F.E. Baralle

High frequency of TARDBP gene mutations in Italian patients with amyotrophic lateral sclerosis

Recent studies identified rare missense mutations in amyotrophic lateral sclerosis (ALS) patients in the TARDBP gene encoding TAR DNA binding protein (TDP)‐43, the major protein of the ubiquitinated inclusions (UBIs) found in affected motor neurons (MNs). The aim of this study was to further define the spectrum of TARDBP mutations in a large cohort of 666 Italian ALS patients (125 familial and 541 sporadic cases). The entire coding region was sequenced in 281 patients, while in the remaining 385 cases only exon 6 was sequenced. In 18 patients, of which six are familial, we identified 12 different heterozygous missense mutations (nine novel) all locating to exon 6, which were absent in 771 matched controls. The c.1144G>A (p.A382T) variation was observed in seven patients, thus representing the most frequent TARDBP mutation in ALS. Analysis of microsatellites surrounding the TARDBP gene indicated that p.A382T was inherited from a common ancestor in 5 of the 7 patients. Altogether, the frequency of TARDBP gene mutations appears to be particularly high in Italian ALS patients compared to individuals of mainly Northern European origin (2.7% vs. 1%). Western blot analysis of lymphocyte extracts from two patients carrying the p.A382T and p.S393L TARDBP mutations showed the presence of lower molecular weight TDP‐43 bands, which were more abundant than observed in healthy controls and patients negative for TARDBP mutations. In conclusion, this report contributes to the demonstration of the causative role of the TARDBP gene in ALS pathogenesis and indicates that mutations may affect the stability of the protein even in nonneuronal tissues. Hum Mutat 0, 1–7, 2009.

Autoregulation of TDP-43 mRNA levels involves interplay between transcription, splicing, and alternative polyA site selection

TDP-43 is a critical RNA-binding factor associated with pre-mRNA splicing in mammals. Its expression is tightly autoregulated, with loss of this regulation implicated in human neuropathology. We demonstrate that TDP-43 overexpression in humans and mice activates a 3 untranslated region (UTR) intron, resulting in excision of the proximal polyA site (PAS) pA(1). This activates a cryptic PAS that prevents TDP-43 expression through a nuclear retention mechanism. Superimposed on this process, overexpression of TDP-43 blocks recognition of pA(1) by competing with CstF-64 for PAS binding. Overall, we uncover complex interplay between transcription, splicing, and 3 end processing to effect autoregulation of TDP-43.

Regulation of the fibronectin EDA exon alternative splicing. Cooperative role of the exonic enhancer element and the 5′ splicing site

Alternatively spliced exons generally contain weak splicing sites, and exonic and/or intronic regulatory elements recognised by trans‐acting auxiliary splicing factors. The EDA exon of the fibronectin gene is a typical example of an exon bearing a purine‐rich exon splicing enhancer (ESE) element recognised by members of the SR phosphoprotein family. The regulatory region that governs splicing in the human EDA exon also contains an exon splicing silencer (ESS) element. We have cloned the mouse EDA genomic region, and we show that the ESE and the ESS elements, although they have base differences, can be replaced by the human elements without significant change in the exon inclusion/exclusion ratio. This fact suggests a common splicing regulatory mechanism across species. We demonstrate in vivo the functional activity of the mouse ESE element in splicing. We also show that the trans‐acting factors recognising this element cooperate with the 5′ splicing site of the EDA exon to facilitate proper exon recognition. Indeed, a strong 5′ splicing site overrides the ESE function in exon recognition. However, the presence of a strong 3′ splicing site is not sufficient to compensate for the absence of the splicing enhancer. Our data provide in vivo evidence of the interplay between the exonic splicing regulatory elements and the splicing sites, leading finally to subtle regulation of alternative splicing.

Hepatitis C genotypes in patients with dual hepatitis B and C virus infection

In patients with chronic hepatitis B and C virus (HBV, HCV) infection, an inverse relationship in the replicative activity of the two viruses has been reported. In the present study the genotype of HCV was evaluated in 34 consecutive cases found with hepatitis B surface antigen (HBsAg) and anti‐HCV in the serum, in order to identify its possible influence in determining the pattern of HBV/HCV interaction. Nineteen patients were HCV‐RNA positive and could be genotyped: 8 were infected by HCV‐1 (3 by HCV‐1a and 5 by HCV‐1b), 10 by HCV‐2, and only 1 by HCV‐3. Among these, 3 were HBV‐DNA positive, compared to 10 of 15 HCV‐RNA‐negative patients (P = 0.003), and all 3 were coinfected with HCV‐2.

