HLA-B*57 and IFNL4-related polymorphisms are associated with protection against HIV-1 disease progression in controllers

Background

HIV-1-controllers maintain HIV-1 viremia at low levels (normally <2000 HIV-RNA copies/mL) without antiretroviral treatment. However, some HIV-1-controllers have evidence of immunologic progression with marked CD4⁺T-cell decline. We investigated host genetic factors associated with protection against CD4⁺T-cell loss in HIV-1-controllers.

Methods

We analysed the association of interferon lambda 4 (IFNL4)-related polymorphisms and HLA-B haplotypes within Long Term Non-Progressor HIV-1-controllers ((LTNP-C), defined by maintaining CD4⁺T-cells counts >500 cells/mm³ for more than 7 years after HIV-1 diagnosis) versus non-LTNP-C, who developed CD4⁺T-cells counts <500 cells/mm³ Both a Spanish study cohort (n=140) and an international validation cohort (n=914) were examined. Additionally, in a subgroup of individuals HIV-1-specific T-cell responses and soluble cytokines were analysed RESULTS: HLA-B*57 was independently associated with the LTNP-C phenotype (OR=3.056 (1.029-9.069) p=0.044 and OR=1.924 (1.252-2.957) p=0.003) while IFNL4 genotypes represented independent factors for becoming non-LTNP-C (TT/TT, ss469415590, OR=0.401 (0.171-0.942) p=0.036 or A/A, rs12980275, OR=0.637 (0.434-0.934) p=0.021) in the Spanish and validation cohort, respectively, after adjusting for sex, age at HIV-1 diagnosis, IFNL4-related polymorphisms and different HLA-B haplotypes. LTNP-C showed lower plasma IP-10 (p=0.019) and higher IFN-γ (p=0.02) levels than the HIV-1-controllers with diminished CD4⁺T-cell numbers. Moreover, LTNP-C exhibited higher quantities of IL2⁺CD57^- and IFN-γ⁺CD57^- HIV-1-specific CD8⁺T-cells (p=0.002 and 0.041, respectively) than non-LTNP-C.

Conclusions

We have defined genetic markers able to segregate stable HIV-1-controllers from those who experience CD4⁺T-cell decline. These findings allow for identification of HIV-1-controllers at risk for immunologic progression, and provide avenues for personalized therapeutic interventions and precision medicine for optimizing clinical care of these individuals.

The STAT4 gene influences the genetic predisposition to systemic sclerosis phenotype

The aim of this study was to investigate the possible role of STAT4 gene in the genetic predisposition to systemic sclerosis (SSc) susceptibility or clinical phenotype. A total of 1317 SSc patients [896 with limited cutaneous SSc (lcSSc) and 421 with diffuse cutaneous SSc (dcSSc)] and 3113 healthy controls, from an initial case-control set of Spanish Caucasian ancestry and five independent cohorts of European ancestry (The Netherlands, Germany, Sweden, Italy and USA), were included in the study. The rs7574865 polymorphism was selected as STAT4 genetic marker. We observed that the rs7574865 T allele was significantly associated with susceptibility to lcSSc in the Spanish population [P = 1.9 x 10(-5) odds ratio (OR) 1.61 95% confidence intervals (CI) 1.29-1.99], but not with dcSSc (P = 0.41 OR 0.84 95% CI 0.59-1.21). Additionally, a dosage effect was observed showing individuals with rs7574865 TT genotype higher risk for lcSSc (OR 3.34, P = 1.02 x 10(-7) 95% CI 2.11-5.31). The association of the rs7574865 T allele with lcSSc was confirmed in all the replication cohorts with different effect sizes (OR ranging between 1.15 and 1.86), as well as the lack of association of STAT4 with dcSSc. A meta-analysis to test the overall effect of the rs7574865 polymorphism showed a strong risk effect of the T allele for lcSSc susceptibility (pooled OR 1.54 95% CI 1.36-1.74; P < 0.0001). Our data show a strong and reproducible association of the STAT4 gene with the genetic predisposition to lcSSc suggesting that this gene seems to be one of the genetic markers influencing SSc phenotype.

A large multicentre analysis of CTGF -945 promoter polymorphism does not confirm association with systemic sclerosis susceptibility or phenotype

OBJECTIVE

To conduct a replication study to investigate whether the -945 CTGF genetic variant is associated with systemic sclerosis (SSc) susceptibility or specific SSc phenotype.

METHODS

The study population comprised 1180 patients with SSc and 1784 healthy controls from seven independent case-control sets of European ancestry (Spanish, French, Dutch, German, British, Swedish and North American). The -945 CTGF genetic variant was genotyped using a Taqman 5' allelic discrimination assay.

