Methylation Data Processing Protocol & Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage

AbstractOne challenge in conducting DNA methylation-based epigenome-wide association studies (EWAS) is the appropriate cleaning and quality-checking of the methylation values to minimize biases and experimental artifacts, while simultaneously retaining potential biological signals. These issues are compounded in studies that include multiple tissue types, and/or tissues for which reference data are unavailable to assist in adjusting for cell-type mixture, for example cerebral spinal fluid (CSF). For our study that evaluated blood and CSF taken from aneurysmal subarachnoid hemorrhage (aSAH) patients, we developed a protocol to clean and quality-check genome-wide methylation levels and compared the methylomic profiles of the two tissues to determine whether blood is a suitable surrogate for CSF. CSF samples were collected from 279 aSAH patients longitudinally during the first 14 days of hospitalization, and a subset of 88 of these patients also provided blood samples within the first two days. Quality control (QC) procedures included identification and exclusion of poor performing samples and low-quality probes, functional normalization, and correction for cell-type heterogeneity via surrogate variable analysis (SVA). Significant differences in rates of poor sample performance was observed between blood (1.1% failing QC) and CSF (9.12% failing QC; p = 0.003). Functional normalization increased the concordance of methylation values among technical replicates in both CSF and blood. Likewise, SVA improved the asymptotic behavior of the test of association in a simulated EWAS under the null hypothesis. To determine the suitability of blood as a surrogate for CSF, we calculated the correlation of adjusted methylation values between blood and CSF globally and by genomic regions. Overall, mean correlation (r < 0.26) was low, suggesting that blood is not a suitable surrogate for global methylation in CSF. However, differences in the magnitude of the correlation were observed by genomic region (CpG island, shore, shelf, open sea; p < 0.001 for all) and orientation with respect to nearby genes (3’ UTR, transcription start site, exon, body, 5’ UTR; p < 0.01 for all). In conclusion, the correlation analysis and QC pipelines indicated that DNA extracted from blood was not, overall, a suitable surrogate for DNA extracted from CSF in aSAH methylomic studies.

Download Full-text

Methylation Data Processing Protocol and Comparison of Blood and Cerebral Spinal Fluid Following Aneurysmal Subarachnoid Hemorrhage

Frontiers in Genetics ◽

10.3389/fgene.2020.00671 ◽

2020 ◽

Vol 11 ◽

Cited By ~ 1

Author(s):

Annie I. Arockiaraj ◽

Dongjing Liu ◽

John R. Shaffer ◽

Theresa A. Koleck ◽

Elizabeth A. Crago ◽

...

Keyword(s):

Subarachnoid Hemorrhage ◽

Data Processing ◽

Cerebral Spinal Fluid ◽

Aneurysmal Subarachnoid Hemorrhage ◽

Spinal Fluid ◽

Methylation Data ◽

Data Processing Protocol

Download Full-text

Analysis of cerebral spinal fluid and plasma after aneurysmal subarachnoid hemorrhage by evaluating a metabolomic profile as biomarkers for early detection of arterial vasospasm

European Journal of Anaesthesiology ◽

10.1097/00003643-201306001-00319 ◽

2013 ◽

Vol 30 ◽

pp. 103-103

Author(s):

T. Triglia ◽

L. Velly ◽

J. C. Martin ◽

N. Bruder ◽

M. C. Alessi

Keyword(s):

Subarachnoid Hemorrhage ◽

Early Detection ◽

Cerebral Spinal Fluid ◽

Aneurysmal Subarachnoid Hemorrhage ◽

Spinal Fluid ◽

Metabolomic Profile ◽

Arterial Vasospasm

Download Full-text

Long-term Elevated Siglec-10 in Cerebral Spinal Fluid Heralds Better Prognosis for Patients with Aneurysmal Subarachnoid Hemorrhage

10.21203/rs.3.rs-29769/v2 ◽

2020 ◽

Keyword(s):

Subarachnoid Hemorrhage ◽

Cerebral Spinal Fluid ◽

Aneurysmal Subarachnoid Hemorrhage ◽

Spinal Fluid

Abstract The authors have requested that this preprint be withdrawn due to erroneous posting.

Download Full-text

Metabolite Profiling the Cerebral Spinal Fluid in Subarachnoid Hemorrhage: Insights into Patient Outcomes

Neurosurgery ◽

10.1093/neuros/nyz310_305 ◽

2019 ◽

Vol 66 (Supplement_1) ◽

Author(s):

Matthew J Koch ◽

Zsuzsanna Ament ◽

Christina Hansen ◽

Matthew Bevers ◽

Christopher J Stapleton ◽

...