IN VIVO TRANSLATIONAL EFFICIENCY OF DIFFERENT HEPATITIS C VIRUS 5'-UTRS

Initiation of translation in hepatitis C virus (HCV) is dependent on the presence of an internal ribosome entry site (IRES) contained in its 341‐nt‐long 5′‐untranslated region (UTR). This region is very conserved among different isolates and has been used to classify HCV isolates in six different genotypes. These genotypes differ in nucleotide sequence that generally preserve the IRES structure. However, the small differences seen may be biologically and clinically significant as the HCV strains seem to differ from each other in several important ways, such as the behaviour of the viral infection and the response to interferon therapy. Therefore, differences in translational initiation efficiency amongst the various genotypes could provide an explanation for these phenomena. Using a bicistronic expression system we have compared the in vivo translational ability of the three most common European genotypes of HCV (1, 2, and 3). The results show that genotype 3 is less able than 1 and 2 to promote translation initiation. In addition, by site‐directed mutagenesis of the sequence of the IRES domain III apical stem loop structure, we have shown that the conservation of the primary nucleotide sequence and not only the structure, is important for the conservation of IRES function.

The neutralizing antibody response against a conserved region of human immunodeficiency virus type 1 gp41 (amino acid residues 731-752) is uniquely directed against a conformational epitope

Amino acids 731-752 (731PRGPDRPEGIEEEGGERDRDRS752) of the transmembrane glycoprotein gp41 of human immunodeficiency virus type 1 (HIV-1) are conserved in most virus isolates and are controversially reported to be implicated in virus neutralization. The humoral response in infected patients against this region is poor and humans immunized with gp160 show high levels of antibodies against the peptide but poor neutralization titres. Nonetheless, several groups have succeeded in obtaining neutralizing antibodies against this sequence using different antigen-presenting systems. In order to identify the sequence(s) against which the neutralizing response was generated, we used the flock house virus (FHV) antigen-presenting system to analyse neutralizing antisera from mice immunized with a cowpea mosaic virus (CPMV) chimera expressing the 731-752 sequence. Data show that the neutralizing response is uniquely directed against a conformational epitope mapping to the ERDRD portion of this sequence, although the major antibody response, which is non-linear, and is not neutralizing, is against an IEEE epitope. These results provide an explanation for the controversy regarding the immunogenicity of this region of gp41 and suggest that this conformational epitope, in the absence of the non-neutralizing epitope, should be considered for a subunit vaccine. In addition, this study highlights the usefulness of antigen-presenting systems that preserve epitope conformation in the investigation of immune responses.

Conformational display of two neutralizing epitopes of HIV-1 gp41 on the Flock House virus capsid protein

We have developed an antigen presenting system based on the capsid protein of the Flock House virus (FHV) and used it to display, in different positions on its external surface, two neutralizing epitopes found at residues 735-752 of HIV-1 gp160. We have compared the immunoreactivity of these FHV chimeric proteins and of the corresponding synthetic peptide using a panel of neutralizing mouse monoclonal antibodies (mAbs) directed against two distinct sequences (IEEE and ERDRD) contained in this epitope of the gp41 region. We have observed that both the FHV chimeric protein and the synthetic peptide are clearly detected in ELISA procedures by the mAbs recognizing the sequence IEEE. The denaturation of these recombinant proteins had little effect on the recognition pattern of this group of monoclonals, suggesting minor conformational requirements for the display of this epitope. The FHV chimeric proteins were also recognized by the mAbs directed against the ERDRD epitope, whereas the corresponding synthetic peptide was not recognized. In this case, denaturation of these recombinant proteins completely abolished the reactivity of the second group of mAbs, arguing for the existence of strong conformational constraints. Additionally, we have investigated whether an isolated loop structure from the FHV protein was sufficient to provide the conformational requirements for the presentation of these epitopes. These experiments have shown that the stabilized loop structure, although improving the presentation of both epitopes, is not as efficient as the native loop in the intact FHV protein. The data obtained with these mAbs support the recently observed limitations in the use of synthetic peptides for the screening of the immune response against conformational epitopes. The establishment of appropriate tools able to present epitope sequences in a structure resembling the native conformation will be useful for accurate epidemiological studies and for the design of new epitope-specific vaccines.

