Endoplasmic reticulum aminopeptidase 1 polymorphism Ile276Met is associated with atopic dermatitis and affects the generation of an HLA-C associated antigenic epitope in vitro

BACKGROUND

Atopic dermatitis (AD) is a common inflammatory skin disease of complex aetiology, with interactions between susceptibility genes and environmental factors. We have previously described a protective effect of the KIR2DS1 gene encoding the natural killer cell receptor, whose ligands are HLA-C molecules. Here, we found an association of HLA-C*05:01 allele with AD. KIR-HLA-C interactions are affected by peptides presented by HLA-C. The generation of these peptides is strongly influenced by endoplasmic reticulum aminopeptidases 1 and 2 (ERAP1 and ERAP2). Expression and activity of ERAP molecules depend on the polymorphisms of their genes.

OBJECTIVE

Possible associations of several single nucleotide polymorphisms (SNPs) in the ERAP1 and ERAP2 genes with susceptibility to AD.

METHODS

Peripheral blood DNA isolation from 318 patients and 549 controls. PCR-SSO or PCR-SSP for HLA-C typing; TaqMan Genotyping Assay for ERAP typing.

RESULTS

Only one SNP in the ERAP1 gene, rs26618T>C, causing the amino acid change Ile276Met, had an association with AD. To gain insight on the functional role of this SNP, we produced recombinant variants differing only at position 276 (Ile or Met) and tested their aminopeptidase activity against a N-terminally extended precursor LIVDRPVTLV of the HLA-C*05:01 epitope IVDRPVTLV. Both ERAP1 variants were able to efficiently generate the epitope, although the 276Ile allotype was able to do this about 50% faster. Furthermore, both variants were quite inefficient in further degradation of the mature epitope. Finally, we found that the effect of 276Met on susceptibility to AD was seen only in KIR2DS1-negative individuals, not protected by this KIR.

CONCLUSION

Associations of HLA-C*05:01 allele and rs26618T>C (Ile276Met) ERAP1 polymorphism with AD, and a significant difference between these two ERAP1 variants in their ability to generate an epitope for the HLA-C*05:01 molecule was found.

KIF5A de novo mutation associated with myoclonic seizures and neonatal onset progressive leukoencephalopathy

The KIF5A gene (OMIM 602821) encodes a neuron-specific kinesin heavy chain involved in intracellular transport of mitochondria and other cargoes. KIF5A protein comprises the N terminal motor domain, the stalk domain and the C-terminal cargo binding domain. The binding between KIF5A and its cargoes is mediated by kinesin adaptor proteins such as TRAK1 and TRAK2. Numerous missense KIF5A mutations in the motor and stalk domains cause spastic paraplegia type 10 (SPG10, OMIM 604187). Conversely, the role of loss-of-function mutations, especially those affecting the cargo binding domain, is unclear. We describe a novel de novo KIF5A p.Ser974fs/c.2921delC mutation found by whole exome sequencing in a patient with a congenital severe disease characterized by myoclonic seizures and progressive leukoencephalopathy. Since this phenotype differs considerably from the KIF5A/SPG10 disease spectrum we propose that the KIF5A p.Ser974fs and possibly other mutations which lead to truncation of the C-terminal tail of the protein cause a novel disorder. We speculate that the unique effect of the C-terminal truncating KIF5A mutations may result from the previously described complex role of this protein domain in binding of the TRAK2 and possibly other kinesin adaptor protein(s).

Spondyloepimetaphyseal dysplasia with neurodegeneration associated with AIFM1 mutation - a novel phenotype of the mitochondrial disease