RESULTS

An independent association study showed in all the case-control cohorts no association of the CTGF -945 polymorphism with SSc susceptibility. These findings were confirmed by a meta-analysis giving a pooled OR = 1.12 (95% CI 0.99 to 1.25), p = 0.06. Investigation of the possible contribution of the -945 CTGF genetic variant to SSc phenotype showed that stratification according to SSc subtypes (limited or diffuse), selective autoantibodies (anti-topoisomerase I or anticentromere) or pulmonary involvement reached no statistically significant skewing.

CONCLUSION

The results do not confirm previous findings and suggest that the CTGF -945 promoter polymorphism does not play a major role in SSc susceptibility or clinical phenotype.

Interactive effects of immunoglobulin gamma and human leucocyte antigen genotypes on clearance and persistence of infection with hepatitis C virus

Particular alleles of human leucocyte antigen (HLA) and immunoglobulin gamma (GM) and immunoglobulin kappa (KM) allotypes (polymorphic determinants of IgG heavy chains and kappa-type light chains, respectively) are associated with the outcome of several infections. To examine their role in the outcome of hepatitis C virus (HCV) infection, we genotyped 50 individuals with resolved and 117 with persistent HCV infection. None of the GM, KM or HLA-C genotypes by themselves were associated with the resolution or persistence of HCV infection. However, particular combinations of HLA and GM genotypes were associated significantly with the outcome of HCV infection. Subjects with the HLA C1C1 genotype, in the absence of GM ff, were more than seven times [odds ratio (OR) 7.15] as likely to have persistent infection as the subjects who lacked both these genotypes. The presence of GM ff, in the absence of HLA C1C2, was associated with the resolution of infection (OR 0.27). The absence of GM fz, in the presence of HLA C2C2, was also associated with the resolution of infection (OR 0.27). Compared to the subjects who lacked both these genotypes, subjects with GM fz, in the absence of HLA C1C2, were almost four times as likely to have persistent infection (OR 3.91); similarly, subjects with HLA C1C2, in the absence of GM fz, were almost three times as likely to have persistent infection (OR 2.80). These results show, for the first time, interactive effects of GM and HLA genotypes in the outcome of HCV infection.

Contribution of MHC class I region to genetic susceptibility for giant cell arteritis

OBJECTIVE

The aim of this study was to assess the potential contribution of HLA-class I MICA and HLA-B gene polymorphisms towards the pathogenesis of giant cell arteritis (GCA).

METHODS

Ninety-eight biopsy-proven GCA patients and 225 ethnically matched controls from Lugo, Northwest Spain, were genotyped for the MICA-TM microsatellite polymorphism using a polymerase chain reaction (PCR)-based method. Genotyping of HLA-B was performed using PCR and detection with a reverse sequence-specific oligonucleotide (SSO) probes system.

RESULTS

A significant difference in the distribution of the alleles of MICA between patient and control groups (P = 0.005) was found. This was due to an increased frequency of the MICA A5 allele in GCA patients compared with controls (26 vs 13.6%; P = 0.0001; P(C) = 0.0005; OR 2.2, 95% CI 1.4-3.4). In addition, the HLA-B*15 allele showed a higher frequency in GCA patients compared with controls (P = 0.004; P(C) = 0.04; OR 2.7, 95% CI 1.3-5.7). Interestingly, the association observed with the MICA A5 allele seems to be independent of linkage disequilibrium with HLA-B, as well as independent of that previously described with HLA-DRB1*04. Remarkably, simultaneous presence of MICA A5 and HLA-B*15 or HLA-DRB1*04 genetic markers leads to an increase in the OR obtained for each individual genetic marker (MICA A5 + B*15 OR 3.2; MICA A5 + DRB1*04 OR 5.8).

CONCLUSIONS

Our results provide the first evidence that the MICA and HLA-B genes are independently associated with the genetic susceptibility to GCA, and suggest that several genes within the MHC might have independent effects in the susceptibility to this systemic vasculitis.

Common ancestral origin of pemphigus vulgaris in Jews and Spaniards: a study using microsatellite markers

Pemphigus is a group of autoimmune blistering diseases of the skin and mucous membranes. The association of pemphigus with human leukocyte antigen (HLA) is widely accepted. It was described in many ethnic groups and in most countries of the world. Studies showed that the associated HLA haplotype in Jewish pemphigus vulgaris (PV) patients is HLA-B38, DRB1*0402, and DQB1*0302; or HLA-B35, DRB1*0402, and DQB1*0302. Similar associations with class II genes were found in Spanish non-Jewish PV patients. As Jews lived in Spain for hundreds of years and many converted to Christianity, the presence of the same HLA haplotype in the Jewish and Spanish PV suggests that they may share the same founder. Microsatellite markers which span the entire major histocompatibility complex (MHC) locus were used as genetic probes. They were utilized to dissect the MHC region in the search for possible common haplotypes, besides HLA, which may provide an answer to this question. It was found that in both cohorts, in addition to HLA class II genes, there are probably genes in the class I region which are associated with PV. Alleles belonging to the associated markers were used to construct haplotypes and to estimate genetic distances. The distance between the two PV cohorts is relatively short, but the distance between the Jewish patients and the Jewish controls is greater compared to the distance between Spanish patients and Spanish controls. In both PV populations, the same microsatellite haplotypes in addition to a common class II haplotype were found, suggesting that both patient populations originated from the same genetic stock and, therefore, share the same ancestral disease gene.

