A temporal developmental map separates human NK cells from noncytotoxic ILCs through clonal and single-cell analysis.

ABSTRACT: Natural killer (NK) cells represent the cytotoxic member within the innate lymphoid cell (ILC) family that are important against viral infections and cancer. Although the NK cell emergence from hematopoietic stem and progenitor cells through multiple intermediate stages and the underlying regulatory gene network has been extensively studied in mice, this process is not well characterized in humans. Here, using a temporal in vitro model to reconstruct the developmental trajectory of NK lineage, we identified an ILC-restricted oligopotent stage 3a CD34-CD117+CD161+CD45RA+CD56- progenitor population, that exclusively gave rise to CD56-expressing ILCs in vitro. We also further investigated a previously nonappreciated heterogeneity within the CD56+CD94-NKp44+ subset, phenotypically equivalent to stage 3b population containing both group-1 ILC and RORγt+ ILC3 cells, that could be further separated based on their differential expression of DNAM-1 and CD161 receptors. We confirmed that DNAM-1hi S3b and CD161hiCD117hi ILC3 populations distinctively differed in their expression of effector molecules, cytokine secretion, and cytotoxic activity. Furthermore, analysis of lineage output using DNA-barcode tracing across these stages supported a close developmental relationship between S3b-NK and S4-NK (CD56+CD94+) cells, whereas distant to the ILC3 subset. Cross-referencing gene signatures of culture-derived NK cells and other noncytotoxic ILCs with publicly available data sets validated that these in vitro stages highly resemble transcriptional profiles of respective in vivo ILC counterparts. Finally, by integrating RNA velocity and gene network analysis through single-cell regulatory network inference and clustering we unravel a network of coordinated and highly dynamic regulons driving the cytotoxic NK cell program, as a guide map for future studies on NK cell regulation.

The role of serum and bronchoalveolar lavage fluid chitotriosidase activity on diagnosis, disease characteristics and prognosis of sarcoidosis.

Introduction: Sarcoidosis is a multisystem granulomatous disease with an unpredictable clinical course. Chitotriosidase is a chitinase mainly expressed by activated macrophages. Increased chitotriosidase activity has been reported in serum and bronchoalveolar lavage (BAL) of sarcoidosis patients compared to healthy controls. This study aims to evaluate the role of serum and BAL chitotriosidase activity on diagnosis, disease characteristics, and prognosis of sarcoidosis. Materials and Methods: Patients referred with suspected sarcoidosis or other interstitial lung disease were prospectively included in the study. All patients underwent bronchoscopy with BAL. Serum and BAL chitotriosidase activity, BAL differential cell counts, and lymphocyte phenotypes were determined. Sarcoidosis patients were followed up regularly. Result: Forty-two sarcoidosis and 28 non-sarcoidosis patients were included in the study. Serum chitotriosidase activity was higher in sarcoidosis group 247.5 (2.78-461) vs 108 (2.78-272) nmol/h/mL (p< 0.001). BAL chitotriosidase activity tended to be higher in sarcoidosis group 11 (2-308) vs 6.95 (2.27-44) nmol/h/mg but was not found to be statistically significant (p= 0.11). Serum and BAL chitotriosidase activities were correlated with each other (p= 0.023, r= 0.355). No significant difference was found between the diagnostic performance of BAL CD4/CD8 ratio and serum chitotriosidase activity (p= 0.079). Serum chitotriosidase and ACE activities were correlated with each other (p= 0.004, r= 0.457). No significant difference was found between serum or BAL chitotriosidase activity and stage or extrapulmonary involvement. Serum chitotriosidase activity was higher in patients who needed systemic therapy at diagnosis (p= 0.046). However, no significant difference was found between serum or BAL chitotriosidase activities and disease progression (p= 0.395 and p= 0.723, respectively). Conclusions: Serum chitotriosidase activity can be helpful in the differential diagnosis of sarcoidosis with a similar diagnostic performance with BAL CD4/CD8 ratio. Although serum chitotriosidase activity at diagnosis does not predict progressive disease, it is associated with the need for systemic therapy at diagnosis. Serial chitotriosidase measurements may be useful in monitoring disease progression during follow-up.

