scholarly journals Temporal Stability and Determinants of White Blood Cell DNA Methylation in the Breakthrough Generations Study

2014 ◽  
Vol 24 (1) ◽  
pp. 221-229 ◽  
Author(s):  
James M. Flanagan ◽  
Mark N. Brook ◽  
Nick Orr ◽  
Katarzyna Tomczyk ◽  
Penny Coulson ◽  
...  
2018 ◽  
Author(s):  
Meaghan J Jones ◽  
Louie Dinh ◽  
Hamid Reza Razzaghian ◽  
Olivia de Goede ◽  
Julia L MacIsaac ◽  
...  

AbstractBackgroundDNA methylation profiling of peripheral blood leukocytes has many research applications, and characterizing the changes in DNA methylation of specific white blood cell types between newborn and adult could add insight into the maturation of the immune system. As a consequence of developmental changes, DNA methylation profiles derived from adult white blood cells are poor references for prediction of cord blood cell types from DNA methylation data. We thus examined cell-type specific differences in DNA methylation in leukocyte subsets between cord and adult blood, and assessed the impact of these differences on prediction of cell types in cord blood.ResultsThough all cell types showed differences between cord and adult blood, some specific patterns stood out that reflected how the immune system changes after birth. In cord blood, lymphoid cells showed less variability than in adult, potentially demonstrating their naïve status. In fact, cord CD4 and CD8 T cells were so similar that genetic effects on DNA methylation were greater than cell type effects in our analysis, and CD8 T cell frequencies remained difficult to predict, even after optimizing the library used for cord blood composition estimation. Myeloid cells showed fewer changes between cord and adult and also less variability, with monocytes showing the fewest sites of DNA methylation change between cord and adult. Finally, including nucleated red blood cells in the reference library was necessary for accurate cell type predictions in cord blood.ConclusionChanges in DNA methylation with age were highly cell type specific, and those differences paralleled what is known about the maturation of the postnatal immune system.


Author(s):  
Mitali Ray ◽  
Lacey W. Heinsberg ◽  
Yvette P. Conley ◽  
James M. Roberts ◽  
Arun Jeyabalan ◽  
...  

Objective: We utilized epigenome-wide DNA methylation data to estimate/compare white blood cell (WBC) proportions in plasma across preeclamptic (case) and uncomplicated, normotensive (control) pregnancy. Methods: We previously collected methylation data using Infinium MethylationEPIC Beadchips during the three trimesters in 28 cases and 28 controls (21 Black, 7 White participants/group). We employed the Houseman regression calibration method to estimate and compare neutrophil, monocyte, B cell, NK cell, CD4+ T and CD8+ T cell proportions across pregnancy and between cases and controls. Results: We observed changes in WBC proportions across pregnancy within cases and controls that varied by cell type and race. Neutrophils represented the largest WBC mean proportion in all three trimesters for cases (Mean+/-SD: 67.2+/-9.6% to 74.4+/-12%) and controls (64.2+/-11% to 74.0+/-7.9%). Mean B cell proportions were significantly lower in cases than controls in Trimester 1 (5.25+/-0.02% versus 6.30+/-0.02%, p=0.02). The remaining mean cell proportions did not significantly differ in the overall sample. Stratified analyses revealed race-specific differences. In White participants (n=14): (1) neutrophil proportions were significantly higher in cases in Trimester 1 (p=0.04), but significantly lower in Trimester 2 (p=0.02), (2) B cell proportions were significantly lower in cases in Trimester 1 (p=0.001). No significant differences were detected among Black participants (n=42). Conclusions: Although chronic inflammation characterizes preeclampsia, few studies have investigated WBCs across pregnancy. We report differences between cases and controls across pregnancy. Our findings in a small sample demonstrate the need for additional studies investigating the relationship between race and WBCs in pregnancy, which could provide insight into preeclampsia pathophysiology.


