Transcriptional profiling of macrophages derived from monocytes and iPS cells identifies a conserved response to LPS and novel alternative transcription

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Alasoo, Kaur ^a   Martinez, Fernando O ^b   Hale, Christine ^a   Gordon, Siamon ^c   Powrie, Fiona ^d   Dougan, Gordon ^a   Mukhopadhyay, Subhankar ^a,c,d   Gaffney, Daniel J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

^c UNIVERSITY OF OXFORD   (United Kingdom)

^d UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

3' UNTRANSLATED REGION; CHEMOKINE; LIPOPOLYSACCHARIDE; RNA; TRANSCRIPTOME;

3' UNTRANSLATED REGION; CELL CULTURE; CHEMISTRY; CYTOLOGY; DRUG EFFECTS; GENE EXPRESSION PROFILING; GENETICS; HUMAN; INDUCED PLURIPOTENT STEM CELL; ISOLATION AND PURIFICATION; MACROPHAGE; METABOLISM; MONOCYTE; PROMOTER REGION; SEQUENCE ANALYSIS;

3' UNTRANSLATED REGIONS; CELLS, CULTURED; CHEMOKINES; GENE EXPRESSION PROFILING; HUMANS; INDUCED PLURIPOTENT STEM CELLS; LIPOPOLYSACCHARIDES; MACROPHAGES; MONOCYTES; PROMOTER REGIONS, GENETIC; RNA; SEQUENCE ANALYSIS, RNA; TRANSCRIPTOME;

EID: 84938319366     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep12524     Document Type: Article

References (53)

