A fast and reliable method for detecting SNP rs67384697 (Hsa-miR-148a binding site) by a single run of allele-specific real-time PCR

HLA. 2020 Sep;96(3):312-322. doi: 10.1111/tan.13971. Epub 2020 Jul 15.

Abstract

Surface expression of human leukocyte antigen (HLA)-class I molecules is critical for modulating T/natural killer lymphocytes' effector functions. Among HLA molecules, HLA-C, the most recently evolved form of class I antigens, is subjected to both transcriptional and multiple post-transcriptional regulation mechanisms affecting its cell surface expression. Among the latter a region placed in the 3' untranslated region of HLA-C transcript contains the single nucleotide polymorphism (SNP) rs67384697 "G-ins/del" that has been found to be strictly associated with surface levels of HLA-C allomorphs because of the effect on the binding site of a microRNA (Hsa-miR-148a). Higher expression of HLA-C has been proved to influence HIV-1 infection via a better control of viremia and a slower disease progression. More importantly, the analysis of SNP rs67384697 "G-ins/del" combined with the evaluation of the HLA-Bw4/-Bw6 C1/C2 supratype, as well as the killer immunoglobulin-like receptor genetic asset, has proved to be pivotal in defining the status of Elite Controllers in the Caucasian population. Here we describe a new reliable and fast method of allele-specific real-time PCR to monitor the integrity/disruption of the binding site of the microRNA Hsa-miR-148a in a high-throughput format that can be easily applied to studies involving large cohorts of individuals.

Keywords: AIDS; HLA-C expression; Hsa-miR-148a; SNP genotyping; allele-specific qPCR; autoimmune diseases.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Binding Sites
  • Humans
  • MicroRNAs* / genetics
  • Polymorphism, Single Nucleotide*
  • Real-Time Polymerase Chain Reaction

Substances

  • MicroRNAs