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.

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.

scholarly journals The Numerical Predominance and Large Transcriptome Differences of Neutrophils in Peripheral Blood Together Inevitably Account for a Reported Pulmonary Tuberculosis Signature

2017 ◽  
Vol 2017 ◽  
pp. 1-8 ◽  
Author(s):  
Kang Wu ◽  
Ka-Wing Wong ◽  
Wang-Long Deng ◽  
Hao Zhang ◽  
Jing Li ◽  
...  
Keyword(s):  
T Cells ◽  
Pulmonary Tuberculosis ◽  
Cd8 T Cells ◽  
Whole Blood ◽  
Peripheral Blood ◽  
Cd4 T Cells ◽  
Cell Types ◽  
Transcriptional Responses ◽  
Inducible Genes ◽  
Transcript Signature

Previous transcriptomic analysis revealed a 393-transcript signature (PTBsig), which is dominated by interferon inducible genes, in whole blood of pulmonary tuberculosis (PTB) patients. Comparisons with a limited set of interferon-driven genes among separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils indicated that the signature is due to changes in neutrophils, the overwhelmingly predominant cell type. By extending the analysis to the entire 393 transcripts of PTBsig and by switching the cell proportions between separated monocytes, CD4+ T cells, CD8+ T cells, and neutrophils, we create putative PTBsig for whole blood (pPTBsig) in which CD4+ or CD8+ T cells or monocytes predominated or in which the cell proportions were unchanged. These putative signatures are then compared to the actual reported PTBsig. We show that, because of their predominance in peripheral blood and their larger transcriptional responses, neutrophils were indeed almost exclusively responsible for PTBsig. We caution that the functional significance of changes in other cell types might escape notice in transcriptome analysis that is based upon whole blood.

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 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.

scholarly journals Evidence for peripheral blood B lymphocyte but not T lymphocyte involvement in multiple myeloma

Blood ◽  
1987 ◽  
Vol 70 (5) ◽  
pp. 1550-1553 ◽  
Author(s):  
J Berenson ◽  
R Wong ◽  
K Kim ◽  
N Brown ◽  
A Lichtenstein
Keyword(s):  
Multiple Myeloma ◽  
T Cell ◽  
T Cell Receptor ◽  
Peripheral Blood ◽  
B Lymphocyte ◽  
Plasma Cells ◽  
Receptor Gene ◽  
Cell Receptor ◽  
Peripheral Blood Lymphocytes ◽  
Immunoglobulin Gene

Because there is controversy regarding whether subsets of peripheral blood lymphocytes (PBLs) are part of the malignant clone in patients with multiple myeloma, we studied this question by immunoglobulin and T cell receptor gene analysis. Southern blot analysis with antibody probes demonstrated clonal immunoglobulin gene rearrangements in PBLs of seven of nine patients that were identical to those seen in their marrow plasma cells. Circulating plasma cells were not detected in any of these patients. In contrast, no patient demonstrated clonally rearranged T cell receptor genes. In one sequentially studied patient, PBLs obtained at diagnosis when he had stage I (Durie-Salmon) contained only germline DNA, while analysis of PBLs at relapse (stage III) revealed a clonally rearranged band. These data confirm the notion that circulating lymphocytes in patients with myeloma are part of the malignant clone and, furthermore, these malignant cells are of B cell rather than T cell lineage.

scholarly journals Deep Optical Blood Analysis: COVID-19 Detection as a Case Study in Next Generation Blood Screening

2021 ◽  
Author(s):  
Colin L Cooke ◽  
Kanghyum Kim ◽  
Shiqi Xu ◽  
Amey Chaware ◽  
Xing Yao ◽  
...  
Keyword(s):  
Blood Cell ◽  
Cell Morphology ◽  
Peripheral Blood ◽  
Peripheral Blood Smear ◽  
Cell Types ◽  
Multiple Instance Learning ◽  
Blood Analysis ◽  
Learning Approaches ◽  
Diagnostic Efficacy ◽  
Peripheral Blood Smears

A wide variety of diseases are commonly diagnosed via the visual examination of cell morphology within a peripheral blood smear. For certain diseases, such as COVID-19, morphological impact across the multitude of blood cell types is still poorly understood. In this paper, we present a multiple instance learning-based approach to aggregate high-resolution morphological information across many blood cells and cell types to automatically diagnose disease at a per-patient level. We integrated image and diagnostic information from across 236 patients to demonstrate not only that there is a significant link between blood and a patient's COVID-19 infection status, but also that novel machine learning approaches offer a powerful and scalable means to analyze peripheral blood smears. Our results both backup and enhance hematological findings relating blood cell morphology to COVID-19, and offer a high diagnostic efficacy; with a 79% accuracy and a ROC-AUC of 0.90.

scholarly journals MicroRNA levels quantified in whole blood varies from PBMCs

F1000Research ◽  
2014 ◽  
Vol 3 ◽  
pp. 183 ◽  
Author(s):  
Sadaf Atarod ◽  
Hannah Smith ◽  
Anne Dickinson ◽  
Xiao-Nong Wang
Keyword(s):  
Whole Blood ◽  
Peripheral Blood ◽  
Mononuclear Cells ◽  
Human Peripheral Blood ◽  
Cell Types ◽  
Microrna Expression ◽  
Peripheral Blood Mononuclear ◽  
Total Rna ◽  
Disease Stages ◽  
Different Cell Types

MicroRNAs are non-coding RNAs that negatively regulate mRNA expression and play significant roles in both health and disease. Differential microRNA expression has been used to aid diagnosis and discriminate disease stages. The accuracy and reliability of microRNA expression measurement is of utmost importance. Quantification of microRNA expression in human peripheral blood is commonly detected using total RNA extracted via different methods. To date, no convincing data are available showing whether microRNA quantification results can be influenced by the use of total RNA extracted from whole blood or peripheral blood mononuclear cells (PBMCs). This study examined miR-146a-5p and miR-155-5p expression using total RNA extracted in parallel from whole blood and PBMCs of 14 healthy volunteers. The data showed that the quantification of miRNA using total RNA extracted from whole blood varied from that of PBMCs, indicating that the miRNA expression was a result of all the different cell-types present in whole blood. Our results suggested that the source of total RNA and the statistical analyses performed are crucial considerations when designing miRNA research.

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