Control of nucleo-cytoplasmic HLA-DRA mRNA partitioning by interaction of a retention signal with compartmentalized proteins

Donor Specific Antibodies are not only directed against HLA-DR: Minding your Ps and Qs

During solid organ transplantation, interactions between recipient and donor immune cells occur chiefly in the allograft microvasculature. All three HLA class II antigens, DR, DP and DQ, have been detected on renal EC with a markedly increased expression of HLA class II observed in renal allografts undergoing rejection. Recent studies of donor-specific antibodies (DSA) have exposed the prevalence of de novo DSA directed against HLA-DQ, as well as a strong association between these antibodies and allograft damage. The HLA-DQ molecule can be distinguished from the other class II antigens by its transcription, expression and peptide repertoire. The distinct intragraft expression and immunogenicity of HLA-DQ may contribute to the incidence of HLA-DQ DSA, as well as directing the DSA-mediated damage. The possibility of HLA class II antigen-specific signaling in EC may reveal different mechanisms of allograft damage that act in tandem with complement-dependent injury. This review addresses the features of the HLA-DQ heterodimer that may underlie the high incidence of HLA-DQ directed DSA and their association with allograft damage. We also consider existing data in hematopoietic stem cell transplantation concerning HLA directed DSA.

Co-regulated expression of alpha and beta mRNAs encoding HLA-DR surface heterodimers is mediated by the MHCII RNA operon

Major histocompatibility complex class II (MHCII) molecules are heterodimeric surface proteins involved in the presentation of exogenous antigens during the adaptive immune response. We demonstrate the existence of a fine level of regulation, coupling the transcription and processing of mRNAs encoding α and β chains of MHCII molecules, mediated through binding of their Untraslated Regions (UTRs) to the same ribonucleoproteic complex (RNP). We propose a dynamic model, in the context of the 'MHCII RNA operon' in which the increasing levels of DRA and DRB mRNAs are docked by the RNP acting as a bridge between 5'- and 3'-UTR of the same messenger, building a loop structure and, at the same time, joining the two chains, thanks to shared common predicted secondary structure motifs. According to cell needs, as during immune surveillance, this RNP machinery guarantees a balanced synthesis of DRA and DRB mRNAs and a consequent balanced surface expression of the heterodimer.

EBP1 and DRBP76/NF90 binding proteins are included in the major histocompatibility complex class II RNA operon

Major histocompatibility complex class II mRNAs encode heterodimeric proteins involved in the presentation of exogenous antigens during an immune response. Their 3'UTRs bind a protein complex in which we identified two factors: EBP1, an ErbB3 receptor-binding protein and DRBP76, a double-stranded RNA binding nuclear protein, also known as nuclear factor 90 (NF90). Both are well-characterized regulatory factors of several mRNA molecules processing. Using either EBP1 or DRBP76/NF90-specific knockdown experiments, we established that the two proteins play a role in regulating the expression of HLA-DRA, HLA-DRB1 and HLA-DQA1 mRNAs levels. Our study represents the first indication of the existence of a functional unit that includes different transcripts involved in the adaptive immune response. We propose that the concept of 'RNA operon' may be suitable for our system in which MHCII mRNAs are modulated via interaction of their 3'UTR with same proteins.

Intragenic amplification and formation of extrachromosomal small circular DNA molecules from the PIP gene on chromosome 7 in primary breast carcinomas

The PIP gene is expressed in exocrine glands and, in pathologic conditions, in breast cysts and breast cancers exhibiting apocrine features. It is localized on the long arm of chromosome 7, a region frequently alterated in mammary tumors. We previously described an abnormal restriction pattern of the PIP gene in 33% of prostate carcinomas analyzed. Here, we analyze the structure of the PIP gene in primary breast carcinomas. We report that part of the 3' end, including exon 3, intron C, two-thirds of exon 4 and a small portion of intron B, is amplified and involved in the formation of extrachromosomal spcDNA molecules in 3/14 (21.4%) breast cancers analyzed. The involvement of a well-defined intragenic region of a gene in the formation of spcDNA appears to be unprecedented. Since spcDNA has been suggested to serve as an enhancer of genetic instability, the PIP gene may be the target of genomic variability processes in breast cancer.

