Elsevier

Human Immunology

Volume 80, Issue 2, February 2019, Pages 112-119
Human Immunology

HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels

https://doi.org/10.1016/j.humimm.2018.10.016Get rights and content

Abstract

HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from −1893 to −943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named Fdistal-C. This haplotype is associated with F01:01:02 alleles, while alleles from the F01:01:01 or F01:03 groups present closely related promoter sequences. Fdistal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. Fdistal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that Fdistal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with Fdistal-C and F01:01:02 alleles.

Introduction

HLA-F is a conserved non-classical HLA class I gene presenting a differentiated expression profile when compared with other HLA class I genes. HLA-F is expressed intracellularly in lymphocytes and monocytes, but it can be detected at the cell surface upon activation [1], [2], [3]. The tissue-specific expression has been reported on tonsil, spleen, thymus [1], trophoblasts [4], [5], and fetal liver [2], [6]. HLA-F expression was also reported for different cell lines, including EBV-transformed lymphoblastoid and monocytic cell lines [7], B, and HUT-78 cell lines [1], J82 transitional cell carcinoma, MOLT-3T cell leukemia, JEG choriocarcinoma, BeWo choriocarcinoma, and 3A-subE SV40 transformed [5]. Moreover, HLA-F expression was detected for gastric, non-small-cell lung and breast cancer [8], [9], [10], and also on esophageal squamous cell carcinoma [11].

Unlike other HLA class I molecules, HLA-F can be exported to the cell surface by a mechanism that is independent of loading with peptides in the endoplasmic reticulum but depends on the HLA-F cytoplasmic tail [12]. HLA-F also presents an intracellular function, associated with other HLA class I molecules at the “open conformer” mode. HLA-F may play a role in the stabilization of open conformers, or even participating in a recycling mechanism of these molecules, possibly being associated with the cross-presentation of exogenous antigens [13], [14]. HLA class I molecules in an “open conformer” manner, including HLA-F, may interact with KIR receptors, thus modulating NK cell function [13], [15], [16]. Moreover, the HLA-F peptide-binding groove is different from those of other class I genes [17]. Because of a mutation (R62W) leading to an open-ended groove that can accommodate long peptides, HLA-F presents peptides of unconventional length [13], [17].

Although its exact function is not well established, HLA-F may present tolerogenic and immunomodulatory properties as other non-classical HLA class I molecules since (a) HLA-F interacts with Natural Killer receptors (NKRs), such as ILT2, ILT4, KIR2DS4, KIR3DL2, KIR3DL1, and KIR3DS1 [1], [13], [15], [16], [17], [18]; (b) HLA-F variants were associated with implantation success during pregnancy [19]; (c) HLA-F is expressed on trophoblasts [4], [5], together with HLA-G, HLA-E and HLA-C [4]; (d) HLA-F molecule is quite conserved at the DNA and protein levels, as also observed for HLA-G and HLA-E [20], [21], [22], [23], [24], [25], [26]; (e) HLA-F is highly conserved among primates, including humans, bonobos, gorillas, orangutans, and chimpanzees, suggesting a critical function in the immune response [25], [27], [28], [29].

Regarding its genetic diversity, there are 31 different HLA-F sequences (or alleles) encoding 6 different full-length proteins described so far at the International Immunogenetics database (IPD-IMGT/HLA, version 3.33.0). However, due to the lack of studies addressing HLA-F variability in worldwide populations, HLA-F might be even more polymorphic. So far, only one study has evaluated HLA-F variability by using massively parallel sequencing in a population-level approach [20], revealing the presence of many new HLA-F alleles. Nevertheless, most of these new alleles encode the same HLA-F molecules already reported, emphasizing that HLA-F is indeed the most conserved HLA class I gene. In addition, there is a lack of studies addressing the HLA-F promoter structure. Variability at the regulatory segments may directly influence the HLA-F expression quantitatively and qualitatively. Here we evaluated the variability and haplotype structure of the HLA-F distal promoter segment in the same Brazilian samples already characterized for the proximal promoter and the coding region [20], correlating the HLA-F haplotypes with mRNA expression levels.