1. Wynn, T. A., Chawla, A. & Pollard, J. W. Macrophage biology in development, homeostasis and disease. Nature 496, 445-455 (2013).
2. Murray, P. J. & Wynn, T. A. Protective and pathogenic functions of macrophage subsets. Nat. Rev. Immunol. 11, 723-737 (2011).
3. Adati, N., Huang, M.-C., Suzuki, T., Suzuki, H. & Kojima, T. High-resolution analysis of aberrant regions in autosomal chromosomes in human leukemia THP-1 cell line. BMC Res. Notes 2, 153 (2009).
4. Schildberger, A., Rossmanith, E., Eichhorn, T., Strassl, K. & Weber, V. Monocytes, peripheral blood mononuclear cells, and THP-1 cells exhibit different cytokine expression patterns following stimulation with lipopolysaccharide. Mediators Inflamm. 2013, 697972 (2013).
5. Schroder, K. et al. Conservation and divergence in Toll-like receptor 4-regulated gene expression in primary human versus mouse macrophages. Proc. Natl. Acad. Sci. USA. 109, E944-53 (2012).
6. Lyakh, L. A. et al. Adenovirus type 5 vectors induce dendritic cell differentiation in human CD14(+ ) monocytes cultured under serum-free conditions. Blood 99, 600-608 (2002).
7. Muruve, D. A. et al. The inflammasome recognizes cytosolic microbial and host DNA and triggers an innate immune response. Nature 452, 103-107 (2008).
8. Karlsson, K. R. et al. Homogeneous monocytes and macrophages from human embryonic stem cells following coculture-free differentiation in M-CSF and IL-3. Exp. Hematol. 36, 1167-1175 (2008).
9. Van Wilgenburg, B., Browne, C., Vowles, J. & Cowley, S. A. Efficient, long term production of monocyte-derived macrophages from human pluripotent stem cells under partly-defined and fully-defined conditions. PLoS One 8, e71098 (2013).
10. Jiang, Y. et al. Derivation and functional analysis of patient-specific induced pluripotent stem cells as an in vitro model of chronic granulomatous disease. Stem Cells 30, 599-611 (2012).
11. Love, M. I., Huber, W. & Anders, S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 15, 550 (2014).
12. Zlotnik, A. & Yoshie, O. The chemokine superfamily revisited. Immunity 36, 705-716 (2012).
13. Wang, E. T. et al. Alternative isoform regulation in human tissue transcriptomes. Nature 456, 470-476 (2008).
14. Carpenter, S., Ricci, E. P., Mercier, B. C., Moore, M. J. & Fitzgerald, K. A. Post-transcriptional regulation of gene expression in innate immunity. Nat. Rev. Immunol. 14, 361-376 (2014).
15. Turro, E. et al. Haplotype and isoform specific expression estimation using multi-mapping RNA-seq reads. Genome Biol. 12, R13 (2011).
16. Wagner, G. P., Kin, K. & Lynch, V. J. Measurement of mRNA abundance using RNA-seq data: RPKM measure is inconsistent among samples. Theory Biosci. 131, 281-285 (2012).
17. Gonzalez-Porta, M., Frankish, A., Rung, J., Harrow, J. & Brazma, A. Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene. Genome Biol. 14, R70 (2013).
18. Turro, E., Astle, W. J. & Tavaré, S. Flexible analysis of RNA-seq data using mixed effects models. Bioinformatics 30, 180-188 (2014).
19. Venables, J. P. et al. MBNL1 and RBFOX2 cooperate to establish a splicing programme involved in pluripotent stem cell differentiation. Nat. Commun. 4, 2480 (2013).
20. Lambert, N. et al. RNA Bind-n-Seq: quantitative assessment of the sequence and structural binding specificity of RNA binding proteins. Mol. Cell 54, 887-900 (2014).
21. Lappalainen, T. et al. Transcriptome and genome sequencing uncovers functional variation in humans. Nature 501, 506-511 (2013).
22. The ENCODE Project Consortium. An integrated encyclopedia of DNA elements in the human genome. Nature 489, 57-74 (2012).
23. Gautier, E. L. et al. Gene-expression profiles and transcriptional regulatory pathways that underlie the identity and diversity of mouse tissue macrophages. Nat. Immunol. 13, 1118-1128 (2012).
24. Gosselin, D. et al. Environment drives selection and function of enhancers controlling tissue-specific macrophage identities. Cell 159, 1327-1340 (2014).
25. Lavin, Y. et al. Tissue-resident macrophage enhancer landscapes are shaped by the local microenvironment. Cell 159, 1312-1326 (2014).
26. Ginhoux, F. et al. Fate mapping analysis reveals that adult microglia derive from primitive macrophages. Science 330, 841-845 (2010).
27. Mantovani, A., Biswas, S. K., Galdiero, M. R., Sica, A. & Locati, M. Macrophage plasticity and polarization in tissue repair and remodelling. J. Pathol. 229, 176-185 (2013).
28. Schmieder, A., Michel, J., Schönhaar, K., Goerdt, S. & Schledzewski, K. Differentiation and gene expression profile of tumorassociated macrophages. Semin. Cancer Biol. 22, 289-297 (2012).
29. Cailhier, J. F. et al. Conditional macrophage ablation demonstrates that resident macrophages initiate acute peritoneal inflammation. The Journal of Immunology 174, 2336-2342 (2005).
30. Soehnlein, O. & Lindbom, L. Phagocyte partnership during the onset and resolution of inflammation. Nat. Rev. Immunol. 10, 427-439 (2010).
31. Gundra, U. M. et al. Alternatively activated macrophages derived from monocytes and tissue macrophages are phenotypically and functionally distinct. Blood 123, e110-22 (2014).
32. Jakubzick, C. et al. Minimal differentiation of classical monocytes as they survey steady-state tissues and transport antigen to lymph nodes. Immunity 39, 599-610 (2013).
33. Klimchenko, O. et al. Monocytic cells derived from human embryonic stem cells and fetal liver share common differentiation pathways and homeostatic functions. Blood 117, 3065-3075 (2011).
34. Yu, L. et al. Induction of a unique isoform of the NCOA7 oxidation resistance gene by interferon ?-1b. J. Interferon Cytokine Res. (2014). doi: 10.1089/jir.2014.0115.
35. Shao, W., Halachmi, S. & Brown, M. ERAP140, a conserved tissue-specific nuclear receptor coactivator. Mol. Cell. Biol. 22, 3358-3372 (2002).
36. Johansson, M. et al. The two variants of oxysterol binding protein-related protein-1 display different tissue expression patterns, have different intracellular localization, and are functionally distinct. Mol. Biol. Cell 14, 903-915 (2003).
37. Ngo, M. & Ridgway, N. D. Oxysterol binding protein-related protein 9 (ORP9) is a cholesterol transfer protein that regulates Golgi structure and function. Mol. Biol. Cell 20, 1388-1399 (2009).
38. Sandberg, R., Neilson, J. R., Sarma, A., Sharp, P. A. & Burge, C. B. Proliferating cells express mRNAs with shortened 3? untranslated regions and fewer microRNA target sites. Science 320, 1643-1647 (2008).
39. Mayr, C. & Bartel, D. P. Widespread shortening of 3? UTRs by alternative cleavage and polyadenylation activates oncogenes in cancer cells. Cell 138, 673-684 (2009).
40. Gupta, I. et al. Alternative polyadenylation diversifies post-transcriptional regulation by selective RNA-protein interactions. Mol. Syst. Biol. 10, (2014).
41. O'Neill, L. A., Sheedy, F. J. & McCoy, C. E. MicroRNAs: the fine-tuners of Toll-like receptor signalling. Nat. Rev. Immunol. 11, 163-175 (2011).
42. Miura, P., Shenker, S., Andreu-Agullo, C., Westholm, J. O. & Lai, E. C. Widespread and extensive lengthening of 3? UTRs in the mammalian brain. Genome Res. 23, 812-825 (2013).
43. Wehrspaun, C. C., Ponting, C. P. & Marques, A. C. Brain-expressed 3? UTR extensions strengthen miRNA cross-talk between ion channel/transporter encoding mRNAs. Front. Genet. 5, (2014).
44. Vallier, L. et al. Signaling pathways controlling pluripotency and early cell fate decisions of human induced pluripotent stem cells. Stem Cells 27, 2655-2666 (2009).
45. Rouhani, F. et al. Genetic background drives transcriptional variation in human induced pluripotent stem cells. PLoS Genet. 10, e1004432 (2014).
46. Martinez, F. O., Gordon, S., Locati, M. & Mantovani, A. Transcriptional profiling of the human monocyte-to-macrophage differentiation and polarization: new molecules and patterns of gene expression. The Journal of Immunology 177, 7303-7311 (2006).
47. Martinez, F. O. Analysis of gene expression and gene silencing in human macrophages. Curr. Protoc. Immunol. Chapter 14, Unit 14.28.1-23 (2012).
48. Kim, D. et al. TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol. 14, R36 (2013).
49. Liao, Y., Smyth, G. K. & Shi, W. featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics 30, 923-930 (2014).
50. Reimand, J., Arak, T. & Vilo, J. g:Profiler-A web server for functional interpretation of gene lists (2011 update). Nucleic Acids Res. 39, W307-15 (2011).
51. Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841-842 (2010).
52. Langmead, B., Trapnell, C., Pop, M. & Salzberg, S. L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10, R25 (2009).
53. Katz, Y., Wang, E. T., Airoldi, E. M. & Burge, C. B. Analysis and design of RNA sequencing experiments for identifying isoform regulation. Nat. Methods 7, 1009-1015 (2010).