Radiomics-Based Intracranial Thrombus Features on CT and CTA Predict Recanalization with Intravenous Alteplase in Patients with Acute Ischemic Stroke

BACKGROUND AND PURPOSE

Thrombus characteristics identified on non-contrast CT (NCCT) are potentially associated with recanalization with intravenous (IV) alteplase in patients with acute ischemic stroke (AIS). Our aim was to determine the best radiomics-based features of thrombus on NCCT and CT angiography associated with recanalization with IV alteplase in AIS patients and proximal intracranial thrombi.

MATERIALS AND METHODS

With a nested case-control design, 67 patients with ICA/M1 MCA segment thrombus treated with IV alteplase were included in this analysis. Three hundred twenty-six radiomics features were extracted from each thrombus on both NCCT and CTA images. Linear discriminative analysis was applied to select features most strongly associated with early recanalization with IV alteplase. These features were then used to train a linear support vector machine classifier. Ten times 5-fold cross-validation was used to evaluate the accuracy of the trained classifier and the stability of the selected features.

RESULTS

Receiver operating characteristic curves showed that thrombus radiomics features are predictive of early recanalization with IV alteplase. The combination of radiomics features from NCCT, CTA, and radiomics changes is best associated with early recanalization with IV alteplase (area under the curve = 0.85) and was significantly better than any single feature such as thrombus length (P < .001), volume (P < .001), and permeability as measured by mean attenuation increase (P < .001), maximum attenuation in CTA (P < .001), maximum attenuation increase (P < .001), and assessment of residual flow grade (P < .001).

CONCLUSIONS

Thrombus radiomics features derived from NCCT and CTA are more predictive of recanalization with IV alteplase in patients with acute ischemic stroke with proximal occlusion than previously known thrombus imaging features such as length, volume, and permeability.

Genomics and response to long-term oxygen therapy in chronic obstructive pulmonary disease

Chronic obstructive pulmonary disease (COPD) is a leading cause of death worldwide, and long-term oxygen therapy has been shown to reduce mortality in COPD patients with severe hypoxemia. However, the Long-term Oxygen Treatment Trial (LOTT), a large randomized trial, found no benefit of oxygen therapy in COPD patients with moderate hypoxemia. We hypothesized that there may be differences in response to oxygen which depend on genotype or gene expression. In a genome-wide time-to-event analysis of the primary outcome of death or hospitalization in 331 subjects, 97 single nucleotide polymorphisms (SNPs) showed evidence of interaction with oxygen therapy at P < 1e-5, including 7 SNPs near arylsulfatase B (ARSB; P = 6e-6). In microarray expression profiling on 51 whole blood samples from 37 individuals, at screening and/or at 12-month follow-up, ARSB expression was associated with the primary outcome depending on oxygen treatment. The significant SNPs were conditional expression quantitative trait loci for ARSB expression. In a network analysis of genes affected by long-term oxygen, two observed clusters including 26 co-expressed genes were enriched in mitochondrial function. Using data from the observational COPDGene Study, we validated the expression of 25 of these 26 genes, plus ARSB. The effect of long-term oxygen therapy in COPD varied based on ARSB expression and genotype. ARSB has previously been shown to be associated with hypoxemia in human bronchial and colonic epithelial cells and in a mouse model. In peripheral blood, long-term oxygen treatment affected expression of mitochondrial-related genes, a biologically relevant pathway in COPD. SNPs and expression of ARSB are associated with response to long-term oxygen in COPD. The ARSB SNPs were expression quantitative trait loci depending on oxygen therapy. Genes differentially expressed by long-term oxygen were enriched in mitochondrial functions. This suggests a potential biomarker to personalize use of long-term oxygen in COPD.

Phylogenetic classification of hemagglutinin gene of H9N2 avian influenza viruses isolated in China during 2012-2016 and evaluation of selected candidate vaccine strains

H9N2 subtype avian influenza virus (AIV) was the highly contagious pathogen which has caused severe losses in the poultry industry throughout China in recent years. Using current epidemic viruses as vaccine was an effective way to prevent infection of H9N2 subtype AIV. In this study, a total of 23 H9N2 subtype AIV strains were isolated in 200 samples from 13 provinces of China during 2012-2016. The sequencing and phylogenetic analysis of the hemagglutinin gene sequence of the isolation strains showed that 22 isolation strains were clustered to h9.4.2.5 lineage, while only 1 belonged to h9.4.2.6. The data of cross-HI, neutralization and cross-immune protection shown that the A/chicken/Hunan/HN/2015 (HN) and A/chicken/Shandong/SD/2014 (SD) strains as vaccine could effectively protect present viruses infection compared with other strains. These results indicated that current epidemic viruses were mainly belong to h9.4.2.5 lineage and HN and SD strains as candidate vaccine strains were potentiality for the protection of present H9N2 subtype AIV infection.

Myelin oligodendrocyte glycoprotein antibody-associated demyelination: comparison between onset phenotypes

BACKGROUND AND PURPOSE

The aim of this study was to analyse the clinical and prognostic features of myelin oligodendrocyte glycoprotein (MOG) antibody-associated demyelination with different onset phenotypes.

METHODS

A total of 52 MOG-IgG-seropositive patients were divided into four groups: (i) optic neuritis (ON) at onset (MOG-ON⁺ , n = 23), (ii) transverse myelitis (TM) at onset (MOG-TM⁺ , n = 12), (iii) pure brain symptoms at onset (MOG-ON^- -TM^- , n = 14) and (iv) both ON and TM at onset (n = 3). This final group was not included in further analyses. Data were collected through medical records and regular follow-up.

RESULTS

Median age at presentation was 24 (range, 3-63) years in the whole cohort (50% female). MOG-ON^- -TM^- patients had the youngest age of onset across the three groups. Patients with MOG-TM⁺ tended to relapse more frequently and had a longer interval to first relapse than was observed in MOG-ON⁺ and MOG-ON^- -TM^- patients. High MOG-IgG titres were associated with increased cerebrospinal fluid leukocytes. The likelihood of harbouring transient, low MOG-IgG titres was higher in the MOG-TM⁺ group than in the other groups. After a median disease duration of 20 months, most but not all cases had a favourable outcome, with 8% developing severe visual deficit, 2% becoming wheelchair-dependent and 6% developing cognitive impairment. The onset phenotype appeared to be an important predictor of disability type. Having high MOG-IgG titres (odds ratio, 0.168, P = 0.027) or female gender (odds ratio, 0.270, P = 0.067) was associated with a lower likelihood of complete recovery.

CONCLUSIONS

Onset phenotype may influence long-term presentation, MOG-IgG status as well as outcome. Further large and prospective studies are needed to better clarify the clinical implications of the first demyelinating event.