In 1999, based on a single family, spondyloepimetaphyseal dysplasia (SEMD) with mental retardation (MR) was described as a novel syndrome with probably X-linked recessive inheritance and unknown molecular defect (MIM 300232). Our purpose was to search for the causative defect in the originally described family and in an independently ascertained second family. All patients had slowly progressive neurodegeneration with central and peripheral involvement and identical skeletal dysplasia. Whole exome sequencing performed in two subjects showed a single plausible candidate - the p.Asp237Gly variant in AIFM1 (chr. Xq26.1). The p.Asp237Gly segregated with disease as indicated by linkage analysis [maximum logarithm of odds score (LOD) score at theta 0 for the two families was 3.359]. This variant had not been previously reported and it was predicted to be pathogenic by Polyphen2, SIFT, MutationTaster and Mutation Assessor. AIFM1 encodes mitochondria associated apoptosis-inducing factor. The AIFM1 gene has been linked with COXPD6 encephalomyopathy (MIM 300816), Cowchock syndrome (MIM 310490) and X-linked deafness with neuropathy (DFNX5, MIM 300614), none of which are similar to SEMD-MR. Our results place SEMD as the third instance of a skeletal phenotype associated with a mitochondrial disease (the others being EVEN-PLUS syndrome caused by mutations of HSPA9 and CODAS syndrome due to LONP1 mutations).

Difficulties in recognition of pyruvate dehydrogenase complex deficiency on the basis of clinical and biochemical features. The role of next-generation sequencing

Pyruvate dehydrogenase complex (PDHc) defect is a well-known cause of mitochondrial disorders (MD) with at least six responsible genes (PDHA1, PDHB, DLAT, DLD, PDHX, PDP1). The aim of this work was to assess the diagnostic value of biochemical methods in recognition of PDHc defect in Polish patients with suspicion of MD.

In the first step, Western blot of the E1α subunit was performed on 86 archive muscle bioptates with suspicion of MD. In the second step, Sanger PDHA1 sequencing was performed in 21 cases with low E1α expression. In the third step, 7 patients with negative results of PDHA1 sequencing were subjected to whole-exome sequencing (WES). This protocol revealed 4 patients with PDHA1 and one with DLD mutations. Four additional probands were diagnosed outside the protocol (WES or Sanger sequencing).

The molecular characterization of PDHc defect was conducted in a total of 9 probands: 5 according to and 4 off the protocol. Additionally, two affected relatives were recognized by a family study. Altogether we identified seven different PDHA1 changes, including two novel variants [c.464T > C (p.Met155Thr) and c.856_859dupACTT (p.Arg288Leufs*10)] and one DLD variant.

The lactate response to glucose load in the PDHA1 subset was compared to a subset of non PDHc-related MD. Opposite responses were observed, with an increase of 23% and decrease of 27%, respectively.

The results show that determining lactate response to glucose load and muscle E1α expression may contribute to distinguishing PDHc-related and other MD, however, WES is becoming the method of choice for MD diagnostics.

Novel sporadic and recurrent mutations in KRT5 and KRT14 genes in Polish epidermolysis bullosa simplex patients: further insights into epidemiology and genotype-phenotype correlation

Epidermolysis bullosa simplex (EBS) is a hereditary genodermatosis characterised by trauma-induced intraepidermal blistering of the skin. EBS is mostly caused by mutations in the KRT5 and KRT14 genes. Disease severity partially depends on the affected keratin type and may be modulated by mutation type and location. The aim of our study was to identify the molecular defects in KRT5 and KRT14 in a cohort of 46 Polish and one Belarusian probands with clinical suspicion of EBS and to determine the genotype-phenotype correlation. The group of 47 patients with clinical recognition of EBS was enrolled in the study. We analysed all coding exons of KRT5 and KRT14 using Sanger sequencing. The pathogenic status of novel variants was evaluated using bioinformatical tools, control group analysis (DNA from 100 healthy population-matched subjects) and probands' parents testing. We identified mutations in 80 % of patients and found 29 different mutations, 11 of which were novel and six were found in more than one family. All novel mutations were ascertained as pathogenic. In the majority of cases, the most severe genotype was associated with mutations in highly conserved regions. In some cases, different inheritance mode and clinical significance, than previously reported by others, was observed. We report 11 novel variants and show novel genotype-phenotype correlations. Our data give further insight into the natural history of EBS molecular pathology, epidemiology and mutation origin.

