HLA class II associations with idiopathic nephrotic syndrome in children

HLA Loci and Recurrence of Focal Segmental Glomerulosclerosis in Pediatric Kidney Transplantation

Recurrent focal segmental glomerulosclerosis (FSGS) after kidney transplantation accounts for the majority of allograft failures in children with primary FSGS. Although current research focuses on FSGS pathophysiology, a common etiology and mechanisms of disease recurrence remain elusive.

Novel insights in the genetics of steroid-sensitive nephrotic syndrome in childhood

Steroid-sensitive nephrotic syndrome (SSNS) is the most common form of nephrotic syndrome in childhood and there is growing evidence that genetics play a role in the susceptibility for the disease. Familial clustering has been observed and has led to several studies on familial SSNS trying to identify a monogenic cause of the disease. Until now, however, none of these have provided convincing evidence for Mendelian inheritance. This and the phenotypic variability within SSNS suggest a complex inheritance pattern, where multiple variants and interactions between those and the environment play roles in disease development. Genome-wide association studies (GWASs) have been used to investigate this complex disease. We herein highlight new insights in the genetics of the disease provided by GWAS and identify how these insights fit into our understanding of the pathogenesis of SSNS.

Incidence and Relapse of Idiopathic Nephrotic Syndrome: Meta-analysis

CONTEXT

Idiopathic nephrotic syndrome (INS) in children is a disease with considerable morbidity, yet the incidence and risk for relapse have not been systematically reviewed.

OBJECTIVE

To estimate the overall pooled weighted incidence and risk for relapse of INS in children.

DATA SOURCES

Medline and Embase (until December 2020).

STUDY SELECTION

All studies reporting incidence (per 100 000 children per year) and/or risk for relapse (the proportion of patients who experience ≥1 relapse) of INS in children (age: <18 years) were eligible.

DATA EXTRACTION

After quality assessment, data were extracted: study (design, localization, and sample size) and patient (age, sex, steroid response, and ethnicity) characteristics, incidence, and risk for relapse.

RESULTS

After screening, 73 studies were included for analysis (27 incidence, 54 relapse). The overall pooled weighted estimate and corresponding prediction interval (PI) of the incidence was 2.92 (95% PI: 0.00-6.51) per 100 000 children per year. Higher incidences were found in non-Western countries (P < .001). Incidence tended to be lower in white children, but this was not significant. The overall pooled weighted estimate of the risk for relapse was 71.9% (95% PI: 38.8-95.5). Between 1945 and 2011, incidence did not change (P = .39), yet the risk for relapse decreased significantly (P = .024), from 87.4% to 66.2%.

LIMITATIONS

There was no full-text availability (n = 33), considerable heterogeneity, and limited studies from Africa, Latin America, and Asia.

CONCLUSIONS

INS has a low incidence with ethnic variation but high risk for relapse. Although corticosteroids have significantly reduced the risk for relapse, it remains unacceptably high, underscoring the need for alternative treatment strategies.

Relationships between the clinical phenotypes and genetic variants associated with the immunological mechanism in childhood idiopathic nephrotic syndrome: protocol for a prospective observational single-centre cohort study

INTRODUCTION

Idiopathic nephrotic syndrome (INS) is the most common glomerulopathy that results in childhood chronic kidney disease in China, but the relationships between different clinical phenotypes and immunological genetic variants observed in patients with INS are ambiguous and have not been well studied. A cohort study combined with whole exome sequencing might further identify the effects of immunological genetic variants on clinical phenotypes and treatment outcomes.