Accumulation of mature mRNA in the nuclear fraction of mammalian cells

Little is known about the nuclear mRNA content of mammalian cells. In this study, we analyzed by Northern blotting with a panel of probes the nuclear and cytoplasmic fractions derived from several rodent cell lines. For most of the genes under study, mature mRNAs could easily be detected in the nuclear fraction and accumulated to higher levels than the corresponding precursors. In addition, significant differences in the nucleo-cytoplasmic partition of mature mRNAs were observed between genes as well as between cell types (NIH 3T3, CTLL-2, D3-ES, PC-12), indicating that this nuclear accumulation of mRNA is regulated. Thus, while it is usually considered that splicing is the limiting step of pre-mRNA processing, these results point towards transport or nuclear retention of mRNA as a key determinant of nuclear mRNA metabolism.

Polymorphism in the 5' terminal region of the mRNA of HLA-DQA1 gene: identification of four groups of transcripts and their association with polymorphism in the alpha 1 domain

Relative to other loci in the MHC, the HLA-DQ locus exhibits an exceptional degree of polymorphism of both A1 and B1 genes, particularly in the region coding for alpha and beta chains. Diversification of the association between different alpha and beta molecules either in cis or in trans contributes to the structural diversity of the repertoire of cell-surface class II protein's in the population. In addition, structural allelic polymorphisms in the 5' regulatory region of both DQB1 and DQA1 shows several linkage groups with respect to the allelic coding sequence of the respective genes. We describe here the allelic polymorphism in the DQA1 mRNA structure located at the 5' untranslated terminal region. This portion of the mRNA molecule represents, in many genes, a cis-acting regulatory sequence playing a role in the posttranscriptional mechanisms by which gene expression can be modulated. Based on detailed transcriptional analysis, we have been able to define at least four groups of transcripts in DQA1. The mRNA variability was associated with the polymorphism of the second exon of the DQA1 gene, coding for the alpha 1 domain and not with the DNA polymorphism in the 5' regulatory region.

The regulation mechanism of HLA class II gene expression at the level of mRNA stability

The number of major histocompatibility complex (MHC) class II antigens may be regulated at different levels. Although transcriptional regulation has been studied most intensely, evidence for control mechanisms acting on the stability of MHC class II mRNAs has been reported. We have previously shown, in fact, that the half-life of MHC class II mRNA rapidly decreases in Raji cells upon inhibition of translation by cycloheximide; further data indicated that this effect was not correlated with the inhibition of the synthesis of trans-acting protein(s) required for mRNA stability. In the present work, we developed an in vitro mRNA decay assay system to measure HLA-DRA mRNA stability and used inhibitors of protein synthesis affecting different steps of the process of translation in order to discriminate among possible mechanisms determining controlled MHC class II mRNA hydrolysis. We found that HLA-DRA mRNA associated with polysomes derived from cells treated with either puromycin (which causes dispersion of polysomes and accumulation of monosomes) or cycloheximide (which slows down translation causing ribosome stalling) is more rapidly degraded than in the absence of protein synthesis inhibitors. On the basis of our findings, we suggest that arrest of protein synthesis per se exposes the HLA-DRA mRNA molecules to degradative activities co-sedimenting with the polysomal fraction.

Nuclear export pathways of tRNA and 40 S ribosomes include both common and specific intermediates

Different classes of RNAs are exported from Xenopus laevis oocyte nuclei by facilitated pathways. We have performed kinetic competition analyses to investigate the relationship between the export pathways of microinjected tRNA and ribosomal subunits. Saturating concentrations of ribosomal subunits do not compete tRNA export. Thus, the saturable factor in the ribosomal subunit export pathway is not limiting for tRNA export. The co-microinjection of ribosomal subunits did, however, stimulate the rate of tRNA export. Co-injected mRNA also stimulated tRNA export. tRNA export itself displays positive cooperative export kinetics that are abrogated by saturating concentrations of rRNA. These results are consistent with the existence of common high affinity RNA-binding sites that can be titrated with tRNA, rRNA or ribosomal subunits, and mRNA. Furthermore, high concentrations of tRNA are also shown to have moderate inhibitory effects on 40 S subunit export, indicating a lower affinity common intermediate also shared by mRNA.