Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation

Baechler, Emily C.; Batliwalla, Franak; Karypis, George; Gaffney, Patrick M.; Moser, Kathy L.; Ortmann, Ward; Espe, Karl J.; Balasubramanian, S.; Hughes, Karis M. H.; Chan, Joanne; Begovich, Ann B.; Chang, Sheng Yung; Gregersen, Peter K.; Behrens, Timothy W.

doi:10.1038/sj.gene.6364098

Cited by 148 publications

(139 citation statements)

References 22 publications

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“…However, Siglec-1 is not one of the genes shown to have such variability. Another report has shown that certain genes are highly induced if a delay occurs prior to RNA processing (51). In comparison with studies that examined gene expression after overnight incubation, all of the samples in our study were processed in an identical manner within 30 minutes after blood withdrawal.…”

Section: Discussionmentioning

confidence: 99%

A macrophage marker, siglec‐1, is increased on circulating monocytes in patients with systemic sclerosis and induced by type i interferons and toll‐like receptor agonists

York¹,

Nagai²,

Mangini³

et al. 2007

Arthritis & Rheumatism

288

228

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Objective. Microarray analyses of peripheral blood leukocytes have shown that patients with systemic lupus erythematosus express increased levels of type I interferon (IFN)-regulated genes. In this study we examined gene expression by peripheral blood mononuclear cells (PBMCs) from patients with systemic sclerosis (SSc) to better understand the dysregulation of the immune system in this disease. Methods. PBMC gene expression was analyzed by microarray and confirmed by real-time polymerase chain reaction (PCR). Surface protein expression of

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Section: Discussionmentioning

confidence: 99%

A macrophage marker, siglec‐1, is increased on circulating monocytes in patients with systemic sclerosis and induced by type i interferons and toll‐like receptor agonists

York¹,

Nagai²,

Mangini³

et al. 2007

Arthritis & Rheumatism

288

228

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“…Recently, Baechler and coworkers [27,28] demonstrated the activation of IFN-inducible genes in peripheral blood cells of patients with severe lupus nephritis. Genes regulated by IFN-a/b (class I) and IFN-c (class II) included immune modulators and regulatory factors.…”

Section: Discussionmentioning

confidence: 99%

Interferon regulatory factor‐1 gene deletion decreases glomerulonephritis in MRL/lpr mice

et al. 2006

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To investigate the role of interferon regulatory factor-1 (IRF-1) in the development of lupus nephritis, IRF-1 -/-genotype mice were bred onto the MRL/lpJfas lpr (MRL/lpr) background. We examined kidney mesangial cell function and disease progression. Endpoints evaluated included inflammatory mediators, autoantibody production, immune complex deposition, renal pathology, T cell subset analysis, and duration of survival. Mesangial cells cultured from IRF-1 -/-mice produced significantly lower levels of nitric oxide and IL-12 but not TNF-a when stimulated with LPS + IFN-c. IRF-1 -/-mice showed less aggravated dermatitis compared to the wild-type mice. Anti-doublestranded DNA production and proteinuria were significantly decreased in IRF-1 -/-mice compared to IRF-1 +/+ mice. IgG and C3 deposition as well as glomerulonephritis were decreased in IRF-1 -/-mice at 26 wk of age compared to the IRF-1 +/+ mice. Splenic CD4 -CD8 -CD44 + T cells were decreased while CD4 + CD25 + T cells were increased in the IRF-1 -/-mice when compared to IRF-1 +/+ mice. Survival rates (ED 50 ) were 22 wk for IRF-1 +/+ mice and 45 wk for IRF-1 -/-mice. These findings suggest an important role of IRF-1 in mediating renal disease in MRL/lpr mice. IntroductionThe etiology of systemic lupus erythematosus remains an enigma although genetic factors influenced by environmental agents appear to trigger the disease. Clearly, B cells, T cells, and macrophages play important roles in the development of lupus pathology [1][2][3].Chronic expression of Th1 cytokines secreted by Th cells is particularly harmful due to their influence on the initiation and promotion of tissue destruction [4,5]. Cytokines, including IFN-c, promote inflammation and provide a positive amplification loop responsible for escalating autoimmune kidney damage [6].MRL/lpr mice develop glomerulonephritis and vasculitis at an early age (4-5 months) [7]. Renal disease is characterized by the early influx of activated T cells and macrophages into the kidney. Activated T cells secrete IFN-c, which induces macrophages to express CSF-1, IL-1b, and TNF-a. Macrophages accumulate in the kidney during inflammation and generate IFN-a, TNF-a, and reactive oxygen species. Locally produced chemokines, particularly monocyte chemoattractant protein (MCP)-1, are also instrumental in attracting and maintaining cellular influx [8] -12 [20]. In the IRF-1 -/-NOD mouse, insulitis and diabetes were decreased accompanied by an increased survival [21]. Additional studies have suggested a role of IRF-1 and IFN-regulated genes in mediating human lupus [22][23][24]. Based on the knowledge that IRF-1 modulates inflammatory mediator production, we sought to determine whether IRF-1 gene deletion alters the severity of lupus nephritis in MRL/lpr mice. Results IRF-1 MRL/lpr mouse phenotypeTo determine the role of IRF-1 in autoimmune disease, IRF-1-knockout mice were backcrossed for eight generations to the MRL/lpr mice. After eight backcrosses, the littermates were intercrossed to yield cohorts for these studies....

