scholarly journals Epigenome-wide association study using prediagnostic bloods identifies a new genomic region (near TMEM204 and IFT140) associated with pancreatic cancer risk

2020 ◽  
Author(s):  
Dominique S. Michaud ◽  
Mengyuan Ruan ◽  
Devin C. Koestler ◽  
Dong Pei ◽  
Carmen J. Marsit ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Dna Methylation ◽  
Study Design ◽  
Peripheral Blood ◽  
Association Studies ◽  
Health Study ◽  
Blood Collection ◽  
Blood Draw ◽  
Prospective Study Design

AbstractBackgroundEpigenome-wide association studies (EWAS) using peripheral blood have identified specific sites of DNA methylation associated with risk of various cancers and may hold promise to identify novel biomarkers of risk; however, few studies have been performed for pancreatic cancer and none using a prospective study design.MethodsUsing a nested case-control study design, incident pancreatic cancer cases and matched controls were identified from participants who provided blood at baseline in three prospective cohort studies (Nurses’ Health Study, Health Professionals Follow-up Study and Physicians’ Health Study). DNA methylation levels were measured in DNA extracted from leukocytes using the Illumina MethylationEPIC array. Average follow-up period for this analysis was 13 years.ResultsA region in chromosome 16 near genesTMEM204 and IFT140 was identified as being differentially methylated in cases and controls. For some CpGs in the region, the associations were stronger with shorter time to diagnosis (e.g., OR= 5.95, 95% CI = 1.52-23.12, for top vs bottom quartile, for <5 years between blood draw and cancer diagnosis) but associations remained significantly higher even when cases were diagnosed over 10 years after blood collection. Statistically significant differences in DNA methylation levels were also observed in the gastric secretion pathway using GSEA analysis.ConclusionsChanges in DNA methylation in peripheral blood may mark alterations in metabolic or immune pathways (potentially including alterations in immune subtypes) that play a role in pancreatic cancer. Identifying new biological pathways in carcinogenesis of pancreatic cancer using EWAS approach could provide new opportunities for improving treatment and prevention.

scholarly journals Epigenome-Wide Association Study Using Prediagnostic Bloods Identifies New Genomic Regions Associated With Pancreatic Cancer Risk

2020 ◽  
Vol 4 (5) ◽  
Author(s):  
Dominique S Michaud ◽  
Mengyuan Ruan ◽  
Devin C Koestler ◽  
Dong Pei ◽  
Carmen J Marsit ◽  
...  
Keyword(s):  
Pancreatic Cancer ◽  
Dna Methylation ◽  
Study Design ◽  
Peripheral Blood ◽  
Association Studies ◽  
Gene Set Enrichment Analysis ◽  
Blood Collection ◽  
Blood Draw ◽  
Genomic Regions ◽  
Prospective Study Design

Abstract Background Epigenome-wide association studies using peripheral blood have identified specific sites of DNA methylation associated with risk of various cancers and may hold promise to identify novel biomarkers of risk; however, few studies have been performed for pancreatic cancer and none using a prospective study design. Methods Using a nested case-control study design, incident pancreatic cancer cases and matched controls were identified from participants who provided blood at baseline in 3 prospective cohort studies. DNA methylation levels were measured in DNA extracted from leukocytes using the Illumina MethylationEPIC array. Average follow-up period for this analysis was 13 years. Results Several new genomic regions were identified as being differentially methylated in cases and controls; the 5 strongest associations were observed for CpGs located in genes TMEM204/IFT140, MFSD6L, FAM134B/RETREG1, KCNQ1D, and C6orf227. For some CpGs located in chromosome 16p13.3 (near genes TMEM204 and IFT140), associations were stronger with shorter time to diagnosis (eg, odds ratio [OR] = 5.95, 95% confidence interval [CI] = 1.52 to 23.12, for top vs bottom quartile, for &lt;5 years between blood draw and cancer diagnosis), but associations remained statistically significantly higher even when cases were diagnosed over 10 years after blood collection. Statistically significant differences in DNA methylation levels were also observed in the gastric secretion pathway using Gene Set Enrichment Analysis (GSEA) analysis. Conclusions Changes in DNA methylation in peripheral blood may mark alterations in metabolic or immune pathways that play a role in pancreatic cancer. Identifying new biological pathways in carcinogenesis of pancreatic cancer using epigenome-wide association studies approach could provide new opportunities for improving treatment and prevention.