METHODS AND ANALYSIS

We describe a 3 year prospective observational single-centre cohort study to be conducted in the Children's Hospital of Chongqing Medical University in China. This study will recruit and investigate 336 patients with childhood-onset INS presenting with different clinical phenotypes. Whole exome sequencing will be conducted when patients progress to a confirmed clinical phenotype during follow-up. Relevant clinical and epidemiological data, as well as conventional specimens, will be collected at study entry and 1 month, 3 months, 6 months, 1 year, 2 years and 3 years after disease onset. After this cohort is generated, the immunological genetic variants of steroid-sensitive nephrotic syndrome without frequent relapse, steroid-resistant nephrotic syndrome and steroid-dependent/frequent relapse nephrotic syndrome will be evaluated.

ETHICS AND DISSEMINATION

The study protocol is approved by Ethics Committee of Children's Hospital of Chongqing Medical University (reference number 2018-140). The results will be disseminated through peer-reviewed journals and conference presentations.

TRIAL REGISTRATION NUMBER

ChiCTR1800019795.

Phospholipase C-Gamma 2 Activity in Familial Steroid-Sensitive Nephrotic Syndrome

BACKGROUND

Familial Steroid-sensitive Nephrotic Syndrome (SSNS) is rare, complicating the identification of candidate genes. A recent population-based approach study of SSNS identified HLA-DQA1 and Phospholipase C-Gamma 2 (PLCG2) missense coding variants as candidate loci. PLCG2 is a signaling molecule regulated by phosphorylation and is critical for Ca²⁺ flux in cells of the immune system.

METHODS

In order to detect a candidate gene for familial SSNS, we conducted an whole-exome sequencing in a pedigree consisting of two healthy parents, two non-identical twin brothers with SSNS, and a healthy young sibling. Flow cytometric assays were conducted to investigate the effects of the identified PLCG2 rare variants on B cell receptor-mediated PLCG2 tyrosine 759 phosphorylation, as well as on Ca²⁺ flux.

RESULTS

Two missense rare variants in the PLCG2 gene were detected in the affected twins. An increase in tyrosine phosphorylation of PLCG2 as well as more rapid Ca²⁺ flux were noted in response to stimulation in the affected twins compared to their parents.

CONCLUSIONS

Rare variants in PLCG2 segregated with disease in familial SSNS. Functional studies suggest the combined rare variants result in a gain of function in PLCG2 activity. Taken together, these results support PLCG2 as a possible candidate locus for familial SSNS.

Genetics of Childhood Steroid Sensitive Nephrotic Syndrome: An Update

Advances in genome science in the last 20 years have led to the discovery of over 50 single gene causes and genetic risk loci for steroid resistant nephrotic syndrome (SRNS). Despite these advances, the genetic architecture of childhood steroid sensitive nephrotic syndrome (SSNS) remains poorly understood due in large part to the varying clinical course of SSNS over time. Recent exome and genome wide association studies from well-defined cohorts of children with SSNS identified variants in multiple MHC class II molecules such as HLA-DQA1 and HLA-DQB1 as risk factors for SSNS, thus stressing the central role of adaptive immunity in the pathogenesis of SSNS. However, evidence suggests that unknown second hit risk loci outside of the MHC locus and environmental factors also make significant contributions to disease. In this review, we examine what is currently known about the genetics of SSNS, the implications of recent findings on our understanding of pathogenesis of SSNS, and how we can utilize these results and findings from future studies to improve the management of children with nephrotic syndrome.

Strong Association of the HLA-DR/DQ Locus with Childhood Steroid-Sensitive Nephrotic Syndrome in the Japanese Population

