Clinical exome sequencing is a powerful tool in the diagnostic flow of monogenic kidney diseases: an Italian experience.

BACKGROUND: A considerable minority of patients on waiting lists for kidney transplantation either have no diagnosis (and fall into the subset of undiagnosed cases) because kidney biopsy was not performed or histological findings were non-specific, or do not fall into any well-defined clinical category. Some of these patients might be affected by a previously unrecognised monogenic disease. METHODS: Through a multidisciplinary cooperative effort, we built an analytical pipeline to identify patients with chronic kidney disease (CKD) with a clinical suspicion of a monogenic condition or without a well-defined diagnosis. Following the stringent phenotypical and clinical characterization required by the flowchart, candidates meeting these criteria were further investigated by clinical exome sequencing followed by in silico analysis of 225 kidney-disease-related genes. RESULTS: By using an ad hoc web-based platform, we enrolled 160 patients from 13 different Nephrology and Genetics Units located across the Piedmont region over 15 months. A preliminary "remote" evaluation based on well-defined inclusion criteria allowed us to define eligibility for NGS analysis. Among the 138 recruited patients, 52 (37.7%) were children and 86 (62.3%) were adults. Up to 48% of them had a positive family history for kidney disease. Overall, applying this workflow led to the identification of genetic variants potentially explaining the phenotype in 78 (56.5%) cases. CONCLUSIONS: These results underline the importance of clinical exome sequencing as a versatile and highly useful, non-invasive tool for genetic diagnosis of kidney diseases. Identifying patients who can benefit from targeted therapies, and improving the management of organ transplantation are further expected applications.

Phosphorylated alpha-enolase induces autoantibodies in HLA-DR8 pancreatic cancer patients and triggers HLA-DR8 restricted T-cell activation.

Pancreatic ductal adenocarcinoma (PDAC) is the fourth cause of cancer-induced death in the Western World. In PDAC patients, alpha-enolase (ENOA), a glycolytic enzyme that also acts as plasminogen receptor, is up-regulated and elicits the production of autoantibodies. Our previous studies revealed that most PDAC patients specifically produce antibodies to Serine(419)phosphorylated ENOA (Ser(419)P-ENOA) isoforms (ENOA1,2), and that this humoral response correlates with a better clinical outcome. Since autoantibody production can be influenced by HLA polymorphisms, and the ENOA sequence presents multiple peptides predicted to preferentially bind HLA-DR molecules, including the peptide containing Ser(419), we hypothesized that the presence of autoantibodies against ENOA1,2 is associated with specific HLA-DRB1 alleles. Here, we demonstrate that the HLA-DRB1*08 allele is significantly more frequent in PDAC patients with autoantibodies to ENOA1,2 (ENOA1,2(+), 8%) compared to healthy controls (3%, p=0.0112). We observed that a Ser(419)P-ENOA peptide, bioinformatically predicted to bind with high affinity to the HLA-DR8 allele coded by HLA-DRB1*08:01 or *08:04 alleles, was able to activate specific CD4(+) T cell clones derived from a HLA-DRB1*08:01. Thus complexes of the Ser(419)P-ENOA peptide with the HLA that trigger T-cell signaling might be relevant for induction of anti-tumor immune response.

Estimation of human leukocyte antigen class I and class II high-resolution allele and haplotype frequencies in the Italian population and comparison with other European populations.

The high-resolution (HR) allele and haplotype frequencies of class I and II human leukocyte antigen (HLA) system were determined in the Italian population from a sample of donors recruited in the Italian Bone Marrow Donor Registry (IBMDR). This study analyzed the HLA-A, -B, -C, -DRB1, and -DQB1 loci. Two different samples were used: donors HR typed at least for one allele, usually when selected for donor-recipient matching (respectively: 3596, 7591, 4715, 57345, and 8196), to make a list of the observed alleles and determine the relative frequencies of the alleles in each class of the corresponding antigen; donors HR randomly typed for both the alleles (respectively: 975, 1643, 1569, 22114, and 2087) to estimate the allele and haplotype frequencies, and two loci linkage disequilibrium. The number of alleles showing a frequency >1% on the total number of observed alleles are 18/75 HLA-A, 28/142 -B, 17/57 -C, 23/154 -DRB1, and 13/31 -DQB1. In each locus they account for more than 88% of the total cumulative frequencies. The most frequent alleles are A*02: 01, B*35: 01, C*04:01, DRB1*07:01, DQB1*03:01. The most frequent five-locus haplotype in the 338 donors randomly typed is A*01: 01-C*07:01-B*08: 01-DRB1*03:01-DQB1*02:01. The genetic comparison of the Italian population with 16 European populations shows a south-north gradient.