Abstract MP54: Circulating Prolactin Concentrations and Risk of Type 2 Diabetes in US Women

Circulation ◽  
2018 ◽  
Vol 137 (suppl_1) ◽  
Author(s):  
Jun Li ◽  
Megan S Rice ◽  
Tianyi Huang ◽  
Sue Hankinson ◽  
Charles Clevenger ◽  
...  
Keyword(s):  
Type 2 Diabetes ◽  
Menopausal Status ◽  
Health Study ◽  
Blood Collection ◽  
Plasma Prolactin ◽  
Inverse Association ◽  
Total Plasma ◽  
Blood Draw

Background: Prolactin, a multifunctional hormone, is involved in regulating insulin sensitivity and glucose homeostasis in experimental and cross-sectional human studies. However, whether circulating levels of prolactin are associated with risk of type 2 diabetes (T2D) remains unclear. Methods: We analyzed the prospective relationship between circulating prolactin levels and T2D risk in in the Nurses’ Health Study (NHS) and Nurses’ Health Study II (NHSII) with up to 22 years of follow-up. Total plasma prolactin was measured using immunoassay in 8,637 women free of T2D and cardiovascular disease at baseline blood collection (NHSI: 1989-1990; NHSII: 1996-1999) and a subset of 1,017 NHS women who provided a second blood sample in 2000-2002. In addition, baseline bioactive prolactin levels were measured in a subset of 2,658 women using the Nb2 lymphoma cell bioassay. We calculated hazard ratios (HRs) using Cox regressions. Results: A total of 701 incident T2D cases were documented during 159,517 person-years of follow-up. Circulating prolactin levels were inversely associated with T2D risk; the multivariable HR comparing the highest with the lowest quartile of prolactin levels was 0.71 (95% confidence interval, 0.54-0.93; P trend =0.02). The associations were similar by menopausal status and risk factors ( P >0.70 for interaction). Additional adjustment for sex hormones, growth factors, adipokine, and inflammatory markers did not alter the results. The association of bioactive prolactin with T2D risk was suggestively stronger than that of total prolactin (comparable HR=0.56 vs. 0.82 among the 2,658 women). The inverse association of total plasma prolactin with incident T2D waned linearly with time, with a significant association observed during the first 9 years after blood draw. Conclusion: High circulating prolactin level was independently associated with lower risk of T2D in women. Our findings are consistent with experimental evidence, supporting a possible protective role for prolactin in the pathogenesis of T2D.

scholarly journals Comparison of DNA Methylation Profiles of Hemostatic Genes between Liver Tissue and Peripheral Blood within Individuals

2020 ◽  
Author(s):  
Annelie Angerfors ◽  
Martina Olsson Lindvall ◽  
Björn Andersson ◽  
Staffan Nilsson ◽  
Marcela Davila Lopez ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Peripheral Blood ◽  
Liver Tissue ◽  
Association Studies ◽  
Epidemiological Studies ◽  
Methylation Pattern ◽  
Cpg Dinucleotides ◽  
Phenotypic Differences ◽  
Targeted Bisulfite Sequencing ◽  
Hemostatic Genes

AbstractDNA methylation has become increasingly recognized in the etiology of complex diseases, including thrombotic disorders. Blood is often collected in epidemiological studies for genotyping and has recently also been used to examine DNA methylation in epigenome-wide association studies. DNA methylation patterns are often tissue-specific, thus, peripheral blood may not accurately reflect the methylation pattern in the tissue of relevance. Here, we collected paired liver and blood samples concurrently from 27 individuals undergoing liver surgery. We performed targeted bisulfite sequencing for a set of 35 hemostatic genes primarily expressed in liver to analyze DNA methylation levels of >10,000 cytosine-phosphate-guanine (CpG) dinucleotides. We evaluated whether DNA methylation in blood could serve as a proxy for DNA methylation in liver at individual CpGs. Approximately 30% of CpGs were nonvariable and were predominantly hypo- (<25%) or hypermethylated (>70%) in both tissues. While blood can serve as a proxy for liver at these CpGs, the low variability renders these unlikely to explain phenotypic differences. We therefore focused on CpG sites with variable methylation levels in liver. The level of blood–liver tissue correlation varied widely across these variable CpGs; moderate correlations (0.5 ≤ r < 0.75) were detected for 6% and strong correlations (r ≥ 0.75) for a further 4%. Our findings indicate that it is essential to study the concordance of DNA methylation between blood and liver at individual CpGs. This paired blood–liver dataset is intended as a resource to aid interpretation of blood-based DNA methylation results.