Background Nephrotic syndrome is the most common cause of chronic glomerular disease in children. Most of these patients develop steroid-sensitive nephrotic syndrome (SSNS), but the loci conferring susceptibility to childhood SSNS are mainly unknown.Methods We conducted a genome-wide association study (GWAS) in the Japanese population; 224 patients with childhood SSNS and 419 adult healthy controls were genotyped using the Affymetrix Japonica Array in the discovery stage. Imputation for six HLA genes (HLA-A, -C, -B, -DRB1, -DQB1, and -DPB1) was conducted on the basis of Japanese-specific references. We performed genotyping for HLA-DRB1/-DQB1 using a sequence-specific oligonucleotide-probing method on a Luminex platform. Whole-genome imputation was conducted using a phased reference panel of 2049 healthy Japanese individuals. Replication was performed in an independent Japanese sample set including 216 patients and 719 healthy controls. We genotyped candidate single-nucleotide polymorphisms using the DigiTag2 assay.Results The most significant association was detected in the HLA-DR/DQ region and replicated (rs4642516 [minor allele G], combined P_allelic=7.84×10^-23; odds ratio [OR], 0.33; 95% confidence interval [95% CI], 0.26 to 0.41; rs3134996 [minor allele A], combined P_allelic=1.72×10^-25; OR, 0.29; 95% CI, 0.23 to 0.37). HLA-DRB1*08:02 (Pc=1.82×10^-9; OR, 2.62; 95% CI, 1.94 to 3.54) and HLA-DQB1*06:04 (Pc=2.09×10^-12; OR, 0.10; 95% CI, 0.05 to 0.21) were considered primary HLA alleles associated with childhood SSNS. HLA-DRB1*08:02-DQB1*03:02 (Pc=7.01×10^-11; OR, 3.60; 95% CI, 2.46 to 5.29) was identified as the most significant genetic susceptibility factor.Conclusions The most significant association with childhood SSNS was detected in the HLA-DR/DQ region. Further HLA allele/haplotype analyses should enhance our understanding of molecular mechanisms underlying SSNS.

Molecular and Cellular Mechanisms for Proteinuria in Minimal Change Disease

Minimal Change Disease (MCD) is a clinical condition characterized by acute nephrotic syndrome, no evident renal lesions at histology and good response to steroids. However, frequent recurrence of the disease requires additional therapies associated with steroids. Such multi-drug dependence and frequent relapses may cause disease evolution to focal and segmental glomerulosclerosis (FSGS) over time. The differences between the two conditions are not well defined, since molecular mechanisms may be shared by the two diseases. In some cases, genetic analysis can make it possible to distinguish MCD from FSGS; however, there are cases of overlap. Several hypotheses on mechanisms underlying MCD and potential molecular triggers have been proposed. Most studies were conducted on animal models of proteinuria that partially mimic MCD and may be useful to study glomerulosclerosis evolution; however, they do not demonstrate a clear-cut separation between MCD and FSGS. Puromycin Aminonucleoside and Adriamycin nephrosis are models of glomerular oxidative damage, characterized by loss of glomerular basement membrane polyanions resembling MCD at the onset and, at more advanced stages, by glomerulosclerosis resembling FSGS. Also Buffalo/Mna rats present initial lesions of MCD, subsequently evolving to FSGS; this mechanism of renal damage is clearer since this rat strain inherits the unique characteristic of overexpressing Th2 cytokines. In Lipopolysaccharide nephropathy, an immunological condition of renal toxicity linked to B7-1(CD80), mice develop transient proteinuria that lasts a few days. Overall, animal models are useful and necessary considering that they reproduce the evolution from MCD to FSGS that is, in part, due to persistence of proteinuria. The role of T/Treg/Bcells on human MCD has been discussed. Many cytokines, immunomodulatory mechanisms, and several molecules have been defined as a specific cause of proteinuria. However, the hypothesis of a single cell subset or molecule as cause of MCD is not supported by research and an interactive process seems more logical. The implication or interactive role of oxidants, Th2 cytokines, Th17, Tregs, B7-1(CD80), CD40/CD40L, c-Mip, TNF, uPA/suPAR, Angiopoietin-like 4 still awaits a definitive confirmation. Whole genome sequencing studies could help to define specific genetic features that justify a definition of MCD as a “clinical-pathology-genetic entity.”

