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Long oligonucleotide microarrays for African green monkey gene expression profile analysis

Béatrice Jacquelin^*,, Véronique Mayau^*, Guillaume Brysbaert^¶, Béatrice Regnault, Ousmane M. Diop, Fernando Arenzana-Seisdedos, Lars Rogge^||, Jean-Yves Coppée, Françoise Barré-Sinoussi^*, Arndt Benecke^¶ and Michaela C. Müller-Trutwin^*,1

^* Unité de Régulation des Infections Rétrovirales,

Plateforme Puces à ADN-Genopole,

Laboratoire de Pathologie Virale Moléculaire,

^|| Groupe à 5 ans Immunorégulation, Institut Pasteur, Paris, France;

Laboratoire de Rétrovirologie, Institut Pasteur, Dakar, Senegal; and

^¶ Institut de Recherche Interdisciplinaire-CNRS and Institut des Hautes Études Scientifiques, Bures sur Yvette, France

¹Correspondence: Unité de Régulations des Infections Rétrovirales, Institut Pasteur, 25, rue du Docteur Roux, 75724 Paris cedex 15, France. E-mail: mmuller{at}pasteur.fr

Nonhuman primates, including African green monkey (AGM), are important models for biomedical research. The information on monkey genomes is still limited and no versatile gene expression screening tool is available. We tested human whole genome microarrays for cross-species reactivity with AGM transcripts using both long oligonucleotide arrays (60-mer probes) and short oligonucleotide arrays (25-mer). Using the long oligonucleotide arrays, we detected 4-fold more AGM transcripts than with the short oligonucleotide technology. The number of detected transcripts was comparable to that detected using human RNA, with 87% of the detected genes being shared between both species. The specificity of the signals obtained with the long oligonucleotide arrays was determined by analyzing the transcriptome of concanavalin A-activated CD4⁺ T cells vs. nonactivated T cells of two monkey species AGM and macaque. For both species, the genes showing the most significant changes in expression, such as IL-2R, were those known to be regulated in human CD4⁺ T cell activation. Finally, tissue specificity of the signals was established by comparing the transcription profiles of AGM brain and tonsil cells. In conclusion, the ABI human microarray platform provides a highly valuable tool for the assessment of AGM gene expression profiles. —Jacquelin, B., Mayau, V., Brysbaert, G., Regnault, B., Diop, O. M., Arenzana-Seisdedos, F., Rogge, L., Coppée, J-Y., Barré-Sinoussi, F., Benecke, A., Müller-Trutwin, M. C. Long oligonucleotide microarrays for African green monkey gene expression profile analysis.

Key Words: nonhuman primate • macaque • CD4⁺ T cell • brain • tonsil