID or persistent COVID. The aim of this study is to describe persisting symptoms 6 months after COVID-19 diagnosis in a prospective cohort in the Northwest Spain. This is a prospective cohort study performed in the COHVID-GS. This cohort includes patients in clinical follow-up in a health area of 569,534 inhabitants after SARS-CoV-2/COVID-19 diagnosis. Clinical and epidemiological characteristics were collected during the follow up. A total of 248 patients completed 6 months follow-up, 176 (69.4%) required hospitalization and 29 (10.2%) of them needed critical care. At 6 months, 119 (48.0%) patients described one or more persisting symptoms. The most prevalent were: extra-thoracic symptoms (39.1%), chest symptoms (27%), dyspnoea (20.6%), and fatigue (16.1%). These symptoms were more common in hospitalized patients (52.3% vs. 38.2%) and in women (59.0% vs. 40.5%). The multivariate analysis identified COPD, women gender and tobacco consumption as risk factors for long COVID. Persisting symptoms are common after COVID-19 especially in hospitalized patients compared to outpatients (52.3% vs. 38.2%). Based on these findings, special attention and clinical follow-up after acute SARS-CoV-2 infection should be provided for hospitalized patients with previous lung diseases, tobacco consumption, and women

Mediastinal staging for non-small cell lung cancer

The staging of mediastinal lymph nodes for lung cancer is crucial for planning treatments or reinterventions. In potentially curable patients the aim of mediastinal staging is to exclude the presence of malignancy in mediastinal lymph nodes with a high level of accuracy while also considering clinical factors and the balance of the benefits and risks of tissue sampling techniques. Mediastinal staging is based on computed tomography (CT) and positron emission tomography (PET) and can be sufficient when no mediastinal abnormalities are present and the probability of unforeseen N2 disease is low. In the case of bulky lymph nodes with a high probability of malignancy in PET-CT, tissue confirmation is not normally required. If mediastinal sampling is needed it can be achieved by endosonographic techniques, including endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) and endoscopic ultrasound-guided fine needle aspiration (EUS-FNA) or a combination of the two. Positive results do not need further confirmation. In the case of negative results, surgical techniques still play a role in the selected cases discussed by multidisciplinary lung cancer committees. New mediastinal surgical techniques including video-assisted cervical mediastinoscopy (VACM), video-assisted mediastinoscopic lymphadenectomy (VAMLA), and transcervical extended mediastinal lymphadenectomy (TEMLA) have been shown to be useful in selected patients. Final pathological staging is based on lymph node removal during surgery and can be achieved by taking one of two approaches: lymph node sampling or systematic lymph node sampling. The accuracy of PET-CT and mediastinal endosonography is lower for mediastinal restaging than it is for surgical techniques; their false positive and false negative (FN) rate is high and so, they require histological confirmation. Here we explain and revise the results from the most recent studies and current international guidelines