Genetics of childhood steroid-sensitive nephrotic syndrome

The pathogenesis of childhood-onset nephrotic syndrome (NS), disparity in incidence of NS among races, and variable responses to therapies in children with NS have defied explanation to date. In the last 20 years over 50 genetic causes of steroid-resistant nephrotic syndrome (SRNS) have been identified, and at least two disease loci for two pathologic variants of SRNS (focal segmental glomerulosclerosis and membranous nephropathy) have been defined. However, the genetic causes and risk loci for steroid-sensitive nephrotic syndrome (SSNS) remain elusive, partly because SSNS is relatively rare and also because cases of SSNS vary widely in phenotypic expression over time. A recent study of a well-defined modest cohort of children with SSNS identified variants in HLA-DQA1 as a risk factor for SSNS. Here we review what is currently known about the genetics of SSNS and also discuss how recent careful phenotypic and genomic studies reinforce the role of adaptive immunity in the molecular mechanisms of SSNS.

Ethnic Differences in Childhood Nephrotic Syndrome

Nephrotic syndrome is a common glomerular disease in children with significant variability in both incidence and steroid responsiveness among various ethnic groups. The average incidence of nephrotic syndrome is 2-16.9 per 100,000 children worldwide. Understanding the variability by ethnicity may point to potential factors leading to nephrotic syndrome, which remains elusive, and may highlight factors accounting for differences in medication response. The emerging role of genetic factors associated with steroid responsive and steroid-resistant forms of nephrotic syndrome within an ethnic group can provide insight into potential biological mechanisms leading to disease. For example, among African-Americans, the risk variants in APOL1 are associated with a more than 10-fold increase in risk of focal segmental glomerulosclerosis and high-risk carriers have a twofold greater risk of progression to end-stage renal disease. Ongoing collaborative studies should consider capturing data on self-reported ethnicity to understand differences in incidence and outcomes. In the future, the availability of whole-genome data will provide an excellent opportunity for new clinical and translational research in childhood nephrotic syndrome and lead to a better understanding of the disease.

HLA-DQA1 and PLCG2 Are Candidate Risk Loci for Childhood-Onset Steroid-Sensitive Nephrotic Syndrome

Steroid-sensitive nephrotic syndrome (SSNS) accounts for >80% of cases of nephrotic syndrome in childhood. However, the etiology and pathogenesis of SSNS remain obscure. Hypothesizing that coding variation may underlie SSNS risk, we conducted an exome array association study of SSNS. We enrolled a discovery set of 363 persons (214 South Asian children with SSNS and 149 controls) and genotyped them using the Illumina HumanExome Beadchip. Four common single nucleotide polymorphisms (SNPs) in HLA-DQA1 and HLA-DQB1 (rs1129740, rs9273349, rs1071630, and rs1140343) were significantly associated with SSNS at or near the Bonferroni-adjusted P value for the number of single variants that were tested (odds ratio, 2.11; 95% confidence interval, 1.56 to 2.86; P=1.68×10(-6) (Fisher exact test). Two of these SNPs-the missense variants C34Y (rs1129740) and F41S (rs1071630) in HLA-DQA1-were replicated in an independent cohort of children of white European ancestry with SSNS (100 cases and ≤589 controls; P=1.42×10(-17)). In the rare variant gene set-based analysis, the best signal was found in PLCG2 (P=7.825×10(-5)). In conclusion, this exome array study identified HLA-DQA1 and PLCG2 missense coding variants as candidate loci for SSNS. The finding of a MHC class II locus underlying SSNS risk suggests a major role for immune response in the pathogenesis of SSNS.