Integrative epigenomic analysis in differentiated human primary bronchial epithelial cells exposed to cigarette smoke

Cigarette smoke (CS) is one of the major risk factors for many pulmonary diseases, including chronic obstructive pulmonary disease (COPD) and lung cancer. The first line of defense for CS exposure is the bronchial epithelial cells. Elucidation of the epigenetic changes during CS exposure is key to gaining a mechanistic understanding into how mature and differentiated bronchial epithelial cells respond to CS. Therefore, we performed epigenomic profiling in conjunction with transcriptional profiling in well-differentiated human bronchial epithelial (HBE) cells cultured in air-liquid interface (ALI) exposed to the vapor phase of CS. The genome-wide enrichment of histone 3 lysine 27 acetylation was detected by chromatin immunoprecipitation followed by next generation sequencing (ChIP-Seq) in HBE cells and suggested the plausible binding of specific transcription factors related to CS exposure. Additionally, interrogation of ChIP-Seq data with gene expression profiling of HBE cells after CS exposure for different durations (3 hours, 2 days, 4 days) suggested that earlier epigenetic changes (3 hours after CS exposure) may be associated with later gene expression changes induced by CS exposure (4 days). The integration of epigenetics and gene expression data revealed signaling pathways related to CS-induced epigenetic changes in HBE cells that may identify novel regulatory pathways related to CS-induced COPD.

[Analysis of clinical characteristics and prognosis of neuromyelitis optic spectrum disease complicated with malignant tumor]

Objective: To investigate the clinical features of patients involved with both malignant tumors and neuromyelitis optica spectrum disorders (NMOSD). Methods: The clinical data of 473 patients with NMOSD admitted into the Third Affiliated Hospital of Sun Yat-sen University and the Department of Neurology, Affiliated Hospital of Guizhou Medical University from June 2012 to March 2017 were retrospectively analyzed. Eleven NMOSD patients complicated with malignant tumors were screened out (3 with breast cancer, 2 with cervical cancer, 2 with rectal cancer, 2 with leukemia, 1 with nasopharyngeal carcinoma, 1 with thyroid cancer). Fifty patients without NMOSD were included as controls. Results: Most of the NMOSD patients were complicated by low-moderately differentiated squamous cell carcinoma/adenocarcinoma, mainly seen in breast, reproductive system, digestive system and hematological system. In terms of sex ratio and autoantibodies, the NMOSD patients with and without malignant tumors showed no significant difference. However, comparing to the patients without malignant tumor, the ones with malignant tumor showed a tendency of lower rate of initial brain symptoms and relapse rate, while with older onset age, higher initial EDSS score, protein content in cerebrospinal fluid (CSF), higher rates of initial symptom resulted from the focus of posterior region of the medulla and of significant image focus. Of the 8 NMOSD patients who diagnosed as malignant tumors in our hospital, 2 with breast cancer and 1 with cervical cancer had a good prognosis (follow-up EDSS score <3). All the 3 patients received aggressive surgery and chemotherapy treatment. However, the other 5 patients had poor prognosis (follow-up EDSS score ≥3 points). All the 11 patients received anti-tumor therapy, 4 patients had first NMOSD attack after anti-tumor treatment and no relapse. Only one case from the remaining 7 patients had relapse; Among the 9 patients received immunosuppressive therapy, 7 patients had no relapse, and 8 cases maintained stable; while, among all the 9 patients received immunosuppressive agents and anti-tumor therapy, only one case had relapse. Conclusions: There are some differences in the clinical features between the NMOSD patients with malignant tumors and the NMOSD patients without malignant tumors. Immunosuppressive therapy can improve the prognosis of patients with NMOSD and tumor, without increasing the risk of malignant tumor. The pathological type, staging and antitumor therapy may influence the prognosis of NMOSD. NMOSD patients with malignant tumor could be treated with anti-tumor and immunosuppressive agents if needed.

Application of empirical Bayes methods to predict the rate of decline in ERG at the individual level among patients with retinitis pigmentosa

Retinitis pigmentosa is one of the most common forms of inherited retinal degeneration. The electroretinogram (ERG) can be used to determine the severity of retinitis pigmentosa-the lower the ERG amplitude, the more severe the disease is. In practice for career, lifestyle, and treatment counseling, it is of interest to predict the ERG amplitude of a patient at a future time. One approach is prediction based on the average rate of decline for individual patients. However, there is considerable variation both in initial amplitude and in rate of decline. In this article, we propose an empirical Bayes (EB) approach to incorporate the variations in initial amplitude and rate of decline for the prediction of ERG amplitude at the individual level. We applied the EB method to a collection of ERGs from 898 patients with 3 or more visits over 5 or more years of follow-up tested in the Berman-Gund Laboratory and observed that the predicted values at the last (kth) visit obtained by using the proposed method based on data for the first k-1 visits are highly correlated with the observed values at the kth visit (Spearman correlation =0.93) and have a higher correlation with the observed values than those obtained based on either the population average decline rate or those obtained based on the individual decline rate. The mean square errors for predicted values obtained by the EB method are also smaller than those predicted by the other methods.

[Efficacy and safety of mycophenolate mofetil in treating neuromyelitis optica spectrum disorder: a multicenter, prospective, self-control study in Guangzhou City]

Objective: To evaluate the efficacy and safety of mycophenolate mofetil (MMF) in neuromyelitis optica spectrum disorder (NMOSD). Method: From September 2014 to February 2017, NMOSD patients with seropositive aquaporin4-IgG was enrolled through a multicenter, prospective study, and the annual recurrence rate (ARR), Expanded Disability Status Scale (EDSS) and MMF-related side effects before and after MMF treatment were compared. Results: Ninety patients were enrolled in the study. After being treated for a median of 12 months (1-30 months), the median ARR decreased from 1.1 pre-MMF to 0 post-MMF (P<0.001), and the median EDSS score decreased from 4.0 pre-MMF to 3.0 post-MMF (P<0.001). The EDSS score reduced significantly after 90 days' treatment (P<0.05). The main adverse events included the deranged liver enzymes (19%, 17/90), respiratory infection (11%, 10/90), urinary tract infection (6%, 5/90), varicella-zoster infection (6%, 5/90), anemia (6%, 5/90), leucopenia (6%, 5/90), diarrhea (2%, 2/90), hair loss (1%, 1/90); 11% (10/90) patients experienced severe adverse events, and 6% (5/90) patients discontinued MMF. Conclusions: MMF could significantly reduce the ARR and EDSS score of NMOSD. However, awareness on side effects should be raised.