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“…However, TCGA's single-center approach for AML is not feasible for many studies. Similarly, commercially available PAXgene collection tubes or similar products rapidly stabilize RNA (9,15,33), but also prevent isolation of specific cell populations with a Ficoll gradient or flow sorting. Therefore, we tested the simple expedient of placing whole blood on ice immediately after collection by a phlebotomist.…”

Section: Leukemic Transcriptomes Exhibit Gene Expression Signatures Ofmentioning

confidence: 99%

“…For example, blood collection procedures and the choice of anticoagulant can impact subsequent clinical chemistry assays or affect hematological parameters such as cell number and morphology (6,7). Similarly, blood shipping temperature and the timing of sample processing can affect levels of protein-based biomarkers and other analytes in plasma or serum, alter the transcription (e.g., IL8, IL10, CCR2, SOCS2, or JUN) or splicing (e.g., NF1, PTEN, or ATM) of specific genes, or cause globally decreased/increased transcription or accelerated RNA degradation, depending upon conditions (8)(9)(10)(11)(12)(13)(14)(15).…”

mentioning

confidence: 99%

Sample processing obscures cancer-specific alterations in leukemic transcriptomes

Dvinge

Ries

Ilagan

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Substantial effort is currently devoted to identifying cancer-associated alterations using genomics. Here, we show that standard blood collection procedures rapidly change the transcriptional and posttranscriptional landscapes of hematopoietic cells, resulting in biased activation of specific biological pathways; up-regulation of pseudogenes, antisense RNAs, and unannotated coding isoforms; and RNA surveillance inhibition. Affected genes include common mutational targets and thousands of other genes participating in processes such as chromatin modification, RNA splicing, T-and B-cell activation, and NF-κB signaling. The majority of published leukemic transcriptomes exhibit signals of this incubation-induced dysregulation, explaining up to 40% of differences in gene expression and alternative splicing between leukemias and reference normal transcriptomes. The effects of sample processing are particularly evident in pan-cancer analyses. We provide biomarkers that detect prolonged incubation of individual samples and show that keeping blood on ice markedly reduces changes to the transcriptome. In addition to highlighting the potentially confounding effects of technical artifacts in cancer genomics data, our study emphasizes the need to survey the diversity of normal as well as neoplastic cells when characterizing tumors.leukemia | RNA splicing | nonsense-mediated decay | batch effects

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Expression levels for many genes in human peripheral blood cells are highly sensitive to ex vivo incubation

Cited by 148 publications

References 22 publications

A macrophage marker, siglec‐1, is increased on circulating monocytes in patients with systemic sclerosis and induced by type i interferons and toll‐like receptor agonists

A macrophage marker, siglec‐1, is increased on circulating monocytes in patients with systemic sclerosis and induced by type i interferons and toll‐like receptor agonists

Interferon regulatory factor‐1 gene deletion decreases glomerulonephritis in MRL/lpr mice

Sample processing obscures cancer-specific alterations in leukemic transcriptomes

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