scholarly journals Utilization of Epigenome-wide DNA Methylation for Longitudinal Comparison of White Blood Cell Proportions Across Preeclamptic and Normotensive Pregnancy by Self-Reported Race

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.


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.





2017 ◽  
Vol 11 (11) ◽  
pp. E414-20 ◽  
Author(s):  
Alaina Garbens ◽  
Christopher J.D. Wallis ◽  
Georg Bjarnason ◽  
Girish S. Kulkarni ◽  
Avery B. Nathens ◽  
...  

Introduction: We sought to examine the relationship between preoperative platelet to white blood cell ratio (PLT/WBC), a hematological marker of the systemic inflammatory response, and postoperative infectious complications following radical nephrectomy for localized renal cell carcinoma.Methods: We performed a retrospective cohort study of patients treated with radical nephrectomy for localized kidney cancer between January 1, 2005 and December 31, 2014 (n=6235) using the American College of Surgeons (ACS) National Surgical Quality Improvement Program (NSQIP) database. Univariate and multivariate analyses were used to assess the association between PLT/ WBC ratio and 30-day infectious complications, including surgical site infection, urinary tract infection (UTI), pneumonia, and sepsis. Secondarily, we examined major complications and bleeding requiring transfusion.Results: A lower PLT/WBC ratio was associated with an increased risk of sepsis, pneumonia, and UTI rates (p<0.05 for all). Furthermore, there was a significant trend of decreasing rates of sepsis and pneumonia with increasing PLT/WBC ratio across quintiles (p<0.05 for all). On multivariate analysis, patients with the lowest PLT/WBC ratios (Quintile 1) had a two-fold risk of having a postoperative infectious complication compared to patients in the highest quintile (odds ratio [OR] 2.01; 95% confidence interval [CI] 1.42–2.86; p<0.0001). Patients in Quintile 5 had a higher risk of requiring blood transfusion than those in Quintiles 2‒4 (p<0.05 for all).Conclusions: The PLT/WBC ratio represents a widely available and novel index to predict risk of infectious and bleeding complications in patients undergoing radical nephrectomy. External validation is required and the biological underpinning of this phenomenon requires further study





2019 ◽  
Author(s):  
Lara Nonell ◽  
Juan R González

AbstractDNA methylation plays an important role in the development and progression of disease. Beta-values are the standard methylation measures. Different statistical methods have been proposed to assess differences in methylation between conditions. However, most of them do not completely account for the distribution of beta-values. The simplex distribution can accommodate beta-values data. We hypothesize that simplex is a quite flexible distribution which is able to model methylation data.To test our hypothesis, we conducted several analyses using four real data sets obtained from microarrays and sequencing technologies. Standard data distributions were studied and modelled in comparison to the simplex. Besides, some simulations were conducted in different scenarios encompassing several distribution assumptions, regression models and sample sizes. Finally, we compared DNA methylation between females and males in order to benchmark the assessed methodologies under different scenarios.According to the results obtained by the simulations and real data analyses, DNA methylation data are concordant with the simplex distribution in many situations. Simplex regression models work well in small sample size data sets. However, when sample size increases, other models such as the beta regression or even the linear regression can be employed to assess group comparisons and obtain unbiased results. Based on these results, we can provide some practical recommendations when analyzing methylation data: 1) use data sets of at least 10 samples per studied condition for microarray data sets or 30 in NGS data sets, 2) apply a simplex or beta regression model for microarray data, 3) apply a linear model in any other case.



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


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 &gt;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&lt; 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&lt; 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&lt;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.



Blood ◽  
2021 ◽  
Author(s):  
Megumu Fujihara ◽  
Ritsu Sakata ◽  
Noriaki Yoshida ◽  
Kotaro Ozasa ◽  
Dale L Preston ◽  
...  

Epidemiological data have provided limited and inconsistent evidence on the relationship between radiation exposure and lymphoid neoplasms. We classified 553 lymphoid neoplasm cases diagnosed between 1950 and 1994 in the Life Span Study (LSS) cohort of atomic bomb survivors into WHO subtypes. Mature B-cell neoplasms represented 58%, mature T-cell and NK-cell neoplasms 20%; precursor cell neoplasms, 5%, and Hodgkin lymphoma, 3%; with the remaining 15% classified as non-Hodgkin lymphoid neoplasms or lymphoid neoplasms, not otherwise specified. We used Poisson regression methods to assess the relationship between radiation exposure and the more common subtypes. As in earlier reports, a significant dose response for non-Hodgkin lymphoid neoplasms as a group was seen for males but not females. However, subtype analyses showed that radiation dose was strongly associated with increased precursor cell neoplasms rates, with an estimated excess relative risk per Gy of 16 (95% Confidence interval: 7.0, &gt;533) at age 50. The current data based primarily of tissue-based diagnoses suggest that the association between radiation dose and lymphoid neoplasms as a group is largely driven by the radiation effect on precursor cell neoplasms while presenting no evidence of a radiation dose response for major categories of mature cell neoplasms, either B- or T-/NK-cell, or more specific disease entities (diffuse large B-cell lymphoma, plasma cell myeloma, adult T-cell leukemia/lymphoma) or Hodgkin lymphoma.



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