scholarly journals Telomere length varies substantially between blood cell types in a reptile

2020 ◽  
Vol 7 (6) ◽  
pp. 192136 ◽  
Author(s):  
Mats Olsson ◽  
Nicholas J. Geraghty ◽  
Erik Wapstra ◽  
Mark Wilson
Keyword(s):  
Blood Cell ◽  
Telomere Length ◽  
Whole Blood ◽  
Phylogenetic Analyses ◽  
Natural Populations ◽  
Cell Types ◽  
Tissue Type ◽  
Telomeric Dna ◽  
Blood Cell Type ◽  
Widespread Phenomenon

Telomeres are repeat sequences of non-coding DNA-protein molecules that cap or intersperse metazoan chromosomes. Interest in telomeres has increased exponentially in recent years, to now include their ongoing dynamics and evolution within natural populations where individuals vary in telomere attributes. Phylogenetic analyses show profound differences in telomere length across non-model taxa. However, telomeres may also differ in length within individuals and between tissues. The latter becomes a potential source of error when researchers use different tissues for extracting DNA for telomere analysis and scientific inference. A commonly used tissue type for assessing telomere length is blood, a tissue that itself varies in terms of nuclear content among taxa, in particular to what degree their thrombocytes and red blood cells (RBCs) contain nuclei or not. Specifically, when RBCs lack nuclei, leucocytes become the main source of telomeric DNA. RBCs and leucocytes differ in lifespan and how long they have been exposed to ‘senescence' and erosion effects. We report on a study in which cells in whole blood from individual Australian painted dragon lizards ( Ctenophorus pictus ) were identified using flow cytometry and their telomere length simultaneously measured. Lymphocyte telomeres were on average 270% longer than RBC telomeres, and in azurophils (a reptilian monocyte), telomeres were more than 388% longer than those in RBCs. If this variation in telomere length among different blood cell types is a widespread phenomenon, and DNA for comparative telomere analyses are sourced from whole blood, evolutionary inference of telomere traits among taxa may be seriously complicated by the blood cell type comprising the main source of DNA.

scholarly journals Assessing the co-variability of DNA methylation across peripheral cells and tissues: implications for the interpretation of findings in epigenetic epidemiology

2020 ◽  
Author(s):  
Eilis Hannon ◽  
Georgina Mansell ◽  
Joe Burrage ◽  
Agnieszka Kepa ◽  
Janis Best-Lane ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Cell ◽  
Whole Blood ◽  
Cell Types ◽  
Sample Type ◽  
Cell Type ◽  
Peripheral Tissues ◽  
Multiple Loci ◽  
Blood Cell Type ◽  
Variance Explained

Summary/AbstractBackgroundMost epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated variation is specific to an individual cellular population.MethodsWe collected three peripheral tissues (whole blood, buccal and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array.ResultsWe identified significant differences in both the level and variability of DNAm between different tissues and cell types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, however, the proportion of variance explained was greater than that explained by either buccal or nasal tissues. Instead we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight.ConclusionsWe identified major differences in DNAm between blood cell types and peripheral tissues, with each sample type being characterized by a unique DNAm signature across multiple loci. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and provide important insights for the interpretation of EWAS performed in whole blood.Key MessagesWe identified major differences in DNA methylation between blood cell types and peripheral tissues, with each sample type being characterized by a unique DNA methylation signature across multiple loci.Estimates of DNAmAge and tobacco smoking from DNA methylation data can be highly variable across different sample types collected from the same individual at the same time.While individual blood cell types did predict more of the variation in whole blood compared to buccal epithelial and nasal epithelial cells, the percentage of variance explained was still small.Instead our data indicate that at the majority of sites, variation in multiple blood cell types additively combines to drive variation in DNA methylation in whole blood.There are subset of sites where variable DNA methylation detected in whole blood can be attributed to variation in a single blood cell type.

scholarly journals Assessing the co-variability of DNA methylation across peripheral cells and tissues: Implications for the interpretation of findings in epigenetic epidemiology

PLoS Genetics ◽  
2021 ◽  
Vol 17 (3) ◽  
pp. e1009443
Author(s):  
Eilis Hannon ◽  
Georgina Mansell ◽  
Emma Walker ◽  
Marta F. Nabais ◽  
Joe Burrage ◽  
...  
Keyword(s):  
Dna Methylation ◽  
T Cells ◽  
Blood Cell ◽  
Whole Blood ◽  
Association Studies ◽  
Cell Types ◽  
Peripheral Tissues ◽  
Epigenetic Epidemiology ◽  
Blood Cell Type ◽  
Multiple Cell