Hepatitis C virus 5' untranslated region variability correlates with treatment outcome

Hepatitis C virus (HCV) variability affects viral-host interactions. We analysed HCV 5'untranslated region (5'UTR) in sera and peripheral blood mononuclear cells (PBMC) from chronic hepatitis C patients undergoing antiviral treatment. We studied 139 patients treated with pegylated interferon and ribavirin. The primary endpoint was a sustained virological response (SVR) defined as negative HCV RNA level 24 weeks after the end of therapy. 5'UTR was analysed by single-strand conformational polymorphism (SSCP) and sequencing. The pretreatment SSCP pattern in serum and PBMC differed in 26 (18.7%) patients. During therapy, the SSCP pattern remained stable in 65 (60.8%) patients, number of bands declined in 16 (15.0%), and in 18 (16.8%) patients, changes were qualified as 'shift' indicating change in band positions. In univariate analysis, there was a significant (P ≤ 0.05) positive association between SVR and pretreatment serum and PBMC dissimilarities, initial viral load <10(6) IU/mL, IL-28B CC genotype of the rs12979860 single nucleotide polymorphism and change in the SSCP band pattern (either 'shift' or decline) In multivariable analysis, only low initial viral load, IL-28B genotype, and changes in the SSCP band pattern were independent factors associated with SVR. In conclusion, stability of 5'UTR correlated with infection persistence, while changes correlated with SVR.

Uridine diphosphate glucuronosyltransferase 2B7 variant p.His268Tyr as a predictor of kidney allograft early acute rejection

BACKGROUND

Uridine diphosphate glucuronosyltransferase (UGT2B7) is responsible for conversion of mycophenolic acid to mycophenolic acyl-glucuronide (acylMPAG). Conflicting data exist regarding the role of UGT2B7 p.His268Tyr (802C>T, rs7439366) variant in the clinical course following organ transplantation.

STUDY AIM

The aim of this study was to reveal an association between UGT2B7 p.His268Tyr (802C>T, rs7439366) polymorphism and kidney transplantation outcome. STUDY DESIGN, PATIENTS, AND METHOD: Genomic DNA of 235 kidney transplant recipients was genotyped for UGT2B7 802C>T using TagMan single nucleotide polymorphism (SNP) genotyping assay. Maintenance immunosuppression used mycophenolate mofetil (MMF) and cyclosporine A (n = 137) or tacrolimus (n = 98). Primary end-point was biopsy-confirmed acute rejection within 3 and 12 post-transplantation months. Secondary end-points included gastrointestinal side effects, leukopenia, lymphopenia, neutropenia, and infections. Statistical analysis was performed with the aid of SAS System using kernel-smoothed estimates of acute graft rejection hazard function. The log-rank test and hazard ratio were used to reflect association between UGT2B7 802C>T variant and risk of acute graft rejection.

RESULTS

Within 3 postimplantation months 38 (16.2%) patients experienced acute rejection; 33 were allele C carriers in UGT2B7 802C>T SNP and 5 were TT homozygotes (P < .0457). Allele C-associated risk of rejection was 2.50 and remained between 2.19 and 3.02 after adjustment for clinical confounders, ie, HLA mismatch, panel-reactive antibodies, donor age, repeated transplantation, induction therapy, donor type, delayed graft function, applied calcineurin inhibitor, or MMF dosing. We found no association between the polymorphism and gastrointestinal side effects, leukopenia, lymphopenia, neutropenia, and infections.

CONCLUSION

UGT2B7 802C>T genotyping may help identify patients with excessive early acute rejection risk.

rs3827440, a nonsynonymous single nucleotide polymorphism within GPR174 gene in X chromosome, is associated with Graves' disease in Polish Caucasian population

Recently Chu et al. conducted a two-stage genome wide association study in Chinese that identified a novel X-linked Graves' disease (GD) susceptibility marker at rs3827440 - a nonsynonymous (P162S) nucleotide transition (519C<T) within G protein-coupled receptor 174 (GPR174) gene. We aimed to replicate this finding in Caucasians. Using the TaqMan approach we typed rs3827440 in 560 GD patients from Warsaw and 196 patients from Gliwice as well as ethically matched controls (N = 748, N = 198, respectively). We found an association of the rs3827440 T allele with GD using both an allelic and genotype comparison [odds ratio (OR) = 1.19, 95% confidence interval (CI): 1.03-1.38, P = 0.021; OR=1.32, 95% CI: 1.03-1.69, P = 0.03, respectively]. There was no difference in distribution of rs3827440 alleles/genotypes vs gender, tobacco smoking, ophthalmopathy or age at disease onset. Also, no statistically significant differences were observed after stratifying patients for DRB1*03- or GD-associated variants in CTLA4 or TSHR genes. Our study provides the first replication in a Caucasian population of the association between GD and rs3827440 originally reported among Chinese. Our results also validate statistical methodology used by Chu et al. to detect associations with X-linked markers.