Idiopathic nephrotic syndrome in Polish children - its variants and associations with HLA

HLA-DR and HLA-DQ antigens were investigated in 127 Polish children with idiopathic nephrotic syndrome (INS) followed-up for the median time of 11 years (minimum 7 years). HLA typing was performed using the polymerase chain reaction sequence-specific oligonucleotide probing technique and the microlymphocytotoxicity test. Histopathologic INS categories and a response to therapy were analyzed according to particular HLA associations. The results were compared with 330 healthy individuals. In INS children, we observed an increased frequency of HLA-DR7, DR3/7, DQ2 and DQ8, whereas HLA-DR13, DR15, DQ5 and DQ6 were decreased. In minimal change nephrotic syndrome, a relationship with HLA-DR3, DR7, DR3/7 and DQ2 was found. Evolved from minimal changes, focal segmental glomerulosclerosis was associated with HLA-DR7, while primary focal segmental glomerulosclerosis with HLA-DR4 and DQ8. In steroid-dependence and secondary steroid-resistance, an increased frequency of HLA-DR3, DR7, DR3/7 and DQ2 was documented. In contrast, primary steroid-resistant nephrotic syndrome was associated with HLA-DR4 and DQ8. Steroid-dependent patients bearing HLA-DR3 achieved longer remissions after chlorambucil therapy compared with HLA-DR3-negative. In steroid-resistant focal segmental glomerulosclerosis, a reduced response to cyclosporine A was associated with HLA-DR4. Associations with HLA differentiate between pathoanatomic entities of INS and may influence a response to immunosuppressive therapy.

HLA alleles in frequently relapsing steroid-dependent and -resistant nephrotic syndrome in Egyptian children

The association between HLA class II antigens and childhood primary nephrotic syndrome has been reported in different populations. To investigate this association in Egyptian children, DRB1 alleles were typed by DNA polymerase chain reverse hybridization in 20 frequent relapsers/steroid-dependent and 14 steroid-resistant children with minimal change nephrotic syndrome (MCNS) and 121 unrelated healthy controls from the northern part of Egypt. The strength of the association was expressed as the relative risk (RR) estimated by the odds ratio. The DRBI*07011 allele frequency was significantly higher among patients than controls (78.9% vs. 16%, Pc <0.001). The etiological fraction (EF) was high at 0.75 [RR=20.1, confidence interval (CI)=6.0-66.7]. Similarly, patients with steroid-resistant MCNS had a higher frequency of the DRBI*07011 allele than controls (64.3% vs. 16.5%, P c<0.001). The EF was high at 0.57 (RR=9.6, CI 2.9-31.7). In the whole group of patients the frequency of DRBI*11 alleles was low compared with controls (11.4% vs. 32.2%, P =0.02), but was not significant when P was corrected. In conclusion, the DRBI*07011 allele confers susceptibility to a frequently relapsing and steroid-dependent or steroid-resistant course of childhood MCNS. These patterns of the disease seem to have the same immunogenetic components.

Identification of a novel HLA-DQA1 null allele, DQA1*0403N, from an East African woman

We report a novel DQA1 allele (DQA1*0403N) identified during sequence-based HLA-DQA1 typing of a Kenyan population. The new allele is identical to DQA1*0401 at exon 2 except for a single-nucleotide substitution at codon 53, changing it from lysine to a stop codon (CAA-->TAA). The substitution at codon 53 was confirmed by sequencing two separate polymerase chain reaction products and by sequencing multiple clones obtained following TOPO-TA cloning. The resulting stop codon at position of codon 53 in exon 2 is predicted to produce a non-functional DQA1 alpha-chain. The new allele has been named by the WHO nomenclature committee as DQA1*0403N. This is the first report of a null allele detected in the DQA1 gene.

Dominant T cells in idiopathic nephrotic syndrome of childhood

BACKGROUND

Because of several studies, idiopathic nephrotic syndrome (INS) of childhood is suspected to have an immunologic pathogenesis with T cells playing a major role. To investigate this hypothesis further, we studied the diversity of the CDR3 region of the T-cell receptor (TCR) beta-chain from peripheral T cells isolated from patients with INS.

METHODS

The study was performed over a three-year period to obtain longitudinal data on the repertoire of peripheral T cells. mRNA from peripheral mononuclear cells (PBMCs) of seven INS patients and two healthy controls (NHD) was prepared and analyzed for CDR3 length polymorphism of TCR beta-chain by spectratyping.