Calculation of Biological Variation Components and Reference Change Value for Serum Copper and Zinc.

BACKGROUND: Zinc and copper are among the most important trace elements. Deficiencies of these trace elements cause a wide variety of disorders. The present study aims to report the definitive assessment of biological variation (BV) parameters for these elements as within-subject BV (CVI), between subject BV (CVG), index of individuality (II), and reference change value (RCV) in a Turkish cohort study group. METHODS: Ten blood specimens were collected weekly from 20 healthy volunteers (13 women, 7 men) for 10 weeks. Collected sera were stored at -80°C until the time of analysis. Serum zinc and copper levels were analyzed with atomic absorption spectrometry and ANOVA test was used to calculate the variations. RESULTS: The CVI and CVG for zinc were 6.26% and 23.27%, respectively. Analytical variation (CVA) was calculated as 4.24%. II and RCV for zinc were calculated as 0.26 and 21.51%, respectively. The CVI and CVG for copper were 6.05% and 19.64%, respectively. CVA was calculated as 4.24%. II and RCV for copper were calculated as 0.31 and 20.47%, respectively. CONCLUSIONS: Since II values were less than 0.6 for both analytes, the reference values will be of little use. RCV might be preferred for better evaluation instead.

Diagnostic performance of the RT-qPCR method targeting 85B mRNA in the diagnosis of pulmonary Mycobacterium tuberculosis infection.

BACKGROUND: Several nucleic acid amplification techniques (IS6110, 16S rRNA, and 85B mRNA) were developed for the rapid, direct detection of Mycobacterium tuberculosis. We aimed to assess the diagnostic performance of 85B mRNA-based RT-qPCR by comparing with the real-time PCR COBAS TaqMan MTB Kit while using the BACTEC MGIT 960 method as the gold standard. METHODS: 60 patients with confirmed pulmonary TB and 60 individuals without TB were included as the study and control groups, respectively. Sputum specimens were cultured using LJ and BACTEC MGIT 960 systems. Extracted DNA was used for COBAS PCR in a CONAS TaqMan 48 analyzer. 85B mRNA detection was performed by RT-qPCR. RESULTS: The sensitivity, specificity, positive predictive value, negative predictive value, and accuracy of COBAS TaqMan MTB Test were detected as 93.3%, 83.3%, 84.8%, 92.6%, and 88.3%, respectively. The same diagnostic parameters of RT-qPCR were: 98.3%, 95.0%, 95.2%, 98.3%, and 96.7%, respectively. According to the binary logistic regression analysis, RT-qPCR (OR: 19,924, p<0.001) was identified as the more optimal test. CONCLUSION: RT-qPCR targeting the 85B gene of M. tuberculosis seems to be a more useful and rapid technique than DNA-based methods for detecting live M. tuberculosis bacilli from sputum specimens.

Importance of pulmonary artery to ascending aorta ratio in chronic obstructive pulmonary disease.

INTRODUCTION: Recent articles revealed that an increased main pulmonary artery to ascending aorta ratio (PA/A) in thorax computed tomography (CT) correlated with pulmonary hypertension, and might be linked to a high probability of chronic obstructive pulmonary disease (COPD) exacerbations. OBJECTIVES: In this study, our aim was to evaluate the clinical importance of PA/A in patients with exacerbations of COPD and investigate its relationship with the number of exacerbations in 1 year or short/long-term mortality after hospital discharge. METHODS: One hundred fifty-six patients hospitalized for COPD exacerbations who fulfilled our inclusion criteria were enrolled in the study. We recorded the number of exacerbations in 1 year from hospital records, checked mortality status, and calculated the PA/A ratio from thorax CT images. RESULTS: PA/A ratio positively correlated with the number of hospitalizations for COPD exacerbations and the total number of exacerbations (hospitalized or not) in 1 year, and baseline PaCO2 level during hospitalization (r = 0.376, P < 0.001, r = 0.230, P = 0.004, and r = 0.328, P < 0.001, respectively). There was no relationship between mortality and PA/A. CONCLUSION: Our study showed that PA/A was related with the number of hospitalizations and the total number of exacerbations due to COPD in 1 year. However, there was no relationship between PA/A and mortality.