Comparison of genotyping and serotyping methods for the identification of hepatitis C virus types

The usefulness of identification of hepatitis C virus (HCV) genotype has recently been investigated for the clinical management of patients infected by HCV. In the present study, the HCV genotype infecting 127 patients was determined by two different methods: HCV genotyping using a dot-blot assay with type-specific probes derived from the 5-UTR of HCV genome and HCV serotyping using an ELISA system in which type-specific antibodies against the NS4 region were detected. Overall, a good correlation of the two methods was observed, the main discrepancy being 4 patients with sequence-confirmed HCV-2 (2 cases) and HCV-3 (2 cases) genotypes recognized as HCV-1 by serotyping. Mixed infections were not detected by either method. In 19 PCR negative sera, in which the HCV genotype could not be evaluated, no particular serotype profile was observed. In conclusion, the molecular and serological techniques are almost equivalent in determining the viral type, although in individual cases, especially in PCR negative patients, the clinical meaning of the serotyping result remains to be determined.

Regulation of gene expression by TDP-43 and FUS/TLS in frontotemporal lobar degeneration.

Two proteins have recently received considerable attention in the neurodegenerative research field: TDP-43 and FUS/TLS. The reason is that both proteins have been found to represent major protein components of the intracellular inclusions occurring in the neuronal tissues of patients affected by Fronto Temporal Lobar Degeneration and Amyotrophic Lateral Sclerosis. One of the most interesting features of this discovery is that both proteins have in common several structural properties. In particular, they are multifunctional RNA-binding proteins (RBPs) already known to play a role in several cellular processes such as transcription, pre-mRNA splicing, and mRNA stability. The potential consequences of changes in their intracellular localization and protein modification status (phosphorylation, ubiquitination, and cleavage) on neuronal metabolism represent one of the major research challenges faced today by researchers. There is hope that a detailed knowledge of the gain- or loss-of-function mechanisms mediated by alterations in these proteins in the neuronal environment may provide novel therapeutic strategies for the treatment of these diseases. Here, we aim to provide an updated review of ways by which TDP-43 and FUS/TLS influence gene expression. In particular, we will focus on the characterized properties of both proteins that involve gene transcription and also RNA splicing, transport and stability processes.

Prediction of successful outcome in a randomised controlled trial of the long‐term efficacy of interferon alpha treatment for chronic hepatitis C

To evaluate the efficacy of a 12‐month course of recombinant interferon alpha (IFN‐α2b), and to assess predictive factors of successful response to IFN therapy in chronic active hepatitis C (HCV CAH), 242 patients with histologically proven HCV CAH were assigned randomly to two groups, one treated with IFN‐α2b (3 MU three times weekly, intramuscularly), the other untreated. To determine the efficacy of IFN‐α2b 12 months after therapy, a second liver biopsy was carried out on 100 treated patients and 27 untreated patients. The biochemical, virological, and serological response of patients followed up for at least 50 months after treatment was also evaluated to confirm the efficacy of IFN‐α2b. The genotypes of infecting HCV, anti‐HCV core IgM, and HCV‐RNA concentrations were also analysed and the predictors of response determined by univariate and multivariate analyses. Response was defined in terms of the normalisation of aminotransferase activities and the disappearance of HCV‐RNA. The overall long‐term response was 39.4%. Anti‐HCV core IgM levels were significantly lower in long‐term responders. Patients with increased levels of IgM anti HCV core (>3.8 sample/cut‐off), infected with genotype 1b were nonresponders. Liver histology improved significantly in patients with long‐term response. Multivariate analysis identified three independent predictors of the likelihood of long‐term response to IFN therapy: age younger than 40 years, basal anti‐HCV core IgM levels ≤ 3.8, and genotypes other than 1b. These data indicate that the treatment with IFN‐α2b used in this randomised controlled trial is effective in HCV CAH. Anti‐HCV core IgM was the strongest predictor of long‐term response in the present study. J. Med. Virol. 58:26–34, 1999.