Keyword(s):

Subarachnoid Hemorrhage ◽

Metabolite Profiling ◽

Cerebral Spinal Fluid ◽

Aneurysmal Subarachnoid Hemorrhage ◽

Delayed Cerebral Ischemia ◽

Early Time ◽

Spinal Fluid ◽

Neurologic Outcomes ◽

Phone Calls ◽

Liquid Chromatography Tandem Mass

Abstract INTRODUCTION Aneurysmal subarachnoid hemorrhage (aSAH) continues to have poor neurologic outcomes. Prior studies demonstrate elevations of CSF metabolites, specifically the structurally similar but functionally different Asymmetric and Symmetric Dimethyl Arginine (ADMA, SDMA) may correlate with vasospasm and patient outcome in smaller cohorts of patients. We performed CSF metabolite profiling of subarachnoid hemorrhage to corroborate these findings and further understand the disease. METHODS CSF of 74 aSAH patients were enrolled in a biorepository study between 2011 and 2018 and CSF from 16 electively clipped aneurysms (90 patients total), underwent metabolite profiling. CSF samples were collected at 3 time epochs (early: days 0-5 after aSAH, peak vasospasm: days 6-10, late: days 11-15). Delayed cerebral ischemia, vasospasm, Discharge and 90-d outcome were assessed retrospectively and with patient followup phone calls. CSF samples were analyzed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). A total of 155 metabolites were initially measured and quantified in each sample. Metabolites were tested for association with DCI, vasospasm and outcome using logistic regression and ANOVA performed in R. RESULTS Screening of CSF metabolite levels at 3 time epochs identified 13 candidate metabolites that were correlated with discharge mRS, and mRS at 90 d. Only (SDMA) demonstrated significantly different levels when compared to control cerebral spinal fluid, (P = .009), ADMA was not significantly different, (P = .183). Statistical analysis yielded significant correlation of SDMA concentrations at the “early” time epoch with poor mRS at 90 d on univariate and multivariate analysis (P = .001 and P = .03, respectively), with an odds ratio of 6.5 (95% CI 1.17-36.7). No significant association with vasospasm or DCI was observed. CONCLUSION SDMA, not ADMA, is associated with poor outcome after aSAH in our cohort. Further study of the role of SDMA in aSAH and its potential utility as a biomarker is warranted to better understand and treat this pathology.

Download Full-text

Abstract P133: Epigenome-Wide Association Study of Moderate-Vigorous Physical Activity in Adult African Americans Identifies Loci Near HCCA2

Circulation ◽

10.1161/circ.137.suppl_1.p133 ◽

2018 ◽

Vol 137 (suppl_1) ◽

Author(s):

Steven Nguyen ◽

Weihua Guan ◽

Chong Wu ◽

Megan Grove ◽

Rui Xia ◽

...

Keyword(s):

Physical Activity ◽

Dna Methylation ◽

Leisure Time ◽

Acute Exercise ◽

Association Studies ◽

Vigorous Physical Activity ◽

Genomic Region ◽

Epigenetic Mark ◽

Global Methylation ◽

Exercise Interventions

Regular moderate-vigorous physical activity (MVPA) reduces the risk of cardiovascular and other chronic diseases, among other important benefits at all life stages. It is hypothesized that physical activity may alter disease risk via epigenetic modifications, including potentially long-standing changes in DNA methylation as previous research has shown epigenetic changes following exercise interventions. Most existing reports examine global methylation or study acute exercise effects on DNA methylation. To our knowledge, there are no published epigenome-wide association studies (EWAS) of habitual MVPA. In this analysis, we tested associations between leisure time MVPA and genome-wide variation in CpG methylation, an epigenetic mark, in 2,601 African American participants (1,663 women; mean age 56.6 years) in the Atherosclerosis Risk in Communities (ARIC) study. The Illumina HM450K Bead Chip was used to measure methylation in 471,035 CpG sites in stored frozen leukocyte samples, from visit 2 (1990-1992) or 3 (1993-1995). Linear regression models tested the cross-sectional association of DNA methylation M-value with self-reported leisure time MVPA at the visit of sample collection, modeled as minutes of MVPA per week and by category based on the AHA guidelines for physical activity in adults (none, less than 150, or at least 150 minutes MVPA per week), adjusting for age, sex, body mass index, education, alcohol use in grams per week, smoking status, cancer status, white blood cell count, imputed cell-type proportions using the Houseman method, and batch effects with the top 30 HM450K built-in nonnegative control probe principal components. Three CpGs, cg08269485, cg20272155, and cg08966208, upstream of the cathepsin D encoding gene, CTSD, were observed to be significantly inversely associated (q<0.05, FDR) with MVPA minutes/week. This is a strongly imprinted genomic region (chr11p15.5) and the region has also been reported to include DNA methylation variants that changed in response to an exercise training intervention. Additionally, 163 CpGs that we identified in the literature to be associated with habitual MVPA were also tested using the same models. One CpG, cg07863043, upstream of the adenomatosis polyposis coli gene, APC, in the 5q22.2 genomic region, was observed to be significantly positively associated with achieving at least 150 minutes of MVPA per week compared to none (q=0.0001, FDR). APC encodes a tumor suppressor protein that is an antagonist of the Wnt signaling pathway, and is involved in carcinogenesis and embryonic development. Replication in other populations is ongoing to confirm these findings as well as to identify additional physical activity-related DNA methylation variants.