Genetic variant of C1GalT1 contributes to the susceptibility to IgA nephropathy.

BACKGROUND: IgA nephropathy (IgAN) is a common form of primary glomerulonephritis characterized by diffuse glomerular mesangial IgA1 deposition that leads to mesangial proliferation and chronic glomerular inflammation. Analyses of serum IgA1 from IgAN patients revealed an abnormal galactosylation of the O-linked carbohydrate moieties of IgA that may be a result of altered activity of core 1 beta1,3-galactosyltransferase (C1GalT1). To evaluate the association between C1GalT1 single nucleotide polymorphisms (SNPs) and IgAN, we performed a case control study on cohorts from the Italian population. METHODS: We sequenced C1GalT1 coding and promoter regions in 284 IgAN patients and 210 healthy controls. The functional role of 3' untranslated region (3'UTR) SNPs was studied using electrophoretic mobility shift assays and real-time quantitative PCR. RESULTS: We analyzed 8 SNPs in the C1GalT1 gene: 5 SNPs were in the promoter region and 3 SNPs in the 3'UTR. The allele 1365G in the 3'UTR was significantly more frequent in IgAN patients than in healthy controls. CONCLUSION: The 1365G allele and 1365G/G genotype seem to confer susceptibility to IgAN.

Cytokine gene polymorphisms in hepatitis C virus-related oral lichen planus.

Cytokine polymorphisms may influence both the risk of developing oral lichen planus (OLP) and the outcome of hepatitis C virus (HCV)-infected patients and OLP has been frequently associated with HCV infection. The aim of the present study was to analyse whether cytokine polymorphisms may influence the susceptibility to HCV-related OLP. Thirty-five patients with OLP and chronic HCV infection (OLP-HCV+ve) took part in the study. As controls, 44 patients with OLP but without HCV (OLP-HCV-ve) infection and 140 healthy donors were studied. Thirteen cytokine genes with 22 single nucleotide polymorphisms (SNP) were studied. IFN-gamma UTR 5644 genotype frequencies showed an increase in number of A/T heterozygote in OLP-HCV+ve patients compared with OLP-HCV-ve that approached the statistical significance [P = 0.03, P-corrected (PC) = 0.66]. Contrarily, in OLP-HCV+ve patients, the frequency of genotype -308 G/A of the TNF-alpha was decreased, whereas the genotype -308 G/G was increased compared with OLP-HCV-ve (P = 0.0005, PC = 0.011 and P = 0.0016, PC = 0.0352, respectively). OLP patients with and without HCV infection showed a different genetic cytokine background suggesting distinct pathogenetic mechanisms.

Chronic graft-versus-host disease after reduced-intensity stem cell transplantation versus conventional hematopoietic stem cell transplantation.