RESULTS

All INS patients presented individually skewed spectratype histograms in at least one Vbeta-family. Patients suffering from a frequent relapsing course of INS or a focal global sclerosis showed some alterations to persist in all samples isolated in the observation period (up to 3 years). In addition, sequence analyses of the beta-chain of the TCR CDR3 region confirmed clonal expansion of peripheral T cells in those patients who had displayed spectratype alterations.

CONCLUSIONS

The data give strong evidence for an direct involvement of CD8+ T cells in the complicated course of INS.

High-resolution sequence typing of HLA-DQA1 and -DQB1 exon 2 DNA with taxonomy-based sequence analysis (TBSA) allele assignment

High-resolution DNA sequencing of exon 2 of DQA1 and DQB1 genes that uses a taxonomy-based sequence analysis (TBSA) method to assign alleles was developed. The system uses fewer primers for polymerase chain reaction (PCR) amplification and sequencing than other methods and yields accurate DQA1 and DQB1 typing when either homozygous or heterozygous DNA samples are tested. The approach was initially corroborated by the correct typing of 10 blinded samples that had been previously typed by PCR using sequence-specific oligonucleotide probes (PCR-SSOP) or serology, and subsequently confirmed by sequencing of cloned PCR products. DNA from peripheral blood cell samples of 130 individuals enrolled in a case-control analysis of HLA determinants of abdominal aortic aneurysm were subsequently evaluated. Overall, 8 different DQA1 and 19 DQB1 alleles were identified. All 21 DQA1 heterozygous combinations and 45 of 49 DQB1 heterozygous combinations were successfully resolved with TBSA. The two pairs of heterozygous DQB1 combinations that were not unambiguously typed required sequence specific PCR amplification for correct allele identification. We conclude that the method provides precise analysis for HLA-DQ typing.

DQCAR microsatellite polymorphisms in three selected HLA class II-associated diseases

DQCAR is a very polymorphic CA repeat microsatellite located between the HLA DQA1 and DQB1 gene. Previous studies have shown that specific DQCAR alleles are in tight linkage disequilibrium with known HLA DR-DQ haplotypes. Of special interest was the fact that haplotypes containing long CA repeat alleles (DQCAR > 111) were generally more polymorphic within and across ethnic groups. In these latter cases, several DQCAR alleles were found even in haplotypes containing the same flanking DQA1 and DQB1 alleles. In this work, three HLA class II associated diseases were studied using the DQCAR microsatellite. The aim of this study was to test if DQCAR typing could distinguish haplotypes with the same DRB1, DQA1 and DQB1 alleles in control and affected individuals. To do so, patients with selected HLA DR-DQ susceptibility haplotypes were compared with HLA DR and DQ matched controls. This included: Norwegian subjects with Celiac disease and the HLA DRB1*0301, DQA1*05011, DQB1*02 haplotype; Japanese subjects with Type 1 (insulin-dependent) Diabetes Mellitus and the HLA DRB1*0405, DQA1*0302, DQB1*0401 haplotype; and French patients with corticosensitive Idiopathic Nephrotic Syndrome and the HLA DRB1*0701, DQA1*0201, DQB1*0202 haplotype. These specific haplotypes were selected from our earlier work to include one haplotype bearing a short DQCAR allele (celiac disease and DR3,DQ2-DQCAR99) and two haplotypes bearing long DQCAR alleles (Diabetes Mellitus and DR4,DQ4-DQCAR 113 or 115 Idiopathic Nephrotic syndrome and DR7,DQ2-DQCAR 111-121). Additional DQCAR diversity was found in both control and patients bearing haplotypes with long CA repeat alleles. The results indicate that DQCAR typing did not improve specificity in combination with high resolution DNA HLA typing as a marker for these three disorders.