Robust joint score tests in the application of DNA methylation data analysis

Background

Recently differential variability has been showed to be valuable in evaluating the association of DNA methylation to the risks of complex human diseases. The statistical tests based on both differential methylation level and differential variability can be more powerful than those based only on differential methylation level. Anh and Wang (2013) proposed a joint score test (AW) to simultaneously detect for differential methylation and differential variability. However, AW’s method seems to be quite conservative and has not been fully compared with existing joint tests.

Results

We proposed three improved joint score tests, namely iAW.Lev, iAW.BF, and iAW.TM, and have made extensive comparisons with the joint likelihood ratio test (jointLRT), the Kolmogorov-Smirnov (KS) test, and the AW test. Systematic simulation studies showed that: 1) the three improved tests performed better (i.e., having larger power, while keeping nominal Type I error rates) than the other three tests for data with outliers and having different variances between cases and controls; 2) for data from normal distributions, the three improved tests had slightly lower power than jointLRT and AW. The analyses of two Illumina HumanMethylation27 data sets GSE37020 and GSE20080 and one Illumina Infinium MethylationEPIC data set GSE107080 demonstrated that three improved tests had higher true validation rates than those from jointLRT, KS, and AW.

Conclusions

The three proposed joint score tests are robust against the violation of normality assumption and presence of outlying observations in comparison with other three existing tests. Among the three proposed tests, iAW.BF seems to be the most robust and effective one for all simulated scenarios and also in real data analyses.

Electronic supplementary material

The online version of this article (10.1186/s12859-018-2185-3) contains supplementary material, which is available to authorized users.

Serum cystatin C and anti-N-methyl-D-aspartate receptor encephalitis

BACKGROUND

Cystatin C (CysC) is associated with many neurodegenerative disorders and autoimmune diseases, but its relationship with anti-N-Methyl-D-aspartate receptor (anti-NMDAR) encephalitis is unknown.

METHODS

Serum levels of CysC were determined in 66 patients with anti-NMDAR encephalitis and 115 healthy controls. Of the 66 patients, 30 had a follow-up evaluation at 3 months after admission. Association of CysC with anti-NMDAR encephalitis and its clinical parameters were evaluated in the patients.

RESULTS

The serum levels of CysC were significantly lower in patients with anti-NMDAR encephalitis than in controls (0.70 ± 0.13 vs 0.83 ± 0.17 mg/mL, P < .001). Disease severity and disease duration were significantly associated with CysC levels. Furthermore, a follow-up evaluation revealed that after treatment anti-NMDAR encephalitis patients had significantly increased serum CysC levels (P < .001) and significantly decreased modified Rankin Scale (mRS) scores (P < .001) compared with before treatment. In addition, a significant negative correlation was observed between the change in CysC levels and the change in mRS scores (r = -.700, P < .001).

CONCLUSION

Our results show that the serum levels of CysC are associated with anti-NMDAR encephalitis and its clinical parameters and that the changes in CysC levels correlate with therapeutic effect. Therefore, our findings provide new insights into the association between serum CysC and anti-NMDAR encephalitis.

The effect of interaction between EtOH dosage and exposure time on gene expression in DPSC

Alcohol (EtOH) dosage and exposure time can affect gene expression. However, whether there exists synergistic effect is unknown. Here, we analyzed the hDPSC gene microarray dataset GSE57255 downloaded from Gene Expression Omnibus and found that the interaction between EtOH dosage and exposure time on gene expression are statistically significant for two probes: 201917_s_at near gene SLC25A36 and 217649_at near gene ZFAND5. GeneMania showed that SLC25A36 and ZFAND5 were related to 20 genes, three of which had alcohol-related functions. WebGestalt revealed that the 22 genes were enriched in 10 KEGG pathways, four of which are related to alcoholic diseases. We explored the possible nonlinear interaction effect and got 172 gene probes with significant p-values. However, no significantly enriched pathways based on the 172 probes were detected. Our analyses indicated a possible molecular mechanism that could help explain why alcohol consumption has both deleterious and beneficial effects on human health.

Full-field fabric stress mapping by micro Raman spectroscopy in a yarn push-out test

The full-field stress distribution of a two-dimensional plain fabric was mapped using micro Raman spectroscopy (MRS) through a novel yarn push-out test, simulating a quasi-static projectile impact on the fabric. The stress-strain relationship for a single yarn was established using a digital image correlation method in a single-yarn tensile test. The relationship between Raman peak shift and aramid Kevlar 49 yarn stress was established using MRS in a single-yarn tensile test. An out-of-plane loading test was conducted on an aramid Kevlar 49 plain fabric, and the yarn stress was measured using MRS. From the full-field fabric stress distribution, it can be observed that there is a cross-shaped distribution of high yarn stress; this result would be helpful in further studies on load transfer on a fabric during a projectile impact.

Ensemble genomic analysis in human lung tissue identifies novel genes for chronic obstructive pulmonary disease

BACKGROUND

Genome-wide association studies (GWAS) have identified single nucleotide polymorphisms (SNPs) significantly associated with chronic obstructive pulmonary disease (COPD). However, many genetic variants show suggestive evidence for association but do not meet the strict threshold for genome-wide significance. Integrative analysis of multiple omics datasets has the potential to identify novel genes involved in disease pathogenesis by leveraging these variants in a functional, regulatory context.

RESULTS

We performed expression quantitative trait locus (eQTL) analysis using genome-wide SNP genotyping and gene expression profiling of lung tissue samples from 86 COPD cases and 31 controls, testing for SNPs associated with gene expression levels. These results were integrated with a prior COPD GWAS using an ensemble statistical and network methods approach to identify relevant genes and observe them in the context of overall genetic control of gene expression to highlight co-regulated genes and disease pathways. We identified 250,312 unique SNPs and 4997 genes in the cis(local)-eQTL analysis (5% false discovery rate). The top gene from the integrative analysis was MAPT, a gene recently identified in an independent GWAS of lung function. The genes HNRNPAB and PCBP2 with RNA binding activity and the gene ACVR1B were identified in network communities with validated disease relevance.

CONCLUSIONS

The integration of lung tissue gene expression with genome-wide SNP genotyping and subsequent intersection with prior GWAS and omics studies highlighted candidate genes within COPD loci and in communities harboring known COPD genes. This integration also identified novel disease genes in sub-threshold regions that would otherwise have been missed through GWAS.