Most epigenome-wide association studies (EWAS) quantify DNA methylation (DNAm) in peripheral tissues such as whole blood to identify positions in the genome where variation is statistically associated with a trait or exposure. As whole blood comprises a mix of cell types, it is unclear whether trait-associated DNAm variation is specific to an individual cellular population. We collected three peripheral tissues (whole blood, buccal epithelial and nasal epithelial cells) from thirty individuals. Whole blood samples were subsequently processed using fluorescence-activated cell sorting (FACS) to purify five constituent cell-types (monocytes, granulocytes, CD4+ T cells, CD8+ T cells, and B cells). DNAm was profiled in all eight sample-types from each individual using the Illumina EPIC array. We identified significant differences in both the level and variability of DNAm between different sample types, and DNAm data-derived estimates of age and smoking were found to differ dramatically across sample types from the same individual. We found that for the majority of loci variation in DNAm in individual blood cell types was only weakly predictive of variance in DNAm measured in whole blood, although the proportion of variance explained was greater than that explained by either buccal or nasal epithelial samples. Covariation across sample types was much higher for DNAm sites influenced by genetic factors. Overall, we observe that DNAm variation in whole blood is additively influenced by a combination of the major blood cell types. For a subset of sites, however, variable DNAm detected in whole blood can be attributed to variation in a single blood cell type providing potential mechanistic insight about EWAS findings. Our results suggest that associations between whole blood DNAm and traits or exposures reflect differences in multiple cell types and our data will facilitate the interpretation of findings in epigenetic epidemiology.

scholarly journals Cord blood buffy coat DNA methylation is comparable to whole cord blood methylation

2017 ◽  
Author(s):  
John Dou ◽  
Rebecca J. Schmidt ◽  
Kelly S. Benke ◽  
Craig Newschaffer ◽  
Irva Hertz-Picciotto ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Blood Cell ◽  
Cord Blood ◽  
Whole Blood ◽  
Cell Types ◽  
Buffy Coat ◽  
Sample Type ◽  
Blood Samples ◽  
Cell Composition ◽  
Cell Counts

AbstractBackgroundCord blood DNA methylation is associated with numerous health outcomes and environmental exposures. Whole cord blood DNA reflects all nucleated blood cell types, while centrifuging whole blood separates red blood cells by generating a white blood cell buffy coat. Both sample types are used in DNA methylation studies. Cell types have unique methylation patterns and processing can impact cell distributions, which may influence comparability.ObjectivesTo evaluate differences in cell composition and DNA methylation between buffy coat and whole cord blood samples.MethodsCord blood DNA methylation was measured with the Infinium EPIC BeadChip (Illumina) in 8 individuals, each contributing buffy coat and whole blood samples. We analyzed principal components (PC) of methylation, performed hierarchical clustering, and computed correlations of mean-centered methylation between pairs. We conducted moderated t-tests on single sites and estimated cell composition.ResultsDNA methylation PCs were associated with individual (PPC1=1.4x10-9; PPC2=2.9x10-5; PPC3=3.8x10-5; PPC4=4.2x10-6; PPC5=9.9x10-13), and not with sample type (PPC1-5>0.7). Samples hierarchically clustered by individual. Pearson correlations of mean-centered methylation between paired individual samples ranged from r=0.66 to r=0.87. No individual site significantly differed between buffy coat and whole cord blood when adjusting for multiple comparisons (5 sites had unadjusted P<10-5). Estimated cell type proportions did not differ by sample type (P=0.86), and estimated cell counts were highly correlated between paired samples (r=0.99).ConclusionsDifferences in methylation and cell composition between buffy coat and whole cord blood are much lower than inter-individual variation, demonstrating that both sample preparation types can be analytically combined and compared.