2016 ◽  
Vol 104 (2) ◽  
pp. 518-525 ◽  
Author(s):  
Mathias Rask-Andersen ◽  
Nathalie Bringeland ◽  
Emil K Nilsson ◽  
Marcus Bandstein ◽  
Marcela Olaya Búcaro ◽  
...  

Epigenetics ◽  
2012 ◽  
Vol 7 (8) ◽  
pp. 868-874 ◽  
Author(s):  
Lissette Delgado-Cruzata ◽  
Hui-Chen Wu ◽  
Mary Perrin ◽  
Yuyan Liao ◽  
Maya A. Kappil ◽  
...  

2021 ◽  
Vol 13 (1) ◽  
Author(s):  
Cilla Söderhäll ◽  
Lovisa E. Reinius ◽  
Pertteli Salmenperä ◽  
Massimiliano Gentile ◽  
Nathalie Acevedo ◽  
...  

Abstract Background Methylation of DNA at CpG sites is an epigenetic modification and a potential modifier of disease risk, possibly mediating environmental effects. Currently, DNA methylation is commonly assessed using specific microarrays that sample methylation at a few % of all methylated sites. Methods To understand if significant information on methylation can be added by a more comprehensive analysis of methylation, we set up a quantitative method, bisulfite oligonucleotide-selective sequencing (Bs-OS-seq), and compared the data with microarray-derived methylation data. We assessed methylation at two asthma-associated genes, IL13 and ORMDL3, in blood samples collected from children with and without asthma and fractionated white blood cell types from healthy adult controls. Results Our results show that Bs-OS-seq can uncover vast amounts of methylation variation not detected by commonly used array methods. We found that high-density methylation information from even one gene can delineate the main white blood cell lineages. Conclusions We conclude that high-resolution methylation studies can yield clinically important information at selected specific loci missed by array-based methods, with potential implications for future studies of methylation-disease associations.


Blood ◽  
2021 ◽  
Vol 138 (Supplement 1) ◽  
pp. 1228-1228
Author(s):  
Ming Hong ◽  
Qian Sun ◽  
Wenjie Liu ◽  
Han Zhu ◽  
Yu Zhu ◽  
...  