The phosphatidylinositide 3-kinase (PI3K) signaling pathway is a determinant of zileuton response in adults with asthma

Variable responsiveness to zileuton, a leukotriene antagonist used to treat asthma, may be due in part to genetic variation. While individual SNPs were previously associated with zileuton-related lung function changes, specific quantitative trait loci (QTLs) and biological pathways that may contribute have not been identified. In this study, we investigated the hypothesis that genetic variation within biological pathways is associated with zileuton response. We performed an integrative QTL mapping and pathway enrichment study to investigate data from a GWAS of zileuton response, in addition to mRNA expression profiles and leukotriene production data from lymphoblastoid cell lines (LCLs) (derived from asthmatics) that were treated with zileuton or ethanol (control). We identified 1060 QTLs jointly associated with zileuton-related differential LTB₄ production in LCLs and lung function change in patients taking zileuton, of which eight QTLs were also significantly associated with persistent LTB₄ production in LCLs following zileuton treatment (i.e., ‘poor’ responders). Four nominally significant trans-eQTLs were predicted to regulate three candidate genes (SELL, MTF2, and GAL), the expression of which was significantly reduced in LCLs following zileuton treatment. Gene and pathway enrichment analyses of QTL associations identified multiple genes and pathways, predominantly related to phosphatidyl inositol signaling via PI3K. We validated the PI3K pathway activation status in a subset of LCLs demonstrating variable zileuton-related LTB₄ production, and show that in contrast to LCLs that responded to zileuton, the PI3K pathway was activated in poor responder LCLs. Collectively, these findings demonstrate a role for the PIK3 pathway and its targets as important determinants of differential responsiveness to zileuton.

Deep Learning Methods for Predicting Disease Status Using Genomic Data

Predicting disease status for a complex human disease using genomic data is an important, yet challenging, step in personalized medicine. Among many challenges, the so-called curse of dimensionality problem results in unsatisfied performances of many state-of-art machine learning algorithms. A major recent advance in machine learning is the rapid development of deep learning algorithms that can efficiently extract meaningful features from high-dimensional and complex datasets through a stacked and hierarchical learning process. Deep learning has shown breakthrough performance in several areas including image recognition, natural language processing, and speech recognition. However, the performance of deep learning in predicting disease status using genomic datasets is still not well studied. In this article, we performed a review on the four relevant articles that we found through our thorough literature search. All four articles first used auto-encoders to project high-dimensional genomic data to a low dimensional space and then applied the state-of-the-art machine learning algorithms to predict disease status based on the low-dimensional representations. These deep learning approaches outperformed existing prediction methods, such as prediction based on transcript-wise screening and prediction based on principal component analysis. The limitations of the current deep learning approach and possible improvements were also discussed.

Asthma Is a Risk Factor for Respiratory Exacerbations Without Increased Rate of Lung Function Decline: Five-Year Follow-up in Adult Smokers From the COPDGene Study

BACKGROUND

Previous investigations in adult smokers from the COPDGene Study have shown that early-life respiratory disease is associated with reduced lung function, COPD, and airway thickening. Using 5-year follow-up data, we assessed disease progression in subjects who had experienced early-life respiratory disease. We hypothesized that there are alternative pathways to reaching reduced FEV₁ and that subjects who had childhood pneumonia, childhood asthma, or asthma-COPD overlap (ACO) would have less lung function decline than subjects without these conditions.

METHODS

Subjects returning for 5-year follow-up were assessed. Childhood pneumonia was defined by self-reported pneumonia at < 16 years. Childhood asthma was defined as self-reported asthma diagnosed by a health professional at < 16 years. ACO was defined as subjects with COPD who self-reported asthma diagnosed by a health-professional at ≤ 40 years. Smokers with and those without these early-life respiratory diseases were compared on measures of disease progression.

RESULTS

Follow-up data from 4,915 subjects were examined, including 407 subjects who had childhood pneumonia, 323 subjects who had childhood asthma, and 242 subjects with ACO. History of childhood asthma or ACO was associated with an increased exacerbation frequency (childhood asthma, P < .001; ACO, P = .006) and odds of severe exacerbations (childhood asthma, OR, 1.41; ACO, OR, 1.42). History of childhood pneumonia was associated with increased exacerbations in subjects with COPD (absolute difference [β], 0.17; P = .04). None of these early-life respiratory diseases were associated with an increased rate of lung function decline or progression on CT scans.

CONCLUSIONS

Subjects who had early-life asthma are at increased risk of developing COPD and of having more active disease with more frequent and severe respiratory exacerbations without an increased rate of lung function decline over a 5-year period.

TRIAL REGISTRY

ClinicalTrials.gov; No. NCT00608764; https://clinicaltrials.gov.

Large-scale study of clinical and biochemical characteristics of Chinese patients diagnosed with Krabbe disease

Krabbe disease (KD) is a rare disease caused by the deficiency of β-galactocerebrosidase. This study investigated 22 unrelated Chinese patients, including their clinical presentations, plasma psychosine levels and β-galactocerebrosidase gene mutations. We found the late-onset form of KD present in 82% of the patients in our study, which was more prevalent than in patients from other populations. Plasma psychosine levels were elevated in KD, which were correlated with the severity of clinical presentations. Sanger sequencing identified 8 novel mutations, including 7 missense mutations, p.H253Y, p.S259L, p.P318L, p.F350V, p.T428A, p.L530P, p.G586D, and 1 splicing mutation, c.1251+1G>A. Quantitative real-time polymerase chain reaction (PCR) and multiplex ligation-dependent probe amplification identified a novel exon 12 and 14 deletion, separately. Next generation sequencing, applied at the final step, revealed 2 missense mutant alleles missed using Sanger sequencing. The most common mutation in Chinese population is p.P154H, which accounts for 20.5% of alleles. Consistent with the higher prevalence of the late-onset form of KD, missense mutations predominated in our study, different with the common mutation types in Europe and Japan. This work was the first large-scale study of Chinese KD patients describing their clinical, biochemical and genetic characteristics, which furthered our understanding of this classical neurological lysosomal storage disease.

[Ovarian tumor associated with anti-N-methyl-D-aspartate receptor encephalitis: a report of 15 cases]

Objective: To summarize the clinical features of patients with ovarian tumor and anti-N-methyl-D-aspartate receptor(NMDAR) encephalitis, and to explore the influence of operation patterns on the prognosis. Methods: The clinical information of patients with ovarian tumor and anti-NMDAR encephalitis in The 3rd Affiliated Hospital of Sun Yat-Sen University and The Zhujiang Hospital of Southern Medical University were collected and analyzed. Results: There were 15 patients were enrolled in this study, with the average age of 24.5±5.0 years old. The most frequent first symptom was psychosis. The main clinical features were psychosis, seizures, conscious disturbance, autonomic dysfunction, dyskinesia, central hypoventilation and impaired memory. Most patients' symptoms were relieved after immunotherapy and surgery. The number of favorable prognosis of patients (mRS score 0-2) with ovariectomy was higher than that of the patients with ovarian cystectomy (5 vs 3). But the difference had no statistical significance (P=0.529). Conclusions: For young female patients with psychosis, we should be alert to the possibility of anti-NMDAR encephalitis and screen for tumor. Treated with immunotherapy and operation, most patients can get a favorable prognosis.