Comparison of different methods for telomere length measurement in whole blood and blood cell subsets: Recommendations for telomere length measurement in hematological diseases

2017 ◽  
Vol 56 (9) ◽  
pp. 700-708 ◽  
Author(s):  
Yvonne Lisa Behrens ◽  
Kathrin Thomay ◽  
Maike Hagedorn ◽  
Juliane Ebersold ◽  
Lea Henrich ◽  
...  
Keyword(s):  
Blood Cell ◽  
Telomere Length ◽  
Whole Blood ◽  
Length Measurement ◽  
Hematological Diseases

scholarly journals Hematopoietic Lineage Transcriptome Stability and Representation in PAXgene™ Collected Peripheral Blood Utilising SPIA Single-Stranded cDNA Probes for Microarray

2008 ◽  
Vol 3 ◽  
pp. BMI.S938 ◽  
Author(s):  
Laura Kennedy ◽  
J. Keith Vass ◽  
D. Ross Haggart ◽  
Steve Moore ◽  
Michael E. Burczynski ◽  
...  
Keyword(s):  
Gene Expression ◽  
Blood Cell ◽  
Whole Blood ◽  
Peripheral Blood ◽  
Expression Profiles ◽  
Cell Types ◽  
Great Promise ◽  
Microarray Probe ◽  
Blood Samples ◽  
Transcriptional Profiles

Peripheral blood as a surrogate tissue for transcriptome profiling holds great promise for the discovery of diagnostic and prognostic disease biomarkers, particularly when target tissues of disease are not readily available. To maximize the reliability of gene expression data generated from clinical blood samples, both the sample collection and the microarray probe generation methods should be optimized to provide stabilized, reproducible and representative gene expression profiles faithfully representing the transcriptional profiles of the constituent blood cell types present in the circulation. Given the increasing innovation in this field in recent years, we investigated a combination of methodological advances in both RNA stabilisation and microarray probe generation with the goal of achieving robust, reliable and representative transcriptional profiles from whole blood. To assess the whole blood profiles, the transcriptomes of purified blood cell types were measured and compared with the global transcriptomes measured in whole blood. The results demonstrate that a combination of PAXgene™ RNA stabilising technology and single-stranded cDNA probe generation afforded by the NuGEN Ovation RNA amplification system V2™ enables an approach that yields faithful representation of specific hematopoietic cell lineage transcriptomes in whole blood without the necessity for prior sample fractionation, cell enrichment or globin reduction. Storage stability assessments of the PAXgene™ blood samples also advocate a short, fixed room temperature storage time for all PAXgene™ blood samples collected for the purposes of global transcriptional profiling in clinical studies.

Abstract WP416: Specific Transcriptome Response in Neutrophils, Monocytes and Whole Blood in Human Intracerebral Hemorrhage and Ischemic Stroke of Different Etiologies

Stroke ◽  
2020 ◽  
Vol 51 (Suppl_1) ◽  
Author(s):  
Paulina Carmona-Mora ◽  
Bradley P Ander ◽  
Glen C Jickling ◽  
Xinhua Zhan ◽  
Farah Hamade ◽  
...  
Keyword(s):  
Immune Response ◽  
Ischemic Stroke ◽  
Blood Cell ◽  
Intracerebral Hemorrhage ◽  
Whole Blood ◽  
Peripheral Blood ◽  
Receptor Gene ◽  
Cell Types ◽  
Cell Receptor ◽  
Transcriptional Responses

Understanding transcriptome changes following intracerebral hemorrhage (ICH) and ischemic stroke (IS) of different etiologies, can lead to a better understanding of the molecular and cellular pathways involved in the response to acute brain injury caused by ICH and IS. We characterized the transcriptomic profiles from ICH and different IS etiologies to identify acute molecular changes in isolated monocytes, neutrophils and in whole blood. Peripheral blood was drawn from ICH (6) and IS (33) cases (cardioembolic, large vessel and lacunar) in the first 30 ± 20 hours post-onset of symptoms. We performed whole-genome RNA sequencing of whole blood (WB), and isolated neutrophils and monocytes. Control cases (10) with vascular risk factors (diabetes and/or hypertension and/or hypercholesterolemia) were also included (VRFC). A linear regression model including the interaction diagnosis x sample subtype with p<0.05 and overlap with FDR<0.2, (fold-change>1.2) was used for identifying differentially expressed (DE) genes. Gene ontology and pathway enrichment were performed for investigating the biological context of the DE. We observed specific transcriptional responses for ICH and IS, and within IS etiologies in monocytes, neutrophils and WB. Neutrophils’ response was the strongest with highest number of DE genes in both ICH and IS and its etiologies when compared to VRFC. Most of the changes were cell-type specific and involved immune response and signal transduction pathways. For example, in ICH compared to VRFC, about half of the over-represented pathways were unique to either monocytes or neutrophils. Many pathways over-represented in WB were not over-represented in monocytes or neutrophils, signifying the importance of additional blood cell types in the immune response to ICH and IS. A T-cell receptor gene was DE in WB only, and in opposite directions in ICH and IS when compared to VRFC, thus is a good biomarker candidate. The unique expression changes in neutrophils and monocytes after ICH and IS and its subtypes underscore their involvement in IS and ICH pathophysiology. The large number of unique genes and pathways in whole blood not detected in monocytes or neutrophils signify the contribution of other peripheral blood cell types to the ICH and IS responses.

