HLA-C Level Is Regulated by a Polymorphic Oct1 Binding Site in the HLA-C Promoter Region.
Differential HLA-C levels influence several human diseases, but the mechanisms responsible are incompletely characterized. Using a validated prediction algorithm, we imputed HLA-C cell surface levels in 228 individuals from the 1000 Genomes dataset. We tested 68,726 SNPs within the MHC for association with HLA-C level. The HLA-C promoter region variant, rs2395471, 800 bp upstream of the transcription start site, gave the most significant association with HLA-C levels (p = 4.2 × 10-66). This imputed expression quantitative trait locus, termed impeQTL, was also shown to associate with HLA-C expression in a genome-wide association study of 273 donors in which HLA-C mRNA expression levels were determined by quantitative PCR (qPCR) (p = 1.8 × 10-20) and in two cohorts where HLA-C cell surface levels were determined directly by flow cytometry (n = 369 combined, p < 10-15). rs2395471 is located in an Oct1 transcription factor consensus binding site motif where the A allele is predicted to have higher affinity for Oct1 than the G allele. Mobility shift electrophoresis demonstrated that Oct1 binds to both alleles in vitro, but decreased HLA-C promoter activity was observed in a luciferase reporter assay for rs2395471_G relative to rs2395471_A on a fixed promoter background. The rs2395471 variant accounts for up to 36% of the explained variation of HLA-C level. These data strengthen our understanding of HLA-C transcriptional regulation and provide a basis for understanding the potential consequences of manipulating HLA-C levels therapeutically.
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Nicolas
N
Vince
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Hongchuan
H
Li
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA.
Veron
V
Ramsuran
Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Center for the AIDS Programme of Research in South Africa, University of KwaZuluNatal, Durban 4091, South Africa.
Vivek
V
Naranbhai
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Fuh-Mei
FM
Duh
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Benjamin P
BP
Fairfax
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Bahara
B
Saleh
Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.
Julian C
JC
Knight
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
Stephen K
SK
Anderson
Cancer and Inflammation Program, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA. Electronic address: carringm@mail.nih.gov.
Mary
M
Carrington
D000465:Algorithms; D000483:Alleles; D001665:Binding Sites / Q000235:genetics; D066264:Datasets as Topic; D015894:Genome, Human / Q000235:genetics; D055106:Genome-Wide Association Study; D015236:HLA-C Antigens / Q000096:biosynthesis* / Q000235:genetics*; D006367:HeLa Cells; D006801:Humans; D050811:Octamer Transcription Factor-1 / Q000378:metabolism*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics; D024363:Transcription Initiation Site; D014158:Transcription, Genetic
D015236:HLA-C Antigens; D050811:Octamer Transcription Factor-1