[Clinical characteristics of neuromyelitis optica spectrum disorders associated with syringomyelia]

Objective: To analyze the clinical characteristics of neuromyelitis optica spectrum disorders (NMOSD) associated with syringomyelia (SML). Methods: The clinical manifestations, laboratory parameters and imaging findings of 7 patients with NMOSD associated with SML during June 2008 to August 2016 from The Third Affiliated Hospital of Sun Yat-sen University were retrospectively analyzed. Results: Six patients were female and 1 was male, with ages ranging from 27-67 years, the course of the disease was 3-12 years, recurrence was 2-7 times, all the patients were cerebrospinal fluid oligoclonal bands (CSF OCB) negative, 5 patients were positive for aquaporin-4-antibody/NMO-IgG. Sensory and motor dysfunction, bowel or bladder dysfunction were the common clinical manifestation, and pain was a significant symptom. Syringomyelia was predominantly located in C4-T10, cavity length 2-6 mm, diameter 0.8-3.6 mm; 5 had lobes involvement and 6 had long segmental spinal cord involvement. Conclusions: NMOSD associated with SML had a high frequency of occurrence in female, with the clinical characteristics of limb pain, easy progression, high recurrence rate and disability rate. The anti AQP4 antibody were commonly seen in these patients. Syringomyelia was predominantly located in the lower cervical and upper thoracic spinal cord, the lobar and longitudinally extensive transverse myelitis were frequently found in patients with NMOSD associated with SML.

Transcriptomic Analysis of Lung Tissue from Cigarette Smoke-Induced Emphysema Murine Models and Human Chronic Obstructive Pulmonary Disease Show Shared and Distinct Pathways

Although cigarette smoke (CS) is the primary risk factor for chronic obstructive pulmonary disease (COPD), the underlying molecular mechanisms for the significant variability in developing COPD in response to CS are incompletely understood. We performed lung gene expression profiling of two different wild-type murine strains (C57BL/6 and NZW/LacJ) and two genetic models with mutations in COPD genome-wide association study genes (HHIP and FAM13A) after 6 months of chronic CS exposure and compared the results to human COPD lung tissues. We identified gene expression patterns that correlate with severity of emphysema in murine and human lungs. Xenobiotic metabolism and nuclear erythroid 2-related factor 2-mediated oxidative stress response were commonly regulated molecular response patterns in C57BL/6, Hhip^+/-, and Fam13a^-/- murine strains exposed chronically to CS. The CS-resistant Fam13a^-/- mouse and NZW/LacJ strain revealed gene expression response pattern differences. The Fam13a^-/- strain diverged in gene expression compared with C57BL/6 control only after CS exposure. However, the NZW/LacJ strain had a unique baseline expression pattern, enriched for nuclear erythroid 2-related factor 2-mediated oxidative stress response and xenobiotic metabolism, and converged to a gene expression pattern similar to the more susceptible wild-type C57BL/6 after CS exposure. These results suggest that distinct molecular pathways may account for resistance to emphysema. Surprisingly, there were few genes commonly modulated in mice and humans. Our study suggests that gene expression responses to CS may be largely species and model dependent, yet shared pathways could provide biologically significant insights underlying individual susceptibility to CS.

Genetic Control of Fatty Acid β-Oxidation in Chronic Obstructive Pulmonary Disease

Bioenergetics homeostasis is important for cells to sustain normal functions and defend against injury. The genetic controls of bioenergetics homeostasis, especially lipid metabolism, remain poorly understood in chronic obstructive pulmonary disease (COPD), the third leading cause of death in the world. Additionally, the biological function of most of the susceptibility genes identified from genome-wide association studies (GWASs) in COPD remains unclear. Here, we aimed to address (1) how fatty acid oxidation (FAO), specifically β-oxidation, a key lipid metabolism pathway that provides energy to cells, contributes to cigarette smoke (CS)-induced COPD; and (2) whether-and if so, how-FAM13A (family with sequence similarity 13 member A), a well-replicated COPD GWAS gene, modulates the FAO pathway. We demonstrated that CS induced expression of carnitine palmitoyltransferase 1A (CPT1A), a key mitochondrial enzyme for the FAO pathway, thereby enhancing FAO. Pharmacological inhibition of FAO by etomoxir blunted CS-induced reactive oxygen species accumulation and cell death in lung epithelial cells. FAM13A promoted FAO, possibly by interacting with and activating sirutin 1, and increasing expression of CPT1A. Furthermore, CS-induced cell death was reduced in lungs from Fam13a^-/- mice. Our results suggest that FAM13A, the COPD GWAS gene, shapes the cellular metabolic response to CS exposure by promoting the FAO pathway, which may contribute to COPD development.

Differential connectivity of gene regulatory networks distinguishes corticosteroid response in asthma

BACKGROUND

Variations in drug response between individuals have prevented us from achieving high drug efficacy in treating many complex diseases, including asthma. Genetics plays an important role in accounting for such interindividual variations in drug response. However, systematic approaches for addressing how genetic factors and their regulators determine variations in drug response in asthma treatment are lacking.

OBJECTIVE

We sought to identify key transcriptional regulators of corticosteroid response in asthma using a novel systems biology approach.

METHODS

We used Passing Attributes between Networks for Data Assimilations (PANDA) to construct the gene regulatory networks associated with good responders and poor responders to inhaled corticosteroids based on a subset of 145 white children with asthma who participated in the Childhood Asthma Management Cohort. PANDA uses gene expression profiles and published relationships among genes, transcription factors (TFs), and proteins to construct the directed networks of TFs and genes. We assessed the differential connectivity between the gene regulatory network of good responders versus that of poor responders.

RESULTS

When compared with poor responders, the network of good responders has differential connectivity and distinct ontologies (eg, proapoptosis enriched in network of good responders and antiapoptosis enriched in network of poor responders). Many of the key hubs identified in conjunction with clinical response are also cellular response hubs. Functional validation demonstrated abrogation of differences in corticosteroid-treated cell viability following siRNA knockdown of 2 TFs and differential downstream expression between good responders and poor responders.

CONCLUSIONS

We have identified and validated multiple TFs influencing asthma treatment response. Our results show that differential connectivity analysis can provide new insights into the heterogeneity of drug treatment effects.