An outbreak of multidrug-resistant tuberculosis among a family.

Tuberculosis is a major public health problem and it may be complicated by multidrug-resistant tuberculosis (MDR-TB). Wide transmission among immunocompetent contacts of the index case is possible. If you detect tuberculosis in two contacts of the index case, it is called an outbreak. The aim of our paper is to evaluate the characteristics of a MDR-TB outbreak affecting 7 people in a family treated during 2012-2014 in Istanbul Yedikule Training and Research Hospital for Chest Disease and Thoracic Surgery, Turkey. The cultures, spoligotyping, and DNA fingerprinting revealed the same Mycobacterium tuberculosis species as T1 genotype and ST53 subtype. All patients were negative for human immunodeficiency virus and free of other underlying diseases.

Prevalence and outcomes of comorbid illnesses in elderly patients with respiratory diseases.

AIM: The aim of the present study was to determine the prevalence of comorbidities in very elderly patients hospitalized as a result of acute respiratory diseases and to analyze sex-specific differences, and to examine the effects of these comorbidities on their treatment outcomes. METHODS: A total of 3316 patients were admitted to our pulmonary inpatient clinic between 2009 and 2011, and 243 of them (aged over 80 years) with acute respiratory disease were included in our study. Data were retrospectively collected, and included demographic features, comorbidities, laboratory findings, length of hospital stay and in-hospital mortality. RESULTS: In total of 243, 144 patients (59.3%) were men and 99 patients (40.7%) were women. The mean age was 84 ± 3 years. The prevalence of comorbidity was 75.7% (n = 184). The most common comorbid disease in patients with chronic obstructive pulmonary disease was congestive heart failure (32.9%), and it was chronic obstructive pulmonary disease (49.4%) in patients with pneumonia. The rate of having one comorbidity was 58.2% (n = 107) and 35.3% (n = 65) had two. Approximately half (52.6%) of the in-hospital deaths occurred within the first 48 hours of hospitalization. The number of comorbidities was higher in the deceased patients compared with the living patients (P = 0.01). CONCLUSIONS: The present study showed that the majority of our patients had at least one comorbidity. The first 48 hours of hospitalization was very important, especially for the patients with comorbidities, to determine the need for intensive care unit and prognosis. The coexistence of comorbidities can increase the risk of mortality in the elderly. Geriatr Gerontol Int 2016; 16: 791-796.

Spontaneous Mediastinal Emphysema Associated with the Use of Synthetic Cannabinoid (Bonsai).

Spontaneous Mediastinal Emphysema (SME), which is a rarely seen case is defined as the detection of free air in the mediastinum without any trauma. Although rare, some cases secondary to drug use have been reported. In this study, two SME cases that developed due to the use of a synthetic cannabinoid known as "bonzai", which has recently become widespread in Turkey, are presented. We would like to emphasize that SME should also be considered in the differential diagnosis of patients who present with the symptoms of chest pain and dyspnea and have a history of drug use.

Cathelicidin as a link between sarcoidosis and tuberculosis.