Aggregates of Reticulocytes, Monocytes and Platelets Exist in Whole Blood of Sickle Cell Patients: Roles for Plasma Fibronectin, α4 Integrins and PSGL-1.

Blood ◽  
2005 ◽  
Vol 106 (11) ◽  
pp. 2330-2330
Author(s):  
Julia E. Brittain ◽  
Shantres C. Clark ◽  
Kenneth I. Ataga ◽  
Eugene P. Orringer ◽  
Leslie V. Parise
Keyword(s):  
Sickle Cell Disease ◽  
Blood Cell ◽  
Sickle Cell ◽  
Whole Blood ◽  
Blood Cells ◽  
Cell Types ◽  
Potential Contribution ◽  
Plasma Fibronectin ◽  
Cell Disease ◽  
Color Flow

Abstract Leukocyte and platelets are understudied contributors to the overall pathology of sickle cell disease (SCD). Elevated leukocyte counts are common in these patients and correlate inversely with patient lifespan and overall disease severity. For example, a drop in neutrophil count typically predicts a patient’s response to hydroxyurea, while increased monocyte counts correlate directly with increased reporting of pain crises. Moreover, both RBCs and WBCs have been detected as components in vaso-occlusive blockages in mouse models, where adhesive RBCs appear to interact directly with WBCs at the vaso-occlusive site. Platelets are activated in SCD and are thought to promote the hypercoagulability in these patients. Despite the potential contribution of all blood cells to the pathology of sickle cell disease, neither a mechanism of adhesion between the WBC and RBC nor a role for soluble matrix proteins in this interaction has been elucidated in humans. To detect potential adhesive interactions between the blood cells in SCD, we collected whole blood into anticoagulants that spare divalent cations (PPACK or factor Xa inhibitor) and assayed for heterotypic cell associations by two and three color flow cytometry. Our results indicate that RBCs, WBCs and platelets exist in heterotypic, multi-cellular aggregates in blood from SCD patients but not unaffected (AA) individuals. By detecting monocyte specific markers, we determined that the primary WBC component of these aggregates was the monocyte, and the primary RBC was the young SS “stress” reticulocyte. Using both in vitro RBC/monocyte adhesion studies and whole blood samples, we demonstrate that α4-containing integrins on both SS RBCs and WBCs mediate this interaction by interacting directly with endogenous plasma fibronectin. Furthermore, we show that the α4 integrin on SS RBCs binds to the RGDS site in fibronectin, whereas the α4 integrin on monocytes binds to the CS-1 site in the molecule, suggesting a novel mechanism of interaction between SS RBCs and monocytes via a fibronectin bridge. Antibodies against the CS-1 binding site in fibronectin substantially disrupt the monocyte/RBC interaction in whole blood, further underscoring the role of fibronectin as a linker between the two cell types. However, platelet incorporation in the aggregate was insensitive to inhibition of the α4 integrin, but was sensitive to inhibition of PSGL-1, suggesting that platelet inclusion likely occurs via a P-selectin/PSGL-1-mediated interaction between the platelet and the monocyte. Interestingly, similar aggregates were also detected in two patients with chronic hemolysis and brisk reticulocytosis, potentially extending the relevance of such aggregates beyond SCD. Taken together our results suggest a new adhesive paradigm for SS RBCs and monocytes as central components of heterotypic blood cell aggregates that include platelets and that are present in whole blood of patients with SCD. Our data therefore illustrate a potentially pathological interaction of all major blood cell types in SCD patients that may impact vaso-occlusion and contribute to other erythrocyte disorders.

scholarly journals Correction for both common and rare cell types in blood is important to identify genes that correlate with age