Age, Sexual Dimorphism, and Disease Associations in the Developing Human Fetal Lung Transcriptome

The fetal origins of disease hypothesis suggests that variations in the course of prenatal lung development may affect life-long pulmonary function growth, decline, and pathobiology. Many studies support the existence of differences in the developing lung trajectory in males and females, and sex-specific differences in the prevalence of chronic lung diseases, such as asthma and bronchopulmonary dysplasia. The objectives of this study were to investigate the early developing fetal lung for transcriptomic correlates of postconception age (maturity) and sex, and their associations with chronic lung diseases. We analyzed whole-lung transcriptome profiles of 61 females and 78 males at 54-127 days postconception (dpc) from nonsmoking mothers using unsupervised principal component analysis and supervised linear regression models. We identified dominant transcriptomic correlates for postconception age and sex with corresponding gene sets that were enriched for developing lung structural and functional ontologies. We observed that the transcriptomic sex difference was not a uniform global time shift/lag, rather, lungs of males appear to be more mature than those of females before 96 dpc, and females appear to be more mature than males after 96 dpc. The age correlate gene set was consistently enriched for asthma and bronchopulmonary dysplasia genes, but the sex correlate gene sets were not. Despite sex differences in the developing fetal lung transcriptome, postconception age appears to be more dominant than sex in the effect of early fetal lung developments on disease risk during this early pseudoglandular phase of development.

Metabolomic profiling in a Hedgehog Interacting Protein (Hhip) murine model of chronic obstructive pulmonary disease

Genetic variants annotated to the hedgehog interacting protein (HHIP) are robustly associated with chronic obstructive pulmonary disease (COPD). Hhip haploinsufficiency in mice leads to increased susceptibility towards the development of emphysema following exposure to chronic cigarette smoke (CS). To explore the molecular pathways which contribute to increased susceptibility, we performed metabolomic profiling using high performance liquid chromatography tandem mass spectroscopy (LC/MS-MS) on plasma, urine, and lung tissue of Hhip^+/− heterozygotes and wild type (Hhip^+/+) C57/BL6 mice exposed to either room-air or CS for six months. Univariate comparisons between groups were made with a combined fold change ≥2 and Student’s t-test p-value < 0.05 to denote significance; associations with mean alveolar chord length (MACL), a quantitative measure of emphysema, and gene-by-environment interactions were examined using empiric Bayes-mediated linear models. Decreased urinary excretion of cotinine despite comparable plasma levels was observed in Hhip^+/− heterozygotes; a strong gene-by-smoking association was also observed. Correlations between MACL and markers of oxidative stress such as urinary methionine sulfoxide were observed in Hhip^+/− but not in Hhip^+/+ mice. Metabolite set enrichment analyses suggest reduced antioxidant capacity and alterations in macronutrient metabolism contribute to increased susceptibility to chronic CS-induced oxidative stress in Hhip haploinsufficiency states.

Detecting disease-associated genomic outcomes using constrained mixture of Bayesian hierarchical models for paired data

Detecting disease-associated genomic outcomes is one of the key steps in precision medicine research. Cutting-edge high-throughput technologies enable researchers to unbiasedly test if genomic outcomes are associated with disease of interest. However, these technologies also include the challenges associated with the analysis of genome-wide data. Two big challenges are (1) how to reduce the effects of technical noise; and (2) how to handle the curse of dimensionality (i.e., number of variables are way larger than the number of samples). To tackle these challenges, we propose a constrained mixture of Bayesian hierarchical models (MBHM) for detecting disease-associated genomic outcomes for data obtained from paired/matched designs. Paired/matched designs can effectively reduce effects of confounding factors. MBHM does not involve multiple testing, hence does not have the problem of the curse of dimensionality. It also could borrow information across genes so that it can be used for whole genome data with small sample sizes.

Functional interactors of three genome-wide association study genes are differentially expressed in severe chronic obstructive pulmonary disease lung tissue

In comparison to genome-wide association studies (GWAS), there has been poor replication of gene expression studies in chronic obstructive pulmonary disease (COPD). We performed microarray gene expression profiling on a large sample of resected lung tissues from subjects with severe COPD. Comparing 111 COPD cases and 40 control smokers, 204 genes were differentially expressed; none were at significant GWAS loci. The top differentially expressed gene was HMGB1, which interacts with AGER, a known COPD GWAS gene. Differentially expressed genes showed enrichment for putative interactors of the first three identified COPD GWAS genes IREB2, HHIP, and FAM13A, based on gene sets derived from protein and RNA binding studies, RNA-interference, a murine smoking model, and expression quantitative trait locus analyses. The gene module most highly associated for COPD in Weighted Gene Co-Expression Network Analysis (WGCNA) was enriched for B cell pathways, and shared seventeen genes with a mouse smoking model and twenty genes with previous emphysema studies. As in other common diseases, genes at COPD GWAS loci were not differentially expressed; however, using a combination of network methods, experimental studies and careful phenotype definition, we found differential expression of putative interactors of these genes, and we replicated previous human and mouse microarray results.

Gender Differences in Outcomes and Predictors of All-Cause Mortality After Percutaneous Coronary Intervention (Data from United Kingdom and Sweden)

To determine gender differences and predictors of all-cause mortality (30 days and 1 year) after percutaneous coronary intervention (PCI) in patients with stable angina pectoris and acute coronary syndrome (non-ST-elevation myocardial infarction/unstable angina pectoris and ST-elevation myocardial infarction) in the British Cardiovascular Intervention Society (BCIS) and Swedish Coronary Angiography and Angioplasty Registry (SCAAR) data sets, an analysis of prospectively collected data from 2007 to 2011 was performed. In total, 458,261 patients (BCIS: n = 368,492 [25.9% women]; Sweden: n = 89,769 [27.2% women]) who underwent PCI were included in this analysis. Using multiple regression analysis, in the BCIS registry, female gender was an independent predictor of all-cause mortality at 30 days (odds ratio [OR] 1.15, 95% CI 1.10 to 1.22, p <0.0001) and at 1 year (OR 1.08, 95% CI 1.04 to 1.12, p <0.0001) after PCI for all patients. Likewise, in the SCAAR registry, female gender was an independent predictor of all-cause mortality at 30 days (OR 1.15, 95% CI 1.05 to 1.26, p = 0.002) and 1 year (OR 1.09, 95% CI 1.03 to 1.17, p = 0.006) after PCI for all patients. In both data sets, there was no statistically significant interaction between age and gender for all-cause mortality at 30 days (BCIS, p = 0.59; SCAAR, p = 0.40) and at 1 year (BCIS, p = 0.11; SCAAR, p = 0.83). In conclusion, despite advances in care, women compared with men continue to experience higher all-cause mortality after PCI for coronary artery disease. The patient's age at the time of PCI remains a strong predictive factor of mortality in this population. Strategies and further research are warranted to better address the management of coronary artery disease in women with possibly earlier diagnosis and more tailored treatments.