scholarly journals Epigenome-wide associations between observed maternal sensitivity and offspring DNA methylation: a population-based prospective study in children

2020 ◽  
pp. 1-11
Author(s):  
Lorenza Dall’ Aglio ◽  
Jolien Rijlaarsdam ◽  
Rosa H. Mulder ◽  
Alexander Neumann ◽  
Janine F. Felix ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Stress Responses ◽  
Association Studies ◽  
Maternal Sensitivity ◽  
Population Based ◽  
Epigenetic Mechanism ◽  
Developmental Problems ◽  
Maternal Caregiving ◽  
Typical Variation

Abstract Background Experimental work in animals has shown that DNA methylation (DNAm), an epigenetic mechanism regulating gene expression, is influenced by typical variation in maternal care. While emerging research in humans supports a similar association, studies to date have been limited to candidate gene and cross-sectional approaches, with a focus on extreme deviations in the caregiving environment. Methods Here, we explored the prospective association between typical variation in maternal sensitivity and offspring epigenome-wide DNAm, in a population-based cohort of children (N = 235). Maternal sensitivity was observed when children were 3- and 4-years-old. DNAm, quantified with the Infinium 450 K array, was extracted at age 6 (whole blood). The influence of methylation quantitative trait loci (mQTLs), DNAm at birth (cord blood), and confounders (socioeconomic status, maternal psychopathology) was considered in follow-up analyses. Results Genome-wide significant associations between maternal sensitivity and offspring DNAm were observed at 13 regions (p < 1.06 × 10−07), but not at single sites. Follow-up analyses indicated that associations at these regions were in part related to genetic factors, confounders, and baseline DNAm levels at birth, as evidenced by the presence of mQTLs at five regions and estimate attenuations. Robust associations with maternal sensitivity were found at four regions, annotated to ZBTB22, TAPBP, ZBTB12, and DOCK4. Conclusions These findings provide novel leads into the relationship between typical variation in maternal caregiving and offspring DNAm in humans, highlighting robust regions of associations, previously implicated in psychological and developmental problems, immune functioning, and stress responses.

Prediagnostic Neurofilament Light Chain Levels in Amyotrophic Lateral Sclerosis

Neurology ◽  
2021 ◽  
pp. 10.1212/WNL.0000000000012632
Author(s):  
Kjetil Bjornevik ◽  
Eilis J. O'Reilly ◽  
Samantha Molsberry ◽  
Laurence N. Kolonel ◽  
Loic Le Marchand ◽  
...  
Keyword(s):  
Light Chain ◽  
Conditional Logistic Regression ◽  
Disease Diagnosis ◽  
Health Study ◽  
Plasma Samples ◽  
Blood Draw ◽  
Neurofilament Light Chain ◽  
Neurofilament Light ◽  
Rate Ratios

Objective:To assess whether plasma neurofilament light chain (NfL) levels are elevated before ALS diagnosis and to evaluate whether pre-diagnostic NfL levels are associated with metabolic alterations.Methods:We conducted a matched case-control study nested in three large prospective US cohorts (the Nurses’ Health Study, the Health Professionals Follow-up Study, and the Multiethnic Cohort Study), and identified 84 individuals who developed ALS during follow-up and had available plasma samples prior to disease diagnosis. For each ALS case, we randomly selected controls from those who were alive at the time of the case diagnosis and matched on birth year, sex, race/ethnicity, fasting status, cohort, and time of blood draw. We measured NfL in the plasma samples and used conditional logistic regression to estimate rate ratios (RRs) and 95% confidence intervals (CIs) for ALS, adjusting for body mass index, smoking, physical activity, and urate levels.Results:Higher NfL levels were associated with a higher ALS risk in plasma samples collected within 5 years of the ALS diagnosis (RR per 1 standard deviation [SD] increase: 2.68, 95% CI: 1.18-6.08), but not in samples collected further away from the diagnosis (RR per 1 SD increase 1.16, 95% CI: 0.78-1.73). A total of 21 metabolites were correlated with pre-diagnostic NfL levels in ALS cases (p < 0.05), but none of these remained significant after multiple comparison adjustments.Conclusions:Plasma NfL levels were elevated in pre-diagnostic ALS cases, indicating that NfL may be a useful biomarker already in the earliest stages of the disease.Classification of Evidence:This study provides Class II evidence that plasma NfL levels are elevated in pre-diagnostic ALS patients.

