The HFE gene undergoes alternate splicing processes

HFE gene: Structure, function, mutations, and associated iron abnormalities

The hemochromatosis gene HFE was discovered in 1996, more than a century after clinical and pathologic manifestations of hemochromatosis were reported. Linked to the major histocompatibility complex (MHC) on chromosome 6p, HFE encodes the MHC class I-like protein HFE that binds beta-2 microglobulin. HFE influences iron absorption by modulating the expression of hepcidin, the main controller of iron metabolism. Common HFE mutations account for ~90% of hemochromatosis phenotypes in whites of western European descent. We review HFE mapping and cloning, structure, promoters and controllers, and coding region mutations, HFE protein structure, cell and tissue expression and function, mouse Hfe knockouts and knockins, and HFE mutations in other mammals with iron overload. We describe the pertinence of HFE and HFE to mechanisms of iron homeostasis, the origin and fixation of HFE polymorphisms in European and other populations, and the genetic and biochemical basis of HFE hemochromatosis and iron overload.

Preliminary investigation of bottlenose dolphins (Tursiops truncatus) for hfe gene-related hemochromatosis

Hemochromatosis (iron storage disease) has been reported in diverse mammals including bottlenose dolphins (Tursiops truncatus). The primary cause of excessive iron storage in humans is hereditary hemochromatosis. Most human hereditary hemochromatosis cases (up to 90%) are caused by a point mutation in the hfe gene, resulting in a C282Y substitution leading to iron accumulation. To evaluate the possibility of a hereditary hemochromatosis-like genetic predisposition in dolphins, we sequenced the bottlenose dolphin hfe gene, using reverse transcriptase-PCR and hfe primers designed from the dolphin genome, from liver of affected and healthy control dolphins. Sample size included two case animals and five control animals. Although isotype diversity was evident, no coding differences were identified in the hfe gene between any of the animals examined. Because our sample size was small, we cannot exclude the possibility that hemochromatosis in dolphins is due to a coding mutation in the hfe gene. Other potential causes of hemochromatosis, including mutations in different genes, diet, primary liver disease, and insulin resistance, should be evaluated.

Alternative polyadenylation and nonsense-mediated decay coordinately regulate the human HFE mRNA levels

Nonsense-mediated decay (NMD) is an mRNA surveillance pathway that selectively recognizes and degrades defective mRNAs carrying premature translation-termination codons. However, several studies have shown that NMD also targets physiological transcripts that encode full-length proteins, modulating their expression. Indeed, some features of physiological mRNAs can render them NMD-sensitive. Human HFE is a MHC class I protein mainly expressed in the liver that, when mutated, can cause hereditary hemochromatosis, a common genetic disorder of iron metabolism. The HFE gene structure comprises seven exons; although the sixth exon is 1056 base pairs (bp) long, only the first 41 bp encode for amino acids. Thus, the remaining downstream 1015 bp sequence corresponds to the HFE 3′ untranslated region (UTR), along with exon seven. Therefore, this 3′ UTR encompasses an exon/exon junction, a feature that can make the corresponding physiological transcript NMD-sensitive. Here, we demonstrate that in UPF1-depleted or in cycloheximide-treated HeLa and HepG2 cells the HFE transcripts are clearly upregulated, meaning that the physiological HFE mRNA is in fact an NMD-target. This role of NMD in controlling the HFE expression levels was further confirmed in HeLa cells transiently expressing the HFE human gene. Besides, we show, by 3′-RACE analysis in several human tissues that HFE mRNA expression results from alternative cleavage and polyadenylation at four different sites – two were previously described and two are novel polyadenylation sites: one located at exon six, which confers NMD-resistance to the corresponding transcripts, and another located at exon seven. In addition, we show that the amount of HFE mRNA isoforms resulting from cleavage and polyadenylation at exon seven, although present in both cell lines, is higher in HepG2 cells. These results reveal that NMD and alternative polyadenylation may act coordinately to control HFE mRNA levels, possibly varying its protein expression according to the physiological cellular requirements.

Differential HFE gene expression is regulated by alternative splicing in human tissues

BACKGROUND

The pathophysiology of HFE-derived Hereditary Hemochromatosis and the function of HFE protein in iron homeostasis remain uncertain. Also, the role of alternative splicing in HFE gene expression regulation and the possible function of the corresponding protein isoforms are still unknown. The aim of this study was to gain insights into the physiological significance of these alternative HFE variants.

METHODOLOGY/PRINCIPAL FINDINGS

Alternatively spliced HFE transcripts in diverse human tissues were identified by RT-PCR, cloning and sequencing. Total HFE transcripts, as well as two alternative splicing transcripts were quantified using a real-time PCR methodology. Intracellular localization, trafficking and protein association of GFP-tagged HFE protein variants were analysed in transiently transfected HepG2 cells by immunoprecipitation and immunofluorescence assays. Alternatively spliced HFE transcripts present both level- and tissue-specificity. Concerning the exon 2 skipping and intron 4 inclusion transcripts, the liver presents the lowest relative level, while duodenum presents one of the highest amounts. The protein resulting from exon 2 skipping transcript is unable to associate with β2M and TfR1 and reveals an ER retention. Conversely, the intron 4 inclusion transcript gives rise to a truncated, soluble protein (sHFE) that is mostly secreted by cells to the medium in association with β2M.

