Genetic interrogation for sequence and copy number variants in systemic lupus erythematosus.

Early-onset systemic lupus erythematosus presents with a more severe disease and is associated with a greater genetic burden, especially in patients from Black, Asian or Hispanic ancestries. Next-generation sequencing techniques, notably whole exome sequencing, have been extensively used in genomic interrogation studies to identify causal disease variants that are increasingly implicated in the development of autoimmunity. This Review discusses the known casual variants of polygenic and monogenic systemic lupus erythematosus and its implications under certain genetic disparities while suggesting an age-based sequencing strategy to aid in clinical diagnostics and patient management for improved patient care.

STXBP6 and B3GNT6 Genes are Associated With Selective IgA Deficiency.

Immunoglobulin A Deficiency (IgAD) is a polygenic primary immune deficiency, with a strong genetic association to the human leukocyte antigen (HLA) region. Previous genome-wide association studies (GWAS) have identified five non-HLA risk loci (IFIH1, PVT1, ATG13-AMBRA1, AHI1 and CLEC16A). In this study, we investigated the genetic interactions between different HLA susceptibility haplotypes and non-MHC genes in IgAD. To do this, we stratified IgAD subjects and healthy controls based on HLA haplotypes (N = 10,993), and then performed GWAS to identify novel genetic regions contributing to IgAD susceptibility. After replicating previously published HLA risk haplotypes, we compared individuals carrying at least one HLA risk allele (HLA-B*08:01-DRB1*03:01-DQB1*02:01 or HLA-DRB1*07:01-DQB1*02:02 or HLA-DRB1*01-DQB1*05:01) with individuals lacking an HLA risk allele. Subsequently, we stratified subjects based on the susceptibility alleles/haplotypes and performed gene-based association analysis using 572,856 SNPs and 24,125 genes. A significant genome-wide association in STXBP6 (rs4097492; p = 7.63 × 10-9) was observed in the cohort carrying at least one MHC risk allele. We also identified a significant gene-based association for B3GNT6 (P Gene = 2.1 × 10-6) in patients not carrying known HLA susceptibility alleles. Our findings indicate that the etiology of IgAD differs depending on the genetic background of HLA susceptibility haplotypes.

Histocompatibility Complex Status and Mendelian Randomization Analysis in Unsolved Antibody Deficiency.

The pathogenesis in the majority of patients with common variable immunodeficiency (CVID), the most common symptomatic primary immunodeficiency, remains unknown. We aimed to compare the minor and major histocompatibility complex (MHC) markers as well as polygenic scores of common genetic variants between patients with monogenic CVID and without known genetic mutation detected. Monogenic patients were identified in a CVID cohort using whole exome sequencing. Computational full-resolution MHC typing and confirmatory PCR amplicon-based high-resolution typing were performed. Exome-wide polygenic scores were developed using significantly different variants and multi-variant Mendelian randomization (MR) analyses were used to test the causality of significant genetic variants on antibody levels and susceptibility to infectious diseases. Among 83 CVID patients (44.5% females), monogenic defects were found in 40 individuals. Evaluation of the remaining CVID patients without known genetic mutation detected showed 13 and 27 significantly associated MHC-class I and II alleles, respectively. The most significant partial haplotype linked with the unsolved CVID was W*01:01:01-DMA*01:01:01-DMB*01:03:01:02-TAP1*01:01:01 (P < 0.001), where carriers had a late onset of the disease, only infection clinical phenotype, a non-familial form of CVID, post-germinal center defects and a non-progressive form of their disease. Exclusion of monogenic diseases allowed MR analyses to identify significant genetic variants associated with bacterial infections and improved discrepancies observed in MR analyses of previous GWAS studies with low pleiotropy mainly for a lower respiratory infection, bacterial infection and Streptococcal infection. This is the first study on the full-resolution of minor and major MHC typing and polygenic scores on CVID patients and showed that exclusion of monogenic forms of the disease unraveled an independent role of MHC genes and common genetic variants in the pathogenesis of CVID.

Paroxysmal Movement Disorders: Recent Advances.

