title: Characterization of LEDGF/p75 genetic variants and association with HIV-1 disease progression.
abstract: BACKGROUND
  As Lens epithelium-derived growth factor (LEDGF/p75) is an important co-factor involved in HIV-1 integration, the LEDGF/p75-IN interaction is a promising target for the new class of allosteric HIV integrase inhibitors (LEDGINs). Few data are available on the genetic variability of LEDGF/p75 and the influence on HIV disease in vivo. This study evaluated the relation between LEDGF/p75 genetic variation, mRNA expression and HIV-1 disease progression in order to guide future clinical use of LEDGINs.
  
  
  METHODS
  Samples were derived from a therapy-naïve cohort at Ghent University Hospital and a Spanish long-term-non-progressor cohort. High-resolution melting curve analysis and Sanger sequencing were used to identify all single nucleotide polymorphisms (SNPs) in the coding region, flanking intronic regions and full 3'UTR of LEDGF/p75. In addition, two intronic tagSNPs were screened based on previous indication of influencing HIV disease. LEDGF/p75 mRNA was quantified in patient peripheral blood mononuclear cells (PBMC) using RT-qPCR.
  
  
  RESULTS
  325 samples were investigated from patients of Caucasian (n = 291) and African (n = 34) origin, including Elite (n = 49) and Viremic controllers (n = 62). 21 SNPs were identified, comprising five in the coding region and 16 in the non-coding regions and 3'UTR. The variants in the coding region were infrequent and had no major impact on protein structure according to SIFT and PolyPhen score. One intronic SNP (rs2737828) was significantly under-represented in Caucasian patients (P<0.0001) compared to healthy controls (HapMap). Two SNPs showed a non-significant trend towards association with slower disease progression but not with LEDGF/p75 expression. The observed variation in LEDGF/p75 expression was not correlated with disease progression.
  
  
  CONCLUSIONS
  LEDGF/p75 is a highly conserved protein. Two non-coding polymorphisms were identified indicating a correlation with disease outcome, but further research is needed to clarify phenotypic impact. The conserved coding region and the observed variation in LEDGF/p75 expression are important characteristics for clinical use of LEDGINs.
authors.affiliation: HIV Translational Research Unit, Department of General Internal Medicine and Infectious Diseases, Ghent University Hospital, Ghent, Belgium.
authors.forename: Peter
authors.initials: P
authors.lastname: Messiaen
authors.forename: Ward
authors.initials: W
authors.lastname: De Spiegelaere
authors.forename: Jose
authors.initials: J
authors.lastname: Alcami
authors.forename: Karen
authors.initials: K
authors.lastname: Vervisch
authors.forename: Petra
authors.initials: P
authors.lastname: Van Acker
authors.forename: Bruno
authors.initials: B
authors.lastname: Verhasselt
authors.forename: Pieter
authors.initials: P
authors.lastname: Meuwissen
authors.forename: Esther
authors.initials: E
authors.lastname: Calonge
authors.forename: Nuria
authors.initials: N
authors.lastname: Gonzalez
authors.forename: Felix
authors.initials: F
authors.lastname: Gutierrez-Rodero
authors.forename: Carmen
authors.initials: C
authors.lastname: Rodriguez-Martín
authors.forename: Erica
authors.initials: E
authors.lastname: Sermijn
authors.forename: Bruce
authors.initials: B
authors.lastname: Poppe
authors.forename: Dirk
authors.initials: D
authors.lastname: Vogelaers
authors.forename: Chris
authors.initials: C
authors.lastname: Verhofstede
authors.forename: Linos
authors.initials: L
authors.lastname: Vandekerckhove
mesh_terms: D020413:3' Untranslated Regions; D000328:Adult; D000595:Amino Acid Sequence; D017124:Conserved Sequence; D018450:Disease Progression; D005091:Exons; D005260:Female; D015658:HIV Infections / Q000175:diagnosis / Q000235:genetics* / Q000473:pathology* / Q000821:virology; D015497:HIV-1; D006801:Humans; D036341:Intercellular Signaling Peptides and Proteins / Q000235:genetics*; D007438:Introns; D007963:Leukocytes, Mononuclear / Q000378:metabolism; D008297:Male; D008969:Molecular Sequence Data; D009154:Mutation; D016366:Open Reading Frames; D020641:Polymorphism, Single Nucleotide; D011379:Prognosis; D012333:RNA, Messenger / Q000235:genetics; D017422:Sequence Analysis, DNA
chemical_list: D020413:3' Untranslated Regions; D036341:Intercellular Signaling Peptides and Proteins; D012333:RNA, Messenger; C119380:lens epithelium-derived growth factor