Association of vitamin D receptor genotypes with early onset rheumatoid arthritis

The presence of certain vitamin D receptor (VDR) genotypes has been associated with low bone mineral density (BMD) in elderly populations as well as with accelerated bone loss in patients with rheumatoid arthritis (RA). In the present study, VDR genotypes from 120 Spanish patients with RA were investigated. Three VDR gene polymorphisms (BsmI, ApaI and TaqI) were investigated using polymerase chain reaction followed by enzymatic digestion. The distributions of VDR allelic frequencies were similar in patients and controls and therefore no influence of VDR polymorphisms on rheumatoid arthritis susceptibility could be demonstrated. However, in an analysis of the clinical features of the different VDR-related genetic subgroups, the BB/tt genotype, defined by the BsmI and TaqI restriction site polymorphisms, was identified to be weakly associated with an early onset RA in female patients. This VDR genotype has been associated with a low BMD level in various studies. When patients were stratified according to the presence of the shared HLA epitope SE, it was found that SE + female patients bearing the BB/tt genotype showed the earliest disease onset. The mechanisms by which the VDR polymorphism is associated with RA is unknown, but they could be related to the immunoregulatory properties of vitamin D.

The predictive value of the HLA shared epitope for severity of radiological joint damage in patients with rheumatoid arthritis. A 10 year observational prospective study

OBJECTIVE

To evaluate the clinical importance of the RA "shared epitope" (SE) as a prognostic marker of radiological severity and extension of the disease to large joints in patients with rheumatoid arthritis (RA).

METHODS

Eighty-two patients who met the American College of Rheumatology criteria for RA with a disease duration < 2 years at presentation were included in the study. Radiographs of hands, wrists, feet, shoulders, elbows, hips, and knees were taken at study entry and 8-10 years later. HLA-DRB1 genotypes were determined by polymerase chain reaction-sequence-specific oligonucleotide probes. Radiological severity was assessed in small joints of hands, wrists, and feet. Extension of the disease to large joints was evaluated in radiographs of shoulders, elbows, hips, and knees.

RESULTS

At the end of the study, erythrocyte sedimentation rate (ESR), rheumatoid factor (RF) titer, and percentage of maximum radiological score at baseline were significantly associated with RA severity (p < 0.01, p < 0.01, p < 0.05, respectively). Extension of RA to large joints was related to a higher ESR (p < 0.001) and a lower hemoglobin level (p < 0.01) at baseline. Neither at entry nor at the end of the study was the RA shared epitope predictive for radiologic severity or extension of disease to large joints (p = 0.8, p = 0.3, respectively).

CONCLUSION

Presence of the SE in patients with RA is not a good prognostic marker of radiological severity after a mean followup period of 9 years.

Complex associations between HLA-DRB1 genes and female rheumatoid arthritis: results from a prospective study

We followed 138 Spanish patients (37 men and 101 women) with rheumatoid arthritis (RA) to analyze whether patient sex influenced the HLA-DRB1 associations with disease susceptibility. Results showed that, although a high increase of the shared epitope (SE) was observed in both genders, distribution of HLA-DRB1 specificities differs from males to females: DR1 was increased among male patients, whereas DR4 as well as DR10 were preferentially associated with female RA. To further explore whether this phenomenon operates either on susceptibility or on disease progression, 82 patients (25 males and 57 females) among the whole group were followed during the first 8 to 10 years of their disease. Results from this prospective study showed that the association of the SE with radiological disease severity was found in both male and female patients, although it was stronger among the latter group. Interestingly, DR1- as well as DR4-related alleles contributed to the high frequency of SE among female patients with early small-joints severe RA and/or long-term large-joint erosions. These results suggest that HLA polymorphism might be involved in RA pathogenesis through two mechanisms: (a) in combination with patient sex, operating in disease induction; and (b) independent of patient sex, influencing disease severity and progression.

