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Clinical and Vaccine Immunology, April 2009, p. 567-573, Vol. 16, No. 4
1071-412X/09/$08.00+0     doi:10.1128/CVI.00441-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.

Major Histocompatibility Complex Class II Molecule-Human Immunodeficiency Virus Peptide Analysis Using a Microarray Chip{triangledown} ,{dagger}

Simani Gaseitsiwe,1,2 Davide Valentini,3 Raija Ahmed,1,2 Shahnaz Mahdavifar,1,2 Isabelle Magalhaes,1,2 Johannes Zerweck,4 Mike Schutkowski,4 Emmanuel Gautherot,5 Felix Montero,5 Anneka Ehrnst,1 Marie Reilly,3 and Markus Maeurer1,2*

Department of Microbiology, Tumor and Cell Biology Center (MTC), Karolinska Institutet, Stockholm, Sweden,1 The Swedish Institute for Infectious Disease Control (SMI), Stockholm, Sweden,2 Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden,3 JPT, Berlin, Germany,4 Biomedical Research Division, Beckman Coulter Inc., Marseille, France5

Received 24 November 2008/ Returned for modification 29 December 2008/ Accepted 4 February 2009

Identification of major histocompatibility complex (MHC) class II binding peptides is a crucial step in rational vaccine design and immune monitoring. We designed a novel MHC class II molecule-peptide microarray binding assay and evaluated 346 peptides from already identified human immunodeficiency virus (HIV) epitopes and an additional set (n = 206) of 20-mer peptides, overlapping by 15 amino acid residues, from HIV type 1B (HIV-1B) gp160 and Nef as a paradigm. Peptides were attached via the N-terminal part to a linker that covalently binds to the epoxy glass slide. The 552 peptides were printed in triplicate on a single peptide microarray chip and tested for stable formation of MHC class II molecule-peptide complexes using recombinant soluble DRB1*0101(DR1), DRB1*1501(DR2), and DRB1*0401(DR4) molecules. Cluster analysis revealed unique patterns of peptide binding to all three, two, or a single MHC class II molecule. MHC class II binding peptides reside within previously described immunogenic regions of HIV gp160 and Nef, yet we could also identify new MHC class II binding peptides from gp160 and Nef. Peptide microarray chips allow the comprehensive and simultaneous screening of a high number of candidate peptide epitopes for MHC class II binding, guided by subsequent quality data extraction and binding pattern cluster analysis.

* Corresponding author. Mailing address: Microbiology, Tumor and Cell Biology Center (MTC), Karolinska Institutet and the Swedish Institute for Infectious Disease Control (SMI), Nobels Väg 18, SE-17182 Stockholm, Sweden. Phone: 46 84572650. Fax: 46 8337460. E-mail: markus.maeurer{at}ki.se

{triangledown} Published ahead of print on 18 February 2009.

{dagger} Supplemental material for this article may be found at http://cvi.asm.org/.

Clinical and Vaccine Immunology, April 2009, p. 567-573, Vol. 16, No. 4
1071-412X/09/$08.00+0     doi:10.1128/CVI.00441-08
Copyright © 2009, American Society for Microbiology. All Rights Reserved.





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