Major histocompatibility complex class II molecule-human immunodeficiency virus peptide analysis using a microarray chip.
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.
Gaseitsiwe
Simani
S
Microbiology, Tumor and Cell Biology Center, Karolinska Institutet, Stockholm, Sweden.
Valentini
Davide
D
Ahmed
Raija
R
Mahdavifar
Shahnaz
S
Magalhaes
Isabelle
I
Zerweck
Johannes
J
Schutkowski
Mike
M
Gautherot
Emmanuel
E
Montero
Felix
F
Ehrnst
Anneka
A
Reilly
Marie
M
Maeurer
Markus
M
D018604:Epitope Mapping / Q000379:methods*; D000939:Epitopes / Q000276:immunology*; D006678:HIV / Q000276:immunology*; D019302:HIV Envelope Protein gp160 / Q000276:immunology; D000949:Histocompatibility Antigens Class II / Q000276:immunology* / Q000378:metabolism; D006801:Humans; D010455:Peptides / Q000276:immunology; D040081:Protein Array Analysis / Q000379:methods*; D011485:Protein Binding; D054311:nef Gene Products, Human Immunodeficiency Virus / Q000276:immunology
D000939:Epitopes; D019302:HIV Envelope Protein gp160; D000949:Histocompatibility Antigens Class II; D010455:Peptides; D054311:nef Gene Products, Human Immunodeficiency Virus