Genome-scale transcript analyses in human neutrophils

Genome-Scale Transcript Analyses of Human Neutrophils

Transcriptome analyses of unicellular and multicellular organisms have changed fundamental understanding of biological and pathological processes across multiple scientific disciplines. Over the past 15 years, studies of polymorphonuclear leukocyte (PMN or neutrophil) gene expression on a global scale have provided new insight into the molecular processes that promote resolution of infections in humans. Herein we present methods to analyze gene expression in human neutrophils using Affymetrix oligonucleotide microarrays and next-generation sequencing. Notably, the procedures utilize commercially available reagents and materials and thus represent a standardized approach for evaluating PMN transcript levels.

Genome-scale transcript analyses with human neutrophils

Transcriptome analyses of single- and multicellular organisms have changed fundamental understanding of biological and pathological processes across multiple scientific disciplines. Over the past decade, studies of polymorphonuclear leukocyte (PMN or neutrophil) gene expression on a global scale have provided new insight into the molecular processes that promote resolution of infections in humans. Herein we present methods to analyze gene expression in human neutrophils using Affymetrix oligonucleotide microarrays, which include isolation of high-quality RNA, generation and labeling of cRNA, and GeneChip hybridization and scanning. Notably, the procedures utilize commercially available reagents and materials and thus represent a standardized approach for evaluating PMN transcript levels.

High-purity neutrophil isolation from human peripheral blood and saliva for transcriptome analysis

The oral cavity is a source of readily available neutrophils and can be used as a model to better understand the role of neutrophils in chronic inflammatory diseases such as rheumatoid arthritis, bronchitis, periodontitis, and inflammatory bowel disease. In this chapter we describe reproducible methods to obtain highly purified neutrophil samples from blood and saliva in humans to enable cell analysis using whole-genome microarrays.

Molecular markers and mechanisms of stroke: RNA studies of blood in animals and humans

Whole genome expression microarrays can be used to study gene expression in blood, which comes in part from leukocytes, immature platelets, and red blood cells. Since these cells are important in the pathogenesis of stroke, RNA provides an index of these cellular responses to stroke. Our studies in rats have shown specific gene expression changes 24  hours after ischemic stroke, hemorrhage, status epilepticus, hypoxia, hypoglycemia, global ischemia, and following brief focal ischemia that simulated transient ischemic attacks in humans. Human studies show gene expression changes following ischemic stroke. These gene profiles predict a second cohort with >90% sensitivity and specificity. Gene profiles for ischemic stroke caused by large-vessel atherosclerosis and cardioembolism have been described that predict a second cohort with >85% sensitivity and specificity. Atherosclerotic genes were associated with clotting, platelets, and monocytes, and cardioembolic genes were associated with inflammation, infection, and neutrophils. These gene profiles predicted the cause of stroke in 58% of cryptogenic patients. These studies will provide diagnostic, prognostic, and therapeutic markers, and will advance our understanding of stroke in humans. New techniques to measure all coding and noncoding RNAs along with alternatively spliced transcripts will markedly advance molecular studies of human stroke.

Why is Pseudomonas aeruginosa a pathogen?

Despite the expression of a myriad of virulence factors, healthy individuals are generally able to resist infections with Pseudomonas aeruginosa. Polymorphonuclear leukocyte-dependent killing is the major mechanism responsible for resistance; dysregulation of host defense mechanisms in addition to expression of specific bacterial factors can result in life-threatening infections with this bacterium.