SETTING: Sarcoidosis and tuberculosis share notable clinical, radiological, histological, and immunological similarities. The importance of vitamin D has long been investigated in these two granulomatous lung diseases. Cathelicidin is an antimicrobial peptide of the innate immune system, directly induced by vitD3. OBJECTIVE: To evaluate the role of cathelicidin in sarcoidosis and tuberculosis development. DESIGN: The study included 30 consecutive patients with active lung tuberculosis, 30 patients with sarcoidosis, and 20 healthy controls. 25-hydroxyvitamin D [25(OH)D] and cathelicidin levels were measured in blood samples. RESULTS: Vitamin D levels were significantly higher (p<0.001) in tuberculosis patients (22.5 ± 9.96 ng/ml) than in sarcoidosis patients (11.75 ± 8.92 ng/ml). Severe vitamin D deficiency was as frequent as 47% in sarcoidosis patients compared to only 3% in tuberculosis patients. Cathelicidin levels were significantly higher in the control group (120.37 ± 41.03 pg/ml) than in sarcoidosis (67.68 ± 38.03 pg/ml) and tuberculosis (68.74 ± 39.44 pg/ml) patients (p<0.001). However, no significant difference in cathelicidin levels was observed between tuberculosis and sarcoidosis patients (p=0.966). The optimum cathelicidin cut-off value to distinguish sarcoidosis patients from healthy controls was 107.14 pg/ml (sensitivity 81.5%, specificity 71.2%). CONCLUSION: Cathelicidin appears to play different roles in the development of granulomatous lung disease.

Patient and physician delay in the diagnosis and treatment of non-small cell lung cancer in Turkey.

AIM: The early diagnosis and treatment of lung cancer are important for the prognosis of patients with lung cancer. This study was undertaken to investigate patient and doctor delays in the diagnosis and treatment of NSCLC and the factors affecting these delays. MATERIALS AND METHODS: A total of 1016 patients, including 926 (91.1%) males and 90 (8.9%) females with a mean age of 61.5±10.1 years, were enrolled prospectively in this study between May 2010 and May 2011 from 17 sites in various Turkish provinces. RESULTS: The patient delay was found to be 49.9±96.9 days, doctor delay was found to be 87.7±99.6 days, and total delay was found to be 131.3±135.2 days. The referral delay was found to be 61.6±127.2 days, diagnostic delay was found to be 20.4±44.5 days, and treatment delay was found to be 24.4±54.9 days. When the major factors responsible for these delays were examined, patient delay was found to be more frequent in workers, while referral delay was found to be more frequent in patients living in villages (p<0.05). We determined that referral delay, doctor delay, and total delay increased as the number of doctors who were consulted by patients increased (p<0.05). Additionally, we determined that diagnostic and treatment delays were more frequent at the early tumour stages in NSCLC patients (p<0.05). DISCUSSION: The extended length of patient delay underscores the necessity of educating people about lung cancer. To decrease doctor delay, education is a crucial first step. Additionally, to further reduce the diagnostic and treatment delays of chest specialists, multidisciplinary management and algorithms must be used regularly.

Value of neutrophil/lymphocyte ratio in the differential diagnosis of sarcoidosis and tuberculosis.

INTRODUCTION: The differential diagnosis of sarcoidosis creates a challange due to tuberculosis also having lung and lymph node involvement. Because both diseases show granulomatous inflammation, it may not be possible to distinguish tuberculosis and sarcoidosis in pathological specimens. As a result of the complexity in the differential diagnosis of sarcoidosis and tuberculosis, new markers for differentiation are being investigated. OBJECTIVE: The aim of our study is to investigate the value of neutrophil/lymphocyte ratio (NLR) as a possible marker in differentiating sarcoidosis and tuberculosis. MATERIALS AND METHODS: In our study, 51 acid-fast bacilli (AFB) positive and/or culture-positive patients with pulmonary tuberculosis, ​​40 patients with biopsy-proven sarcoidosis and a control group consisting of 43 patients were included. In our study, information was collected retrospectively based on hospital records. RESULTS: Leukocyte and neutrophil counts, NLR, erythrocyte sedimentation rate (ESR), C-reactive protein (CRP) were significantly higher, and albumin was significantly lower in the tuberculosis group compared with sarcoidosis (for all parameters P < 0.001). The most appropriate cut-off value of NLR to distinguish tuberculosis from sarcoidosis was determined as 2.55. For this cut-off value of NLR there was 79% sensitivity, 69% specificity, 73% positive predictive value (PPV), 75% negative predictive value (NPV), and area under the curve (AUC) was 0.788. For differentiation of sarcoidosis from tuberculosis, accuracy of the NLR test according to this cut-off value was found as 76%. CONCLUSION: NLR as a little known marker in respiratory medicine was found to be supportive in differentiation of tuberculosis and sarcoidosis. More studies on this issue is needed.

