Advertisement

Neutrophil pp 277-298 | Cite as

Genome-Scale Transcript Analyses of Human Neutrophils

  • Scott D. Kobayashi
  • Adeline R. Porter
  • Sarah L. Anzick
  • Dan E. Sturdevant
  • Frank R. DeLeoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 2087)

Abstract

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.

Key words

Neutrophil Microarray Gene expression Affymetrix Next-generation sequencing Transcript Phagocyte Polymorphonuclear leukocytes 

Notes

Acknowledgments

This work was supported by the Intramural Program of the National Institutes of Allergy and Infectious Diseases, NIH.

References

  1. 1.
    Kasprisin DO, Harris MB (1977) The role of RNA metabolism in polymorphonuclear leukocyte phagocytosis. J Lab Clin Med 90:118–124PubMedGoogle Scholar
  2. 2.
    Chang FY, Shaio MF (1990) In vitro effect of actinomycin D on human neutrophil function. Microbiol Immunol 34:311–321CrossRefGoogle Scholar
  3. 3.
    Kasprisin DO, Harris MB (1978) The role of protein synthesis in polymorphonuclear leukocyte phagocytosis II. Exp Hematol 6:585–589PubMedGoogle Scholar
  4. 4.
    Cline MJ (1966) Phagocytosis and synthesis of ribonucleic acid in human granulocytes. Nature 212:1431–1433CrossRefGoogle Scholar
  5. 5.
    Cline MJ (1966) Ribonucleic acid biosynthesis in human leukocytes. Effects of phagocytosis on RNA metabolism. Blood 28:188–200CrossRefGoogle Scholar
  6. 6.
    Jack RM, Fearon DT (1988) Selective synthesis of mRNA and proteins by human peripheral blood neutrophils. J Immunol 140:4286–4293PubMedGoogle Scholar
  7. 7.
    Newburger PE, Dai Q, Whitney C (1991) In vitro regulation of human phagocyte cytochrome b heavy and light chain gene expression by bacterial lipopolysaccharide and recombinant human cytokines. J Biol Chem 266:16171–16177PubMedGoogle Scholar
  8. 8.
    Newburger PE, Ezekowitz RA, Whitney C et al (1988) Induction of phagocyte cytochrome b heavy chain gene expression by interferon gamma. Proc Natl Acad Sci U S A 85:5215–5219CrossRefGoogle Scholar
  9. 9.
    Itoh K, Okubo K, Utiyama H et al (1998) Expression profile of active genes in granulocytes. Blood 92:1432–1441CrossRefGoogle Scholar
  10. 10.
    Subrahmanyam YV, Yamaga S, Prashar Y et al (2001) RNA expression patterns change dramatically in human neutrophils exposed to bacteria. Blood 97:2457–2468CrossRefGoogle Scholar
  11. 11.
    Borjesson DL, Kobayashi SD, Whitney AR et al (2005) Insights into pathogen immune evasion mechanisms: Anaplasma phagocytophilum fails to induce an apoptosis differentiation program in human neutrophils. J Immunol 174:6364–6372CrossRefGoogle Scholar
  12. 12.
    Kobayashi SD, Braughton KR, Palazzolo-Ballance AM et al (2010) Rapid neutrophil destruction following phagocytosis of Staphylococcus aureus. J Innate Immun 2:560–575CrossRefGoogle Scholar
  13. 13.
    Kobayashi SD, Braughton KR, Whitney AR et al (2003) Bacterial pathogens modulate an apoptosis differentiation program in human neutrophils. Proc Natl Acad Sci U S A 100:10948–10953CrossRefGoogle Scholar
  14. 14.
    Kobayashi SD, Voyich JM, Braughton KR et al (2003) Down-regulation of proinflammatory capacity during apoptosis in human polymorphonuclear leukocytes. J Immunol 170:3357–3368CrossRefGoogle Scholar
  15. 15.
    Kobayashi SD, Voyich JM, Braughton KR et al (2004) Gene expression profiling provides insight into the pathophysiology of chronic granulomatous disease. J Immunol 172:636–643CrossRefGoogle Scholar