scholarly journals Dietary Pattern and Risk of Multiple Myeloma in Two Large Prospective US Cohort Studies

2019 ◽  
Vol 3 (2) ◽  
Author(s):  
Dong Hoon Lee ◽  
Teresa T Fung ◽  
Fred K Tabung ◽  
Graham A Colditz ◽  
Irene M Ghobrial ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Dietary Pattern ◽  
Association Studies ◽  
Positive Association ◽  
Healthy Eating Index ◽  
Health Study ◽  
Men Health ◽  
Cox Proportional Hazard Models ◽  
Inflammatory Pattern

AbstractBackgroundThe limited data on specific dietary components and risk of multiple myeloma (MM) show no consistent association. Studies have not examined the association of dietary pattern with MM risk.MethodsIn prospective cohorts of 69 751 women (Nurses’ Health Study, 1984–2014) and 47 232 men (Health Professionals Follow-up Study, 1986–2014), we examined the association between dietary pattern and risk of MM using Cox proportional hazard models. Diet was assessed repeatedly every 4 years with food frequency questionnaires and was used to calculate dietary patterns including the Alternate Healthy Eating Index-2010, Alternate Mediterranean Diet, Dietary Approaches to Stop Hypertension, Prudent and Western patterns, the empirical dietary inflammatory pattern (EDIP), and empirical dietary indices for insulin resistance (EDIR) and hyperinsulinemia (EDIH).ResultsDuring 2 792 257 person-years of follow-up, we identified 478 incident MM cases (215 women, 263 men). In men, high EDIP was statistically significantly associated with a 16% increase in MM risk (hazard ratio [HR] = 1.16, 95% confidence interval [CI] = 1.02 to 1.32 per 1-SD increase). Moreover, EDIR and EDIH had a suggestive positive association (EDIR: HR = 1.09, 95% CI = 0.96 to 1.24; and EDIH: HR = 1.11, 95% CI = 0.97 to 1.28 per 1-SD increase). We observed no other associations with MM risk in men and no associations for any dietary pattern with MM risk in women.ConclusionsWe present the first evidence for a role of diets with higher inflammatory or insulinemic potential in MM development. Further studies are warranted to explore these associations in other populations, including the apparent restriction to men.

Known colorectal cancer susceptibility loci and survival after colorectal cancer diagnosis.

2012 ◽  
Vol 30 (4_suppl) ◽  
pp. 394-394 ◽  
Author(s):  
Amanda Phipps ◽  
Xabier Garcia-Albeniz ◽  
Carolyn Hutter ◽  
Emily White ◽  
Charles S. Fuchs ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Overall Survival ◽  
Fixed Effects ◽  
Cancer Susceptibility ◽  
Association Studies ◽  
Cox Proportional Hazards ◽  
Health Study ◽  
Genome Wide Association Studies ◽  
Increased Risk

394 Background: Beyond clinicopathologic stage, there are few established markers of prognosis in colorectal cancer (CRC). Recent genome-wide association studies have identified 17 germline single nucleotide polymorphisms (SNPs) significantly associated with incident CRC. However, it is unclear if these CRC susceptibility SNPs influence survival after CRC diagnosis. Although the functionality of many of these SNPs remains unknown, a few, including rs4939827 in SMAD7, map to genes with plausible biological mechanisms associated with both cancer risk and prognosis. We examined 17 CRC susceptibility SNPs in relation to survival after CRC diagnosis. Methods: We genotyped 2,611 men and women enrolled in five prospective cohort studies who were diagnosed with invasive CRC during study follow-up: the Physicians’ Health Study (N=281), Health Professionals Follow-up Study (N=268), Nurses’ Health Study (N=367), Vitamins and Lifestyle Study (N=281), and the Women’s Health Initiative (N=1414). Analyses were limited to Caucasians with known vital status, cause of death, and survival time. We used Cox proportional hazards regression to assess associations between each SNP and CRC-specific and overall survival in study-specific models adjusted for age, sex, and stage; SNPs were modeled additively to reflect associations per copy of the minor allele. Study-specific results were combined via fixed-effects meta-analysis. Results: The G allele in rs4939827 was associated with poorer CRC-specific survival [hazard ratio (HR)=1.16, p=0.02] and overall survival (HR=1.13, p=0.03) in CRC patients. The A alleles in rs10795668 and in rs4925386 were associated with a 1.14-fold increased risk of overall mortality (both p-values=0.03) but not CRC-specific mortality. Other evaluated SNPs were not associated with survival. Conclusions: Genetic variation in rs4939827 (SMAD7) is associated with CRC-specific and overall survival. These results suggest that SMAD7 may have a role in CRC progression, and provide proof-of-principle that common germline variation may provide prognostic information beyond traditional considerations such as stage.