Section snippets

HLA-F distal promoter variability and haplotypes

We evaluated the HLA-F distal promoter variability in 204 individuals from the State of São Paulo, Brazil, associating each promoter haplotype with the coding alleles reported for the same samples in a previous study [20]. All participants gave written informed consent to participate in this study, and the UNESP School of Medicine Ethics Committee (#24157413.7.0000.5411) approved this study protocol. HLA-F amplification and sequencing library preparation was performed as described elsewhere [20]

HLA-F promoter variability and extended haplotypes

We evaluated the HLA-F promoter segment between positions −1893 and −943, considering as +1 the Adenine of the first translated ATG. This comprises a promoter segment of 950 bp, henceforth considered as the HLA-F distal promoter. Within this segment, there were 13 variable sites (Table 1), ten of them presenting alternative alleles with frequencies above 15%, and all fitting Hardy-Weinberg equilibrium expectations (P > 0.05). Nine of these variable sites presented the same allele frequencies,

Discussion

Reports on HLA-F variability are quite scarce, mainly when the promoter segment is included. In fact, as far as we know, a single study evaluated the HLA-F promoter, comprehending approximately 2 kb upstream the first translated ATG, but it only explored a few cell lines [25]. This study described a pattern of variation similar to the one detected in this Brazilian population sample. Moreover, only one study evaluated the complete HLA-F coding segment by second-generation sequencing, but the

Acknowledgements

This work was supported by FAPESP/Brazil (Grant# 2013/17084-2). E.C.C. and C.T.M.J. are supported by CNPq/Brazil (Grants# 302590/2016-1 and 309572/2014-2). R.V.B, J.R., T.H.A.L., and L.C.V.C. are supported by the Brazilian Coordination for the Improvement of Higher Education Personnel (CAPES/Brazil).

Conflict of interests

There is no conflict of interest.

References (43)

  • S.J. Gobin et al.

    Transcriptional regulation of the MHC class Ib genes HLA-E, HLA-F, and HLA-G

    Hum. Immunol.

    (2000)
  • E.J. Lepin et al.

    Functional characterization of HLA-F and binding of HLA-F tetramers to ILT2 and ILT4 receptors

    Eur. J. Immunol.

    (2000)
  • S.D. Wainwright et al.

    HLA-F is a predominantly empty, intracellular, TAP-associated MHC class Ib protein with a restricted expression pattern

    J. Immunol.

    (2000)
  • N. Lee et al.

    HLA-F is a surface marker on activated lymphocytes

    Eur. J. Immunol.

    (2010)
  • R. Hackmon et al.

    Definitive class I human leukocyte antigen expression in gestational placentation: HLA-F, HLA-E, HLA-C, and HLA-G in extravillous trophoblast invasion on placentation, pregnancy, and parturition

    Am. J. Reprod. Immunol.

    (2017)
  • A. Ishitani et al.

    Protein expression and peptide binding suggest unique and interacting functional roles for HLA-E, F, and G in maternal-placental immune recognition

    J. Immunol.

    (2003)
  • J.M. Houlihan et al.

    Evidence for the expression of non-HLA-A,-B,-C class I genes in the human fetal liver

    J. Immunol.

    (1992)
  • N. Lee et al.

    HLA-F surface expression on B cell and monocyte cell lines is partially independent from tapasin and completely independent from TAP

    J. Immunol.

    (2003)
  • A. Harada et al.

    Clinical implication of human leukocyte antigen (HLA)-F expression in breast cancer

    Pathol. Int.

    (2015)
  • S. Ishigami et al.

    Human leukocyte antigen (HLA)-E and HLA-F expression in gastric cancer

    Anticancer Res.

    (2015)
  • L.H. Boyle et al.

    Selective export of HLA-F by its cytoplasmic tail

    J. Immunol.

    (2006)
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