Download Full-text

Bilirubin Production and Oxidation in CSF of Patients with Cerebral Vasospasm after Subarachnoid Hemorrhage

Journal of Cerebral Blood Flow & Metabolism ◽

10.1038/sj.jcbfm.9600101 ◽

2005 ◽

Vol 25 (8) ◽

pp. 1070-1077 ◽

Cited By ~ 57

Author(s):

Gail J Pyne-Geithman ◽

Chad J Morgan ◽

Kenneth Wagner ◽

Elizabeth M Dulaney ◽

Janice Carrozzella ◽

...

Keyword(s):

Oxidative Stress ◽

Subarachnoid Hemorrhage ◽

Cerebral Vasospasm ◽

Cerebral Spinal Fluid ◽

Spinal Fluid ◽

Oxidation Products ◽

Mortality And Morbidity ◽

Delayed Cerebral Vasospasm ◽

And Oxidative Stress

Delayed cerebral vasospasm after subarachnoid hemorrhage (SAH) remains a significant cause of mortality and morbidity; however, the etiology is, as yet, unknown, despite intensive research efforts. Research in this laboratory indicates that bilirubin and oxidative stress may be responsible by leading to formation of bilirubin oxidation products (BOXes), so we investigated changes in bilirubin concentration and oxidative stress in vitro, and in cerebral spinal fluid (CSF) from SAH patients. Non-SAH CSF, a source of heme oxygenase I (HO-1), and blood were incubated, and in vitro bilirubin production measured. Cerebrospinal fluid from SAH patients was collected, categorized using stimulation of vascular smooth muscle metabolism in vitro, and information obtained regarding occurrence of vasospasm in the patients. Cerebral spinal fluid was analyzed for hemoglobin, total protein and bilirubin, BOXes, malonyldialdehyde and peroxidized lipids (indicators of an oxidizing environment), and HO-1 concentration. The formation of bilirubin in vitro requires that CSF is present, as well as whole, non-anti-coagulated blood. Bilirubin, BOXes, HO-1, and peroxidized lipid content were significantly higher in CSF from SAH patients with vasospasm, compared with nonvasospasm SAH CSF, and correlated with occurrence of vasospasm. We conclude that vasospasm may be more likely in patients with elevated BOXes. The conditions necessary for the formation of BOXes are indeed present in CSF from SAH patients with vasospasm, but not CSF from SAH patients without vasospasm.

Download Full-text

Nitric Oxide Metabolites in the Cisternal Cerebral Spinal Fluid of Patients with Subarachnoid Hemorrhage

Neurosurgery ◽

10.1097/00006123-199710000-00008 ◽

1997 ◽

Vol 41 (4) ◽

pp. 807-812 ◽

Cited By ~ 43

Author(s):

Yoshio Suzuki ◽

Koji Osuka ◽

Atsushi Noda ◽

Toshihiko Tanazawa ◽

Masakazu Takayasu ◽

...

Keyword(s):

Nitric Oxide ◽

Subarachnoid Hemorrhage ◽

Cerebral Spinal Fluid ◽

Spinal Fluid ◽

Nitric Oxide Metabolites

Download Full-text

Genetic Determinants of Cerebral Vasospasm, Delayed Cerebral Ischemia, and Outcome after Aneurysmal Subarachnoid Hemorrhage

Journal of Cerebral Blood Flow & Metabolism ◽

10.1038/jcbfm.2009.278 ◽

2010 ◽

Vol 30 (4) ◽

pp. 676-688 ◽

Cited By ~ 21

Author(s):

Andrew F Ducruet ◽

Paul R Gigante ◽

Zachary L Hickman ◽

Brad E Zacharia ◽

Eric J Arias ◽

...

Keyword(s):

Subarachnoid Hemorrhage ◽

Cerebral Ischemia ◽

Cerebral Vasospasm ◽

Vascular Reactivity ◽

Aneurysmal Subarachnoid Hemorrhage ◽

Association Studies ◽

Genetic Research ◽

Delayed Cerebral Ischemia ◽

Cerebral Injury ◽

Genetic Determinants

Despite extensive effort to elucidate the cellular and molecular bases for delayed cerebral injury after aneurysmal subarachnoid hemorrhage (aSAH), the pathophysiology of these events remains poorly understood. Recently, much work has focused on evaluating the genetic underpinnings of various diseases in an effort to delineate the contribution of specific molecular pathways as well as to uncover novel mechanisms. The majority of subarachnoid hemorrhage genetic research has focused on gene expression and linkage studies of these markers as they relate to the development of intracranial aneurysms and their subsequent rupture. Far less work has centered on the genetic determinants of cerebral vasospasm, the predisposition to delayed cerebral injury, and the determinants of ensuing functional outcome after aSAH. The suspected genes are diverse and encompass multiple functional systems including fibrinolysis, inflammation, vascular reactivity, and neuronal repair. To this end, we present a systematic review of 21 studies suggesting a genetic basis for clinical outcome after aSAH, with a special emphasis on the pathogenesis of cerebral vasospasm and delayed cerebral ischemia. In addition, we highlight potential pitfalls in the interpretation of genetic association studies, and call for uniformity of design of larger multicenter studies in the future.

Download Full-text