  16. 16.
    Kobayashi SD, Voyich JM, Buhl CL et al (2002) Global changes in gene expression by human polymorphonuclear leukocytes during receptor-mediated phagocytosis: cell fate is regulated at the level of gene expression. Proc Natl Acad Sci U S A 99:6901–6906CrossRefGoogle Scholar
  17. 17.
    Kobayashi SD, Voyich JM, Somerville GA et al (2003) An apoptosis-differentiation program in human polymorphonuclear leukocytes facilitates resolution of inflammation. J Leukoc Biol 73:315–322CrossRefGoogle Scholar
  18. 18.
    Kobayashi SD, Voyich JM, Whitney AR et al (2005) Spontaneous neutrophil apoptosis and regulation of cell survival by granulocyte macrophage-colony stimulating factor. J Leukoc Biol 78:1408–1418CrossRefGoogle Scholar
  19. 19.
    Holland SM, DeLeo FR, Elloumi HZ et al (2007) STAT3 mutations in the hyper-IgE syndrome. N Engl J Med 357:1608–1619CrossRefGoogle Scholar
  20. 20.
    Theilgaard-Monch K, Jacobsen LC, Borup R et al (2005) The transcriptional program of terminal granulocytic differentiation. Blood 105:1785–1796CrossRefGoogle Scholar
  21. 21.
    Theilgaard-Monch K, Knudsen S, Follin P et al (2004) The transcriptional activation program of human neutrophils in skin lesions supports their important role in wound healing. J Immunol 172:7684–7693CrossRefGoogle Scholar
  22. 22.
    Fessler MB, Malcolm KC, Duncan MW et al (2002) Lipopolysaccharide stimulation of the human neutrophil: an analysis of changes in gene transcription and protein expression by oligonucleotide microarrays and proteomics. Chest 121:75S–76SCrossRefGoogle Scholar
  23. 23.
    Tsukahara Y, Lian Z, Zhang X et al (2003) Gene expression in human neutrophils during activation and priming by bacterial lipopolysaccharide. J Cell Biochem 89:848–861CrossRefGoogle Scholar
  24. 24.
    Kluger Y, Tuck DP, Chang JT et al (2004) Lineage specificity of gene expression patterns. Proc Natl Acad Sci U S A 101:6508–6513CrossRefGoogle Scholar
  25. 25.
    Zhang X, Kluger Y, Nakayama Y et al (2004) Gene expression in mature neutrophils: early responses to inflammatory stimuli. J Leukoc Biol 75:358–372CrossRefGoogle Scholar
  26. 26.
    Kobayashi SD, DeLeo FR (2009) Role of neutrophils in innate immunity: a systems biology-level approach. Wiley Interdiscip Rev Syst Biol Med 1:309–333CrossRefGoogle Scholar
  27. 27.
    Nauseef WM (2014) Isolation of human neutrophils from venous blood. Methods Mol Biol 1124:13–18CrossRefGoogle Scholar
  28. 28.
    Siemsen DW, Malachowa N, Schepetkin IA et al (2014) Neutrophil isolation from nonhuman species. Methods Mol Biol 1124:19–37CrossRefGoogle Scholar
  29. 29.
    Kobayashi SD, Sturdevant DE, DeLeo FR (2007) Genome-scale transcript analyses in human neutrophils. Methods Mol Biol 412:441–453CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2020

Authors and Affiliations

  • Scott D. Kobayashi
    • 1
  • Adeline R. Porter
    • 1
  • Sarah L. Anzick
    • 2
  • Dan E. Sturdevant
    • 2
  • Frank R. DeLeo
    • 3
    Email author
  1. 1.Laboratory of Bacteriology, Rocky Mountain LaboratoriesNational Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUSA
  2. 2.Genomics Unit, Rocky Mountain LaboratoriesNational Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUSA
  3. 3.Laboratory of Bacteriology, Rocky Mountain Laboratories, Division of Intramural ResearchNational Institute of Allergy and Infectious Diseases, National Institutes of HealthHamiltonUSA

Personalised recommendations