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Damiano Pellegrino-Coppola ◽  
◽  
Annique Claringbould ◽  
Maartje Stutvoet ◽  
Dorret I. Boomsma ◽  
...  
Keyword(s):  
Gene Expression ◽  
Blood Cell ◽  
Whole Blood ◽  
Cell Types ◽  
Functional Enrichment ◽  
Extended Model ◽  
Initial Model ◽  
Platelet Activity ◽  
Blood Gene Expression ◽  
New Model

Abstract Background Aging is a multifactorial process that affects multiple tissues and is characterized by changes in homeostasis over time, leading to increased morbidity. Whole blood gene expression signatures have been associated with aging and have been used to gain information on its biological mechanisms, which are still not fully understood. However, blood is composed of many cell types whose proportions in blood vary with age. As a result, previously observed associations between gene expression levels and aging might be driven by cell type composition rather than intracellular aging mechanisms. To overcome this, previous aging studies already accounted for major cell types, but the possibility that the reported associations are false positives driven by less prevalent cell subtypes remains. Results Here, we compared the regression model from our previous work to an extended model that corrects for 33 additional white blood cell subtypes. Both models were applied to whole blood gene expression data from 3165 individuals belonging to the general population (age range of 18–81 years). We evaluated that the new model is a better fit for the data and it identified fewer genes associated with aging (625, compared to the 2808 of the initial model; P ≤ 2.5⨯10−6). Moreover, 511 genes (~ 18% of the 2808 genes identified by the initial model) were found using both models, indicating that the other previously reported genes could be proxies for less abundant cell types. In particular, functional enrichment of the genes identified by the new model highlighted pathways and GO terms specifically associated with platelet activity. Conclusions We conclude that gene expression analyses in blood strongly benefit from correction for both common and rare blood cell types, and recommend using blood-cell count estimates as standard covariates when studying whole blood gene expression.

scholarly journals Nucleic Acid-Sensing and Interferon-Inducible Pathways Show Differential Methylation in MZ Twins Discordant for Lupus and Overexpression in Independent Lupus Samples: Implications for Pathogenic Mechanism and Drug Targeting

Genes ◽  
2021 ◽  
Vol 12 (12) ◽  
pp. 1898
Author(s):  
Miranda Marion ◽  
Paula Ramos ◽  
Prathyusha Bachali ◽  
Adam Labonte ◽  
Kip Zimmerman ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nucleic Acid ◽  
Lupus Erythematosus ◽  
Whole Blood ◽  
Cell Types ◽  
Differential Methylation ◽  
European Ancestry ◽  
Tissue Type ◽  
Type I ◽  
Mz Twins

Systemic lupus erythematosus (SLE) is a chronic, multisystem, autoimmune inflammatory disease with genomic and non-genomic contributions to risk. We hypothesize that epigenetic factors are a significant contributor to SLE risk and may be informative for identifying pathogenic mechanisms and therapeutic targets. To test this hypothesis while controlling for genetic background, we performed an epigenome-wide analysis of DNA methylation in genomic DNA from whole blood in three pairs of female monozygotic (MZ) twins of European ancestry, discordant for SLE. Results were replicated on the same array in four cell types from a set of four Danish female MZ twin pairs discordant for SLE. Genes implicated by the epigenetic analyses were then evaluated in 10 independent SLE gene expression datasets from the Gene Expression Omnibus (GEO). There were 59 differentially methylated loci between unaffected and affected MZ twins in whole blood, including 11 novel loci. All but two of these loci were hypomethylated in the SLE twins relative to the unaffected twins. The genes harboring these hypomethylated loci exhibited increased expression in multiple independent datasets of SLE patients. This pattern was largely consistent regardless of disease activity, cell type, or renal tissue type. The genes proximal to CpGs exhibiting differential methylation (DM) in the SLE-discordant MZ twins and exhibiting differential expression (DE) in independent SLE GEO cohorts (DM-DE genes) clustered into two pathways: the nucleic acid-sensing pathway and the type I interferon pathway. The DM-DE genes were also informatically queried for potential gene–drug interactions, yielding a list of 41 drugs including a known SLE therapy. The DM-DE genes delineate two important biologic pathways that are not only reflective of the heterogeneity of SLE but may also correlate with distinct IFN responses that depend on the source, type, and location of nucleic acid molecules and the activated receptors in individual patients. Cell- and tissue-specific analyses will be critical to the understanding of genetic factors dysregulating the nucleic acid-sensing and IFN pathways and whether these factors could be appropriate targets for therapeutic intervention.

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