scholarly journals Competing risk of mortality in association studies of non-fatal events

PLoS ONE ◽  
2021 ◽  
Vol 16 (8) ◽  
pp. e0255313
Author(s):  
Petra Buzkova
Keyword(s):  
Cardiovascular Health ◽  
Association Studies ◽  
Population Based ◽  
Competing Risk ◽  
Health Study ◽  
Cardiovascular Health Study ◽  
Subdistribution Hazard ◽  
Hazard Regression ◽  
Risk Of Mortality

In geriatric research of non-fatal events, participants often die during the study follow-up without having the non-fatal event of interest. Cause-specific (CS) hazard regression and Fine-Gray (FG) subdistribution hazard regression are the two most common estimation approaches addressing such competing risk. We explain how the conventional CS approach and the FG approach differ and why many FG estimates of associations are counter-intuitive. Additionally, we clarify the indirect link between models for hazard and models for cumulative incidence. The methodologies are contrasted on data from the Cardiovascular Health Study, a population-based study in adults aged 65 years and older.

Abstract TP232: A Biomarker Algorithm that Represents Time from Stroke Symptom Onset

Stroke ◽  
2013 ◽  
Vol 44 (suppl_1) ◽  
Author(s):  
Danielle N Doll ◽  
Steven D Brooks ◽  
Stephanie L Rellick ◽  
Reyna L VanGilder ◽  
Alan Cantor ◽  
...  
Keyword(s):  
Gene Expression ◽  
Symptom Onset ◽  
Peripheral Blood ◽  
Stroke Onset ◽  
Stroke Severity ◽  
Blood Draw ◽  
Clinical Covariates ◽  
The Mean ◽  
Mean Time

Background and Purpose: Time of onset is critical when treating ischemic stroke (IS). The purpose of this project was to investigate the use of our 9 gene profile to develop a biomarker algorithm that represents time from stroke onset for use in the clinical setting to improve utilization of tissue plasminogen activator (tPA) and streamline appropriate secondary prevention. Methods: Peripheral blood samples were collected from n=34 IS patients’ ≥18 years of age within 24 hours from symptom onset and 24-48 hours later. Total RNA was extracted from whole blood in Paxgene RNA tubes, amplified, and hybridized to Illumina HumanRef-8v2 bead chips. Gene expression was compared in a univariate manner between patients at both time points using t -test in GeneSpring. Inflation of type one error was corrected by Bonferroni. A linear regression was used to model the change in gene expression as a linear function of time when controlling for age. Results: The mean age of the sample was 71.9± (14.6 sd ) years. Mean time from symptom onset to acute blood draw was 9:29± (6:2 sd ) hours (range 2:35-23:02); to follow up blood draw was 29:24± (7.1 sd ) hours (range 18:45-43:30); and time between acute and follow up blood draw was 19:55± (3.3 sd ) hours (range 13:30-27:32). CA4 and ARG1 expression significantly decreased >1.5 fold, and LY96 expression by >2-fold between baseline and follow up. This decrease in expression was associated with an increase from time of stroke onset and remained significant for only LY96 expression when controlling for age. ARG1 and CA4 expression were significantly lower in older patients. Conclusions: Our profile provides evidence that the expression of LY96 , CA4 , and ARG1 in the peripheral blood may serve as a surrogate for determining the time of stroke onset. In clinical practice, an algorithm based on this biomarker profile and other clinical covariates could be used when time of onset is unknown. To increase the accuracy of our biomarker algorithm, it will be important to determine the effects of age, stroke severity, and other clinical covariates on the expression of these genes over time.

Sign in / Sign up

Export Citation Format

Share Document