Gene Expression Profiling in Blood Provides Reproducible Molecular Insights into Asthma Control

RATIONALE

Maintaining optimal symptom control remains the primary objective of asthma treatment. Better understanding of the biologic underpinnings of asthma control may lead to the development of improved clinical and pharmaceutical approaches.

OBJECTIVES

To identify molecular pathways and interrelated genes whose differential expression was associated with asthma control.

METHODS

We performed gene set enrichment analyses of asthma control in 1,170 adults with asthma, each with gene expression data derived from either whole blood (WB) or unstimulated CD4+ T lymphocytes (CD4), and a self-reported asthma control score representing either the preceding 6 months (chronic) or 7 days (acute). Our study comprised a discovery WB cohort (n = 245, chronic) and three independent, nonoverlapping replication cohorts: a second WB set (n = 448, acute) and two CD4 sets (n = 300, chronic; n = 77, acute).

MEASUREMENTS AND MAIN RESULTS

In the WB discovery cohort, we found significant overrepresentation of genes associated with asthma control in 1,106 gene sets from the Molecular Signatures Database (false discovery rate, <5%). Of these, 583 (53%) replicated in at least one replication cohort (false discovery rate, <25%). Suboptimal control was associated with signatures of eosinophilic and granulocytic inflammatory signals, whereas optimal control signatures were enriched for immature lymphocytic patterns. These signatures included two related biologic processes related to activation by TREM-1 (triggering receptor expressed on myeloid cells 1) and lipopolysaccharide.

CONCLUSIONS

Together, these results demonstrate the existence of specific, reproducible transcriptomic components in blood that vary with degree of asthma control and implicate a novel biologic target (TREM-1).

Integration of metabolomic and transcriptomic networks in pregnant women reveals biological pathways and predictive signatures associated with preeclampsia

INTRODUCTION

Preeclampsia is a leading cause of maternal and fetal mortality worldwide, yet its exact pathogenesis remains elusive.

OBJECTIVES

This study, nested within the Vitamin D Antenatal Asthma Reduction Trial (VDAART), aimed to develop integrated omics models of preeclampsia that have utility in both prediction and in the elucidation of underlying biological mechanisms.

METHODS

Metabolomic profiling was performed on first trimester plasma samples of 47 pregnant women from VDAART who subsequently developed preeclampsia and 62 controls with healthy pregnancies, using liquid-chromatography tandem mass-spectrometry. Metabolomic profiles were generated based on logistic regression models and assessed using Received Operator Characteristic Curve analysis. These profiles were compared to profiles from generated using third trimester samples. The first trimester metabolite profile was then integrated with a pre-existing transcriptomic profile using network methods.

RESULTS

In total, 72 (0.9%) metabolite features were associated (p<0.01) with preeclampsia after adjustment for maternal age, race, and gestational age. These features had moderate to good discriminatory ability; in ROC curve analyses a summary score based on these features displayed an area under the curve (AUC) of 0.794 (95%CI 0.700, 0.888). This profile retained the ability to distinguish preeclamptic from healthy pregnancies in the third trimester (AUC:0.762 (95% CI 0.663, 0.860)). Additionally, metabolite set enrichment analysis identified common pathways, including glycerophospholipid metabolism, at the two time-points. Integration with the transcriptomic signature refined these results suggesting a particular role for lipid imbalance, immune function and the circulatory system.

CONCLUSIONS

These findings suggest it is possible to develop a predictive metabolomic profile of preeclampsia. This profile is characterized by changes in lipid and amino acid metabolism and dysregulation of immune response and can be refined through interaction with transcriptomic data. However validation in larger and more diverse populations is required.

The use of Masson's trichrome staining, second harmonic imaging and two-photon excited fluorescence of collagen in distinguishing intestinal tuberculosis from Crohn's disease

AIM

Differentiation between Crohn's disease (CD) and intestinal tuberculosis (ITB) continues to be difficult. The present study investigated the collagen fibre characteristics of CD and ITB using Masson's trichrome staining, second harmonic generation (SHG) imaging and two-photon excited fluorescence (TPEF) imaging with the aim of distinguishing between them.

METHOD

The characteristics of collagen fibres in intestinal specimens from patients with CD, ITB and healthy controls were compared using Masson's trichrome staining and SHG and TPEF imaging.

RESULTS

Masson's trichrome staining showed that the content of collagen fibre (540.92 [139.61-1681.93] vs 236.17 [72.94-1108.32], P < 0.05) and fibre deposits (888.92 [315.89-3172.9] vs 498.98 [38.82-5802.31], P < 0.05) were both higher in ITB than in CD. The content of collagen fibre (594.677 [139.61-1681.93] vs 107.425 [4.66-988.7], P < 0.05) and fibre deposits (1118.4661 [315.89-5802.31] vs 340.575 [29.62-1188.87], P < 0.05) were significantly higher in lesions with granulomata than in those without. The SHG/TPEF images demonstrated that the percentage of fibrosis in ITB was also significantly higher than in CD (P < 0.05), in both surgical (13.363% ± 5.303% vs 8.322% ± 5.078%, P = 0.044) and endoscopic specimens (mean rank 13.5 vs 7.5, P = 0.023). The SHG/TPEF imaging described different distribution patterns of collagen between CD and ITB; in the former this was irregular in clumps while in ITB the collagen was arranged around caseating granulomata.

CONCLUSION

The evaluation of fibrosis in CD and ITB by Masson's trichrome staining and SHG and TPEF imaging appears to distinguish between these two diseases.

Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations

Background

Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort.

Methods

We assessed DNA methylation from whole blood samples in 362 African-American smokers in the PA-SCOPE cohort using the Illumina Infinium HumanMethylation27 BeadChip Array. Final analysis included 19302 CpG probes annotated to the nearest gene transcript after quality control. We tested methylation associations with COPD case-control status using mixed linear models. Weighted gene comethylation networks were constructed using weighted gene coexpression network analysis (WGCNA) and network modules were analyzed for association with COPD.

Results

There were five differentially methylated CpG probes significantly associated with COPD among African-Americans at an FDR less than 5 %, and seven additional probes that approached significance at an FDR less than 10 %. The top ranked gene association was MAML1, which has been shown to affect NOTCH-dependent angiogenesis in murine lung. Network modeling yielded the “yellow” and “blue” comethylation modules which were significantly associated with COPD (p-value 4 × 10^-10 and 4 × 10^-9, respectively). The yellow module was enriched for gene sets related to inflammatory pathways known to be relevant to COPD. The blue module contained the top ranked genes in the concurrent differential methylation analysis (FXYD1/LGI4, gene significance p-value 1.2 × 10^-26; MAML1, p-value 2.0 × 10^-26; CD72, p-value 2.1 × 10^-25; and LPO, p-value 7.2 × 10^-25), and was significantly associated with lung development processes in Gene Ontology gene-set enrichment analysis.