Is MMP-7 gene polymorphism a possible risk factor for chronic obstructive pulmonary disease in Turkish patients.

Chronic obstructive pulmonary disease (COPD) is a chronic inflammatory disease that leads to fixed narrowing of small airways and alveolar wall destruction (emphysema). This study was performed to test the association between MMP-7 (rs155668818) and MMP-12 (rs56184183) polymorphisms in the MMP-7 gene and COPD risk and its severity in the Turkish population. MMP-7 and MMP-12 polymorphisms were genotyped in 85 patients with COPD and 73 healthy control subjects using real-time polymerase chain reaction analysis. There were significant differences in the distribution of MMP-7 genotypes but not in the frequencies of these alleles between COPD patients and controls (p=0.009, p=0.102, respectively). The MMP-7 AA genotype was found to be associated with an increased risk of COPD (p=0.004; odds ratio: 2.576; confidence interval: 1.297-5.119). The lowest values of forced expiratory volume in 1 s (FEV1), forced vital capacity (FVC), FEV1/FVC in patients with GG homozygosity were determined and these values were statistically significant compared to the control subjects (p<0.001, p<0.001, p<0.001). When the present study groups were analyzed for MMP-12 polymorphism, it was found that all the subjects had wild-type genotype for this polymorphism. These findings have suggested that MMP-7 polymorphism might be associated with the risk and progression of COPD in the Turkish population.

Adapted T cell interferon-gamma release assay for the diagnosis of pleural tuberculosis.

BACKGROUND: Better and more rapid tests are needed for the diagnosis of tuberculous pleural effusion (TPE), given the known limitations of conventional diagnostic tests. OBJECTIVES: To estimate diagnostic accuracy of the QuantiFERON-TB Gold In-Tube (QFT-GIT) test (and its components) using data-derived cutoffs in pleural fluid. METHODS: The QFT-GIT test was performed on whole blood and pleural fluid from 43 patients with TPE and 29 control subjects (non-TPE). To achieve the objective, QFT-GIT test, estimating likelihood ratios and receiver operating curve analysis were performed. RESULTS: The sensitivity and specificity using the QFT-GIT for the diagnosis of TPE were 48.8% and 79.3%, respectively, in pleural fluid. The best cutoff points for tuberculosis (TB) antigen, nil and TB antigen minus nil results were estimated at 0.70, 0.90 and 0.30 IU/ml, respectively. Area under the curve of TB antigen IFN-γ response was 0.86 (CI: 0.76-0.93), nil tube was 0.80 (CI: 0.69-0.89) and TB antigen minus nil tube was 0.82 (CI: 0.72-0.90). When the best cutoff scores of the nil tubes were set at this value, the results of a likelihood ratio of a positive and a negative test were 9.44 (7.4-12.0) and 0.37 (0.09-1.5), respectively. The percentages of indeterminate results in pleural fluid among the TPE cases were 42% (most of them caused by high nil IFN-γ values) using the QFT-GIT test. CONCLUSION: QFT-GIT test or its components have poor accuracy in the diagnosis of TPE, largely because of a high number of indeterminate results due to high background IFN-γ production in the TPE.