Risk factors of charcot neuroarthropathy development in patients with type 2 diabetes

AIM

Charcot neuroarthropathy is a very rare form of diabetic foot syndrome occurring among others in patients with diabetes mellitus. Charcot neuroarthropathy leads to bone tissue destruction and may result in foot amputation. The aim of the study was to identify risk factors of Charcot neuroarthropathy occurrence in patients with diabetic foot and type 2 diabetes.

MATERIALS

The study included 144 patients with type 2 diabetes; 33 with Charcot neuroarthropathy and 111 with diabetic foot of neuropathic origin without neuroarthropathy. The study was perform in Gastroenterology and Metabolic Diseases Department, Medical University of Warsaw, Poland.

RESULTS

The regression analysis showed that Charcot neuroarthropathy occurrence risk factors were: male gender (OR=4.94, 95% CI:1.63-15.03, p=0.003), age (OR=0.92, 95% CI:0.87-0.96, p=0.0001), diabetic foot duration (OR=1.19, 95% CI:1.08-1.32, p=0.00002) and height (OR=1.078, 95% CI:1.019-1.140, p=0.007). A positive effect on Charcot neuroarthropathy presence was exerted by body weight (OR=1.027, 95% CI:1.003-1.051, p=0.03) and hips circumference (OR=1.034, 95% CI:0.997-1.072, p=0.04).

CONCLUSIONS

The existence of the specific factors influencing Charcot neuroarthropathy development may result in earlier identification of patients at risk of its development. There is a necessity to take special care for patients prone to develop Charcot neuroarthropathy in order to prevent its occurrence and severe complications.

The replication of the association of the rs6832151 within chromosomal band 4p14 with Graves' disease in a Polish Caucasian population

Recently Chu et al. conducted a genome-wide association study in a Chinese Han population and identified two novel Graves' disease (GD) susceptibility loci within 4p14 (rs6832151) and 6q27 (rs9355610). Our purpose was to replicate these associations in a Polish Caucasian population. We analyzed rs6832151 and rs9355610 genotypes in a case-control study based on 560 GD patients and 1475 unrelated controls using TaqMan assays. Our study had the power of 0.8 and 0.6 to detect the effects originally reported for rs6832151 and rs9355610, respectively. We found an association between GD and the rs6832151 G allele (odds ratio OR = 1.27, P = 0.002). Analysis of model of inheritance suggested that the dominant model should be preferred (P(fit) = 0.938, OR = 1.39, P = 0.001). For rs9355610 a formally significant effect was observed assuming a recessive model (OR = 1.24, P = 0.028), whereas analysis of allele distribution showed a trend for association (OR = 1.14,95%, P = 0.082). Our findings are the first to show that rs6832151 and possibly rs9355610 contribute to GD pathogenesis also in Caucasians.

Lymphocyte counts in kidney allograft recipients are associated with IMPDH2 3757T>C gene polymorphism

Inosine monophosphate dehydrogenase (IMPDH), the rate-limiting enzyme for de novo synthesis of guanine nucleotides, is required for lymphocyte proliferation. Inhibition of IMPDH by mycophenolic acid (MPA) constitutes part of an immunosuppressive therapy in kidney allograft recipients. The 3757T>C polymorphic variant (rs11706052) of the IMPDH2 gene, which encodes 1 of 2 IMPDH isoenzymes, has been associated with increased IMPDH activity and reduced ability of MPA to exert antiproliferative effects on lymphocytes. The association of IMPDH2 3757T>C SNP with posttransplant courses of kidney allograft recipients remains unclear. Therefore, the aim of the present study was to evaluate associations between this single nucleotide polymorphism and common posttransplant complications among Polish kidney allotransplant recipients. We observed that the frequency of IMPDH2 3757C allele in this group (n=177) did not differ significantly from a control cohort representing the background population of Poland (n=550). There were no significant differences between patients carrying the IMPDH2 3757CT and TT genotypes with respect to acute rejection risk, neutropenia, or incidences of serious infections or gastrointestinal side effects. However, we noted that the 3757C allele was associated with higher lymphocyte counts and a reduced incidence of lymphopenia among kidney allograft recipients. Our findings may be of practical significance to tailor immunosuppressive regimens in kidney transplant recipients.