CONCLUSIONS/SIGNIFICANCE

HFE gene post-transcriptional regulation is clearly affected by a tissue-dependent alternative splicing mechanism. Among the corresponding proteins, a sHFE isoform stands out, which upon being secreted into the bloodstream, may act in remote tissues. It could be either an agonist or antagonist of the full length HFE, through hepcidin expression regulation in the liver or by controlling dietary iron absorption in the duodenum.

The ethnospecific distribution of the HFE haplotypes for IVS2(+4)t/c, IVS4(-44)t/c, and IVS5(-47)g/a in populations of Russia and possible effects of these single-nucleotide polymorphisms in splicing

AIM

The aim of this work was a haplotype analysis of the major mutations (C282Y, H63D, S65C) and IVS2(+4)t/c, IVS4(-44)t/c, and IVS5(-47)a/g polymorphisms of the hemochromatosis HFE gene in populations inhabiting the territories of Russia (Russians, Finno-Ugrians, Central Asians, and Arctic Mongoloids).

METHOD

The hemochromatosis gene (HFE) alleles were detected using the polymerase chain reaction/restriction fragment length polymorphism method.

RESULTS

Of the eight possible intronic haplotype variants, the TTG, TTA, CTA, and CCA were identified. The HFE alleles with the different haplotype variants were distributed in an ethnospecific manner among the populations. Our finding was that every one of the C282Y, H63D, and S65C mutations was in linkage disequilibrium only with one of the intronic haplotype variants: TTG, CTA, and CCA, respectively. The data from context analysis of DNA regions where the examined single-nucleotide polymorphisms are located suggested their involvement in splicing.

CONCLUSIONS

Different genotypes of the HFE gene occur at different frequencies among populations of Russia. Carriers of the specific genotype variants may potentially express distinct sets of alternative HFE mRNAs.

Deletion of murine Smn exon 7 directed to liver leads to severe defect of liver development associated with iron overload

Spinal muscular atrophy (SMA) is characterized by degeneration of lower motor neurons caused by mutations of the survival motor neuron 1 gene (SMN1). SMN is involved in various processes including the formation of the spliceosome, pre-mRNA splicing and transcription. To know whether SMN has an essential role in all mammalian cell types or an as yet unknown specific function in the neuromuscular system, deletion of murine Smn exon 7, the most frequent mutation found among SMA patients, has been restricted to liver. Homozygous mutation results in severe impairment of liver development associated with iron overload and lack of regeneration leading to dramatic liver atrophy and late embryonic lethality of mutant mice. These data strongly suggest an ubiquitous and essential role of full-length SMN protein in various mammalian cell types. In SMA patients, the residual amount of SMN allows normal function of various organs except motor neurons. However, data from mouse and human suggest that other tissues might be involved in severe form of SMA or during prolonged disease course which reinforce the need of therapeutic approaches targeted to all tissues. In addition, liver function of patients should be carefully investigated and followed up before and during therapeutic trials.

Pathogenesis of hereditary hemochromatosis

Hereditary hemochromatosis comprises several inherited disorders of iron homeostasis characterized by increased gastrointestinal iron absorpstion and resultant tissue iron deposition. The identification of HFE and other genes involved in iron metabolism has greatly expanded our understanding of hereditary hemochromatosis. Two major hypotheses have been proposed to explain the pathogenesis of HFE-related hereditary hemochromatosis: the hepcidin hypothesis and the duodenal crypt cell programming hypothesis.

Mechanisms of iron accumulation in hereditary hemochromatosis

Hereditary hemochromatosis (HH) is a common inborn error of iron metabolism characterized by excess dietary iron absorption and iron deposition in several tissues. Clinical consequences include hepatic failure, hepatocellular carcinoma, diabetes, cardiac failure, impotence, and arthritis. Despite the discovery of the mutation underlying most cases of HH, considerable uncertainty exists in the mechanism by which the normal gene product, HFE, regulates iron homeostasis. Knockout of the HFE gene clearly confers the HH phenotype on mice. However, studies on HFE expressed in cultured cells have not yet clarified the mechanism by which HFE mutations lead to increased dietary iron absorption. Recent discoveries suggest other genes, including a second transferrin receptor and the circulating peptide hepcidin, participate in a shared pathway with HFE in regulation of iron absorption. This review summarizes our current understanding of the relationship between iron stores and absorption and presents models to explain the dysregulated iron homeostasis in HH.

Complete Characterization of the 3′ Region of the Human and Mouse Hereditary Hemochromatosis HFE Gene and Detection of Novel Splicing Forms

The human HFE gene was identified in 1996 as the gene whose mutations are responsible for hereditary hemochromatosis in most patients. Expression analysis by Northern blot indicated that the gene was approximately 4.1 kb in length. However, the cDNA reported was only 2716 bp. These results implied that at least 1.4 kb of the mRNA remained to be identified. In the present study, we detected several 3' EST clones while screening the genomic region of the gene in search of potential additional HFE mRNA sequences. Subsequent sequencing of these EST clones and RT-PCR experiments revealed that exon 7 of the HFE gene has, in fact, a length of 1944 bp and it presents two polyadenylation signals. The new human HFE exon 7 region has been screened in non-C282Y HH patients in search for new putative mutations. Mouse 3' RACE experiments also further extend the previously reported mouse HFE exon 6 sequence. Additionally, we report two novel end forms of the human HFE gene detected by 3' RACE experiments and several novel splicing forms identified in the HepG2 cell line.