Association of HLA shared epitope with joint damage progression in rheumatoid arthritis

A nine years prospective study was performed on 82 Spanish rheumatoid arthritis patients with a disease duration of less than two years at the study entry, in order to evaluate the role of HLA markers in the susceptibility and progression of rheumatoid arthritis. Radiological evaluation of disease severity was performed at the time of diagnosis and 9 years later. High resolution HLA-DR typing demonstrated that the presence of the shared epitope (SE) was more frequent among patients (61% vs. 31% in controls; p = 0.00003; OR = 3.48). Fourteen patients carried two SE+ HLA-DRB1 alleles (SE+/+); 36, one single allele (SE+/-) and 32 were SE negative (SE-/-). HLA-DR4 (particularly DRB1*0401 and DRB 1*0405) and HLA-DR10 were increased among patients. At study entry, the frequencies of locally severe (hands and feet) RA were more frequent among SE+/+ patients (79%) than among SE+/- (47%) and SE-/-(44%) patients (p = 0.05; RR = 1.80). After 9 years of disease these differences disappeared, whereas differences in the extent of the disease arise: 79%, 50% and 32% of SE+/+, SE+/- and SE-/- patients respectively showed large joints involvement (shoulders, elbows, hips and knees) (p = 0.01; RR = 2.44 for SE+/+ vs. SE-/-; and p = 0.04; RR = 1.81 for SE+ vs. SE-). These results suggest that the presence of the shared epitope is associated with the extent and progression of radiological joint damage in rheumatoid arthritis.

CTLA4 polymorphisms in Spanish patients with rheumatoid arthritis

Cytotoxic T-lymphocyte antigen 4 (CTLA4) polymorphisms located in the promotor region at positions -318 (C/T) and in exon 1 (49 A/ G) were investigated in 138 Spanish patients (37 men and 101 women) with rheumatoid arthritis and in 305 ethnically-matched healthy controls. When the allelic and genotypic frequencies corresponding to the CTLA4 -318 position were compared, no significant differences between patients and controls were found. However, when the CTLA4 49 A/G polymorphism was analysed, a significant increase of A/G heterozygous individuals among female patients (48.5% vs. 33.8% in controls; P=0.008; OR=2.0) was observed. This increase was absent among males (37.8%, P=NS). Analysis of the CTLA4 49 polymorphism with respect to HLA-DRB1 typing demonstrated a significant increase of A/G heterozygosity in the HLA-DR3-positive patient group compared with HLA-DR3-negative patient group (14/19, 74% vs. 49/119, 41%; P=0.009, OR=4.0). The increase of A/G genotype among HLA-DR3-positive patients was found in both males (4/6, 67%) and females' (10/13, 77%), although statistical differences were only reached in the female group. These results provide new insight into this complex association, confirm previous data from other studies, and suggest that the CTLA4 gene could be involved in the pathogenesis of rheumatoid arthritis.

Autoantibodies to transcriptional regulation proteins DEK and ALY in a patient with systemic lupus erythematosus

A human cDNA expression library that was used to investigate the nature of autoantigens recognized by the serum from a patient with systemic lupus erythematosus revealed the presence of antibodies directed against two transcriptional regulation protein: DEK, a site-specific 45 kD DNA binding protein, likely involved in signal transduction and transcriptional regulation, and a novel 28 kD protein that showed a 94% homology with murine ALY, a nuclear protein that plays a role in regulating the activity of TCRalpha enhancer complex. Whereas autoantibodies directed to epitopes on DEK are commonly found in patients with pauciarticular onset juvenile rheumatoid arthritis, autoantibodies against ALY have not been described and their occurrence has led to the cloning of the cDNA sequence of the first member of the human ALY family.

Cytoplasmic detection of a novel protein containing a nuclear localization sequence by human autoantibodies

A great diversity of antibodies directed to cell proteins has been described in sera of patients with autoimmune diseases. Most of these sera recognize nuclear components, but some others are directed against cytoplasmic autoantigens. Some of the antibodies directed to cytoplasmic autoantigens are well characterized, such as anti-mitochrondial, anti-ribosomal, anti-microsomal and anti-Golgi complex autoantibodies, but the target of many others remains unknown. In the last 5 years we have selected 32 sera with a characteristic speckled cytoplasmic pattern in indirect immunofluorescence (IIF) assay among a total of more than 31,000 sera from patients with any kind of autoimmune manifestation who attend our Connective Tissue Disease Clinic. Using a human cDNA expression library, we have identified a new autoantibody specificity named RCD-8 in five of these sera, directed to one cytoplasmic autoantigen. Affinity-purified antibodies eluted from a positive clone reproduced the same IIF cytoplasmic staining pattern as native serum and reacted with one single band of 160 kD on an immunoblot of HeLa cell extract. The sequence was found homologous to an autoantigen recently reported named Ge-1, and contains a nuclear localization sequence (NLS), an active protein domain made by a contiguous stretch of amino acids which allows the selective entry of the protein into the nucleus. The five patients whose sera exhibited this new autoantibody specificity displayed different autoimmune pathological profiles.