Lack of KIR2DL4 gene in a fertile Caucasian woman

Killer cell immunoglobulin-like receptor (KIR2DL4) gene is present in virtually all humans. It encodes a receptor present on uterine and decidual natural killer (NK) cells and some peripheral blood NK cells. Its only known ligand is human leukocyte antigen-G molecule expressed on extravillous trophoblasts invading the decidua. Therefore, KIR2DL4 has been regarded as a molecule important for successful pregnancy. However, a multiparous woman from Africa, lacking KIR2DL4 gene, was described suggesting that this gene is not absolutely required for successful human reproduction. Here, we describe a Polish woman who delivered a child and who is not only lacking KIR2DL4 gene, but also possessing a KIR genotype virtually identical to that of the African woman mentioned above. Their genotypes are compared with few other KIR2DL4-negative genotypes and haplotypes described so far.

Functionally defective germline variant of sialic acid acetylesterase (Met89Val) is not associated with type 1 diabetes mellitus and Graves' disease in a Polish population

Recently, rare genotypes encoding defective variants of sialic acid acetylesterase (SIAE), such as homozygous Met89Val substitution, were strongly associated [odds ratio (OR) = 8] with a panel of autoimmune diseases including type 1 diabetes mellitus (T1DM). Our purpose was to replicate this finding in T1DM and explore whether Met89Val predisposes to Graves' diseases (GD). We studied 561 GD patients, 379 T1DM patients and 1822 controls. The prevalence of Met89Val homozygosity was similar among patients (GD: 0.4%, n = 2; T1DM: 0.3%, n = 1) and controls (0.4%, n = 7) yielding OR of 0.93 [95% confidence interval (CI): 0.19-4.48, P = 0.9] and 0.69 (95% CI: 0.08-5.59, P = 0.71) for GD and T1DM, respectively. We conclude that further studies are needed before the proposed strong effect of defective SIAE variants on susceptibility to autoimmunity can be universally accepted.

Transferrin hypoglycosylation in hereditary fructose intolerance: using the clues and avoiding the pitfalls

Hereditary fructose intolerance (HFI) is caused by a deficiency of aldolase B due to mutations of the ALDOB gene. The disease poses diagnostic problems because of unspecific clinical manifestations. We report three cases of HFI all of whom had a chronic disease with neurological, nephrological or gastroenterological symptoms, whereas nutritional fructose intolerance, the pathognomonic sign of HFI, was apparent only in retrospect. In all patients a hypoglycosylated pattern of transferrin isoforms was found but was misinterpreted as a sign of CDG Ix. The correct diagnosis was achieved with marked delay (26, 36 and 24 months, respectively) by sequencing of the ALDOB gene two common mutations were identified on both alleles or on one (A150P/A175D, A150P/-, and A150P/A175D). The diagnosis was further supported by normalization of transferrin isoforms on a fructose-free diet. Data available in two patients showed that following the fructose restriction the type I pattern of carbohydrate-deficient transferrin detectable on fructose-containing diet disappeared after 3-4 weeks. These cases illustrate that in the first years of life HFI may show misleading variability in clinical presentation and that protein glycosylation analysis such as transferrin isofocusing may give important diagnostic clues. However, care should be taken not to misinterpret the abnormal results as CDG Ix as well as to remember that a normal profile does not exclude HFI due to the possibility of spontaneous fructose restriction in the diet. The presented data also emphasize the usefulness of ALDOB mutation screening for diagnosis of HFI.