The aim of this study was to retrospectively analyse clinical characteristics of chronic GVHD (cGVHD) and requirements for immunosuppressive treatment (IST) in patients receiving reduced-intensity stem cell transplantation (RIST). About 29 patients who underwent RIST between September 1999 and April 2003 were evaluable for cGVHD; they were compared to an age-matched cohort of 29 patients who received conventional stem cell transplantation (CST).A total of 26 patients in the RIST group and 24 in the CST group developed cGVHD, which was graded as limited disease in 15 (52%) and 12 (41%) cases, respectively, and as extensive disease in 11 (38%) and 12 (41%) cases, respectively. Kaplan-Meier estimates of the risk of cGVHD at 1 year after transplant were 96 and 82%, respectively (p = 0.4). The median day of onset of cGVHD was 117 (range 93-220) in RIST group and 112 (range 77-225) in CST group. The skin was the most common target organ, involving 22 (84%) patients in the RIST group and 17 (71%) in the CST group. The probability of withdrawal from systemic IST at 3 years was 63 and 52% in the two groups, respectively, (p = 0.7). By multivariate analysis, RIST was the only, independent, prognostic factor for the development of refractory cGVHD (p = 0.01).In conclusion, we did not find major differences between patients receiving RIST and CST respect to timing, clinical characteristics and incidence of cGVHD. Refractory disease was more frequently observed in patients receiving RIST, although the probability of withdrawal from systemic IST was not significantly different between the two groups.

Cytokines and chronic rejection: a study in kidney transplant long-term survivors.

BACKGROUND: In part, the long-term survival of kidney transplants depends on the efforts to perform grafts with good human leukocyte antigen (HLA) compatibility, but there are other mechanisms that must induce some sort of tolerance and impair the anti-graft immune reaction. Because cytokines are one of the main components of immune response, we evaluated single nucleotide polymorphisms (SNPs) of several cytokine genes that may influence the production of a given cytokine and therefore the features of immune reactions. METHODS: A total of 416 first cadaveric kidney transplants were monitored for HLA matching. After 10 years, the graft was still functional in 171 of 416 patients; 102 of 171 patients were also typed for cytokine polymorphisms. RESULTS: The mismatch distributions in patients who underwent transplantation were not statistically different from the entire group of patients who underwent transplantation during the same time period. Moreover, it seems that almost all of the HLA class I incompatible long-term survivors are homozygous for GG at the -1082 interleukin (IL)-10 or CC at the -33IL4. CONCLUSIONS: We observed that a match for class I and class II HLA antigens apparently does not favor the long-term survival of transplanted kidneys. In fact, matched grafts are lost before 10 years in the same proportion as the mismatched grafts. We also demonstrated (1) that patients who are homozygous for GG at the SNP -1082IL10 (high IL-10 producers) and HLA class I mismatched (but matched for class II) are protected from chronic rejection, and (2) that patients who are homozygous for CC at the SNP -33IL4 (low IL-4 producers) and HLA class I mismatched (regardless of matching for class II) are protected from chronic rejection.

Tumor necrosis factor-alpha and interferon-gamma polymorphisms contribute to susceptibility to oral lichen planus.

Most lymphocytes in the lamina propria of oral lichen planus (OLP) lesions express and secrete interferon-gamma (IFN-gamma) and tumor necrosis factor-alpha (TNF-alpha), whereas they do not secret interleukin-4 and -10 or transforming growth factor-beta. We analyzed whether the polymorphisms of several cytokines may influence the susceptibility to OLP. Cytokine typing was performed by a sequence-specific PCR assay. Thirteen cytokine genes with 22 single-nucleotide polymorphisms were studied. IFN-gamma UTR 5644 genotype frequencies showed a significant increase in number of T/T homozygotes in OLP patients compared with controls (40.9 vs. 22.9%; p=0.0022). Moreover, in OLP patients, the frequency of the -308A TNF-alpha allele was higher than in the controls (21.6 vs. 9.3%; p < 0.05) causing a significantly increased frequency of the genotype G/A in OLP (43.2 vs. 14.3%; p=0.0002). Because in patients with mucocutaneous lichen planus (LP), the frequency of the -308A TNF-alpha allele was more than double the values in the pure OLP patients (40.9 vs. 15.1%; p=0.003), the -308G/A TNF-alpha genotype showed a significantly higher frequency in patients with mucocutaneous LP than in patients with pure OLP (81.8 vs. 30.3%, p=0.003). In conclusion, we suggest that genetic polymorphism of the first intron of the promoter gene of IFN-gamma may be an important risk factor to develop oral lesions of LP, whereas an increase in the frequency of -308A TNF-alpha allele may best contribute to the development of additional skin involvement.