Conclusion

We identified 12 differentially methylated CpG sites associated with COPD that mapped to biologically plausible genes. Network module comethylation patterns have identified candidate genes that may be contributing to racial differences in COPD susceptibility and severity. COPD-associated comethylation modules contained genes previously associated with lung disease and inflammation and recapitulated known COPD-associated genes. The genes implicated by differential methylation and WGCNA analysis may provide mechanistic targets contributing to COPD susceptibility, exacerbations, and outcomes among African-Americans.

Trial registration

Trial Registration: NCT00774176, Registry: ClinicalTrials.gov, URL: www.clinicaltrials.gov, Date of Enrollment of First Participant: June 2004, Date Registered: 04 January 2008 (retrospectively registered).

Electronic supplementary material

The online version of this article (doi:10.1186/s12931-016-0459-8) contains supplementary material, which is available to authorized users.

[Clinical analysis of acute disseminated encephalomyelitis in 44 cases]

Objective: To investigate the clinical features in 44 patients with acute disseminated encephalomyelitis (ADEM). Methods: Consecutive ADEM patients admitted to Neurology Department of the Third Affiliated Hospital of Sun yat-sen University during August 2009 to July 2014 were enrolled.Clinical and laboratory data of the patients were reviewed and analyzed. Results: Forty-four patients with ADEM based on the 2012 criteria were recruited, including 23 male and 21 female; 9 children, 11 teenagers and 24 adults.There were 23 monophasic ADEM (23/44, 52%) and 21 multiphasic ADEM (21/44, 48%). Fourteen patients (31.8%) had definite incentive factors within 2 weeks preceding the disease onset.The commonest presenting symptoms were fever (20/44, 45%), mental disorder (18/44, 41%), disturbance of consciousness (17/44, 39%) and seizure (12/44, 27%). The average EDSS score was (4.3±1.3), and the average mRS score was (2.7±0.9). Abnormal autoimmune antibodies were detected in 10 patients.Two patients were positive for NMO-IgG, and three patients were positive for oligoclonal bands.On MRI scanning, small lesions were observed in 18 of 44 patients (18/44, 41%); large confluent white matter lesions in 10 patients (10/44, 23%); symmetric bithalamic involvement in 12 patients (12/44, 27%). Patients were mainly treated with intravenous corticosteroids (40/44, 90.9%) and immunoglobulin G ( 13/44, 29.5%) in acute phase.Regular follow-up performed in 29 patients (65.9%), and the average follow-up time was (4.2±2.3) year.A monophasic course was found in 10 patients, and multiphasic course in 19 patients.After (2.5±2.3) years, patients with multiphasic ADEM experienced their first clinical relapse, and the relapse frequency was (3.3±1.4). The average EDSS score was (3.9±2.2), and the mRS score was (2.2±1.3) in their latest relapse.In follow-up MRI for (5.3±1.9) years, lesions in 18 patients (62.1%) were partially ameliorated, while 6 patients (20.7%) persisted, and new lesions appeared in 5 patients (17.2%). For the 13 multiphasic patients with regular treatment, intravenous corticosteroids (13/13, 100.0%) and immunoglobulin G (7/13, 53.8%) were still important treatments in the acute phase, while oral steroids (12/13, 92.3%) plus immunosuppressants including azathioprine, tacrolimus, cyclosporine and rituximab were chosen in the remission phase. Conclusions: ADEM is not uncommon in adults, presenting with multiphasic course, encephalopathy features and disseminated lesions on MRI.As it shows very heterogeneous characteristics, ADEM is best viewed as a "syndrome" rather than a specific disorder.

Asthma Metabolomics and the Potential for Integrative Omics in Research and the Clinic

Asthma is a complex disease well-suited to metabolomic profiling, both for the development of novel biomarkers and for the improved understanding of pathophysiology. In this review, we summarize the 21 existing metabolomic studies of asthma in humans, all of which reported significant findings and concluded that individual metabolites and metabolomic profiles measured in exhaled breath condensate, urine, plasma, and serum could identify people with asthma and asthma phenotypes with high discriminatory ability. There was considerable consistency across the studies in terms of the reported biomarkers, regardless of biospecimen, profiling technology, and population age. In particular, acetate, adenosine, alanine, hippurate, succinate, threonine, and trans-aconitate, and pathways relating to hypoxia response, oxidative stress, immunity, inflammation, lipid metabolism and the tricarboxylic acid cycle were all identified as significant in at least two studies. There were also a number of nonreplicated results; however, the literature is not yet sufficiently developed to determine whether these represent spurious findings or reflect the substantial heterogeneity and limited statistical power in the studies and their methods to date. This review highlights the need for additional asthma metabolomic studies to explore these issues, and, further, the need for standardized methods in the way these studies are conducted. We conclude by discussing the potential of translation of these metabolomic findings into clinically useful biomarkers and the crucial role that integrated omics is likely to play in this endeavor.

The impact of genetic variation and cigarette smoke on DNA methylation in current and former smokers from the COPDGene study

DNA methylation can be affected by systemic exposures, such as cigarette smoking and genetic sequence variation; however, the relative impact of each on the epigenome is unknown. We aimed to assess if cigarette smoking and genetic variation are associated with overlapping or distinct sets of DNA methylation marks and pathways. We selected 85 Caucasian current and former smokers with genome-wide single nucleotide polymorphism (SNP) genotyping available from the COPDGene study. Genome-wide methylation was obtained on DNA from whole blood using the Illumina HumanMethylation27 platform. To determine the impact of local sequence variation on DNA methylation (mQTL), we examined the association between methylation and SNPs within 50 kb of each CpG site. To examine the impact of cigarette smoking on DNA methylation, we examined the differences in methylation by current cigarette smoking status. We detected 770 CpG sites annotated to 708 genes associated at an FDR < 0.05 in the cis-mQTL analysis and 1,287 CpG sites annotated to 1,242 genes, which were nominally associated in the smoking-CpG association analysis (P(unadjusted) < 0.05). Forty-three CpG sites annotated to 40 genes were associated with both SNP variation and current smoking; this overlap was not greater than that expected by chance. Our results suggest that cigarette smoking and genetic variants impact distinct sets of DNA methylation marks, the further elucidation of which may partially explain the variable susceptibility to the health effects of cigarette smoking. Ascertaining how genetic variation and systemic exposures differentially impact the human epigenome has relevance for both biomarker identification and therapeutic target development for smoking-related diseases.