Abstract Introduction: AML is an extremely heterogenous disease which poses fundamental challenges in developing effective treatment regimens, while simultaneously highlighting the critical need for more personalized therapy. This investigation explores AML patients who would benefit the most from the relatively low intensive regimen D-CAG or intensive therapy. Methods: A total of 331 patients with AML who were treated with intensive chemotherapy (young patients, n=179) or D-CAG regimen (older patients, n=152) were enrolled in this study.The young patients received IA regimen (idarubicin 10-12 mg/m 2 on days 1 to 3 and cytarabine 100 mg/m 2/d on days 1 to 7) as induction. A total of 37 patients were recipients of allogeneic hematopoietic stem cell transplantation (allo-HSCT) and 27 patients were recipients of autologous HSCT. Patients who were unsuitable for HSCT were subjected to post-remission therapy consisting of 2-4 courses of intermediate to high dose cytarabine (cytarabine 2-3 g/m 2 twice daily on days 1-3). The D-CAG regimen (decitabine 15 mg/m 2 intravenously on days 1-5, cytarabine 10 mg/m 2 subcutaneous injection twice daily on days 3-9, aclarubicin 8-10 mg/m 2/d on days 3-6, and G-CSF 300 μg/d for priming until white blood cell count was >20×10 9/L) was given to the older patients. An additional 4-6 cycles of D-CAG were administered to those who achieved CR. Those who failed to obtain CR after two cycles of D-CAG were given the option of palliative care or alternative treatments. None of the patients in this subgroup received allo- or auto-HSCT.Clinical outcomes were retrospectively analyzed for patients belonging to the two treatment arms. Results: The median age was 67 (range, 60 to 86 years) and 36 years (range, 14 to 59 years) in D-CAG and IA cohort, respectively. In the D-CAG cohort, there were significantly more patients demonstrating an Eastern Cooperative Oncology Group performance status (ECOG PS) score of 2-3 in contrast to the IA cohort (17.1% vs. 2.2%, P< 0.0001). Conventional cytogenetic examination was conducted in all patients. However, sufficient metaphase data was not available for 15 of these patients. Based on the 2017 ELN cytogenetic risk classification, patients were risk stratified based on the presence of molecular and cytogenetic aberrances upon diagnosis. A total of 114 patients (34.4%) were determined to possess favorable-risk, 106 patients (32.0%) were intermediate-risk and 96 patients (29.0%) were poor-risk. There were significantly more patients in the favorable-risk category and less in the poor-risk category in the IA cohort as in contrast to the D-CAG cohort (favorable-risk: 47.5% vs. 19.1%, P< 0.0001; poor-risk: 21.2% vs. 38.2%, P=0.001). Older patients harbored significantly more complex, monosomal karyotypes and abnormalities in chromosomes 5 and/or 7 (-5/5q- and/or -7/7q-) in comparison to young patients. Clinical features of gender, white blood cell (WBC), hemoglobin and platelet count at diagnosis as well as percentage of blasts in bone marrow, were similar between the two cohorts. Our data revealed that the young patients had significantly better complete remission (CR) rate (80.4% vs.67.1%, P=0.0051) and median overall survival (OS) (38 vs. 15 months, P<0.0001) compared to older patients. However, the objective response rate (ORR) and median OS of the intermediate- and high-risk groups was comparable between older and young patients who were not recipients of allo-HSCT. The median OS was comparable between D-CAG-treated patients with or without FLT3-ITD, DNMT3A, IDH2, TP53 and as well as DNA methylation associated gene mutations, whereas patients treated with intensive therapy who bore these mutations demonstrated markedly lower median OS in contrast to those bore wild-type genes. Individuals with biallelic CEBPA and NRAS mutations were more likely to benefit from intensive chemotherapy regimens. Conclusions: Intensive chemotherapy had little effect on the prognosis of intermediate- or high-risk young patients who did not undergo allo-HSCT. Patients harboring FLT3-ITD, DNMT3A, IDH2, TP53 and DNA methylation associated mutations were found to benefit more from the D-CAG regimen in comparison to intensive chemotherapy. Figure 1 Figure 1. Disclosures No relevant conflicts of interest to declare.


2018 ◽  
Vol 64 (3) ◽  
pp. 566-575 ◽  
Author(s):  
Joana Frobel ◽  
Tanja Božić ◽  
Michael Lenz ◽  
Peter Uciechowski ◽  
Yang Han ◽  
...  

Abstract BACKGROUND White blood cell counts are routinely measured with automated hematology analyzers, by flow cytometry, or by manual counting. Here, we introduce an alternative approach based on DNA methylation (DNAm) at individual CG dinucleotides (CpGs). METHODS We identified candidate CpGs that were nonmethylated in specific leukocyte subsets. DNAm levels (ranging from 0% to 100%) were analyzed by pyrosequencing and implemented into deconvolution algorithms to determine the relative composition of leukocytes. For absolute quantification of cell numbers, samples were supplemented with a nonmethylated reference DNA. RESULTS Conventional blood counts correlated with DNAm at individual CpGs for granulocytes (r = −0.91), lymphocytes (r = −0.91), monocytes (r = −0.74), natural killer (NK) cells (r = −0.30), T cells (r = −0.73), CD4+ T cells (r = −0.41), CD8+ T cells (r = −0.88), and B cells (r = −0.66). Combination of these DNAm measurements into the “Epi-Blood-Count” provided similar precision as conventional methods in various independent validation sets. The method was also applicable to blood samples that were stored at 4 °C for 7 days or at −20 °C for 3 months. Furthermore, absolute cell numbers could be determined in frozen blood samples upon addition of a reference DNA, and the results correlated with measurements of automated analyzers in fresh aliquots (r = 0.84). CONCLUSIONS White blood cell counts can be reliably determined by site-specific DNAm analysis. This approach is applicable to very small blood volumes and frozen samples, and it allows for more standardized and cost-effective analysis in clinical application.


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