PURPOSE OF REVIEW: Recent advancements in next-generation sequencing (NGS) have enabled techniques such as whole exome sequencing (WES) and whole genome sequencing (WGS) to be used to study paroxysmal movement disorders (PMDs). This review summarizes how the recent genetic advances have altered our understanding of the pathophysiology and treatment of the PMDs. Recently described disease entities are also discussed. RECENT FINDINGS: With the recognition of the phenotypic and genotypic heterogeneity that occurs amongst the PMDs, an increasing number of gene mutations are now implicated to cause the disorders. PMDs can also occur as part of a complex phenotype. The increasing complexity of PMDs challenges the way we view and classify them. The identification of new causative genes and their genotype-phenotype correlation will shed more light on the underlying pathophysiology and will facilitate development of genetic testing guidelines and identification of novel drug targets for PMDs.

IL2RG hypomorphic mutation: identification of a novel pathogenic mutation in exon 8 and a review of the literature.

BACKGROUND: Atypical X-linked severe combined immunodeficiency (X-SCID) is a variant of cellular immunodeficiency due to hypomorphic mutations in the interleukin 2 receptor gamma (IL2RG) gene. Due to a leaky clinical phenotype, diagnosis and appropriate treatment are challenging in these patients. CASE PRESENTATION: We report a 16-year-old patient with a Tlow B+ NK+ cellular immunodeficiency due to a novel nonsense mutation in exon 8 (p.R328X) of the IL2RG gene. Functional impairment of the IL2RG was confirmed by IL2-Janus kinase 3-signal transducer and activator of transcription signaling pathway investigation. In addition, the characteristics of the mutations previously described in 39 patients with an atypical phenotype were reviewed and analyzed from the literature. CONCLUSION: This is the first report of an atypical X-SCID phenotype due to an exon 8 mutation in the IL2RG gene. The variability in the phenotypic spectrum of classic X-SCID associated gene highlights the necessity of multi-disciplinary cooperation vigilance for a more accurate diagnostic workup.

Tuberculosis and impaired IL-23-dependent IFN-γ immunity in humans homozygous for a common TYK2 missense variant.

Inherited IL-12Rß1 and TYK2 deficiencies impair both IL-12- and IL-23-dependent IFN-γ immunity and are rare monogenic causes of tuberculosis, each found in less than 1/600,000 individuals. We show that homozygosity for the common TYK2 P1104A allele, which is found in about 1/600 Europeans and between 1/1000 and 1/10,000 individuals in regions other than East Asia, is more frequent in a cohort of patients with tuberculosis from endemic areas than in ethnicity-adjusted controls (P = 8.37 × 10-8; odds ratio, 89.31; 95% CI, 14.7 to 1725). Moreover, the frequency of P1104A in Europeans has decreased, from about 9% to 4.2%, over the past 4000 years, consistent with purging of this variant by endemic tuberculosis. Surprisingly, we also show that TYK2 P1104A impairs cellular responses to IL-23, but not to IFN-α, IL-10, or even IL-12, which, like IL-23, induces IFN-γ via activation of TYK2 and JAK2. Moreover, TYK2 P1104A is properly docked on cytokine receptors and can be phosphorylated by the proximal JAK, but lacks catalytic activity. Last, we show that the catalytic activity of TYK2 is essential for IL-23, but not IL-12, responses in cells expressing wild-type JAK2. In contrast, the catalytic activity of JAK2 is redundant for both IL-12 and IL-23 responses, because the catalytically inactive P1057A JAK2, which is also docked and phosphorylated, rescues signaling in cells expressing wild-type TYK2. In conclusion, homozygosity for the catalytically inactive P1104A missense variant of TYK2 selectively disrupts the induction of IFN-γ by IL-23 and is a common monogenic etiology of tuberculosis.

Targeted next-generation sequencing for genetic diagnosis of 160 patients with primary immunodeficiency in south China.

BACKGROUND: Primary immunodeficiency disorders (PID) is a group of heterogeneous diseases mainly characterized by severe and recurrent infections and an increased susceptibility to lymphoproliferative, atopic, and autoimmune conditions. The clinical diagnosis should preferably be complemented by a genetic diagnosis. To date, PID-related reports from China seldom attempt to make a genetic test for their patients. METHODS: Our study aimed to evaluate demographic data, clinical manifestations, and molecular diagnosis of PID patients from southern China. Moreover, by comparison with previous reports, we provide a picture of the current status of PID in mainland China. A total number of 160 pediatric PID patients (106 males and 54 females) were enrolled, and targeted next-generation sequencing was conducted using 269 PID-related genes and subsequently confirmed by Sanger sequencing and familial segregation analysis. RESULT: The autoinflammatory disease group was the most common subcategory of PID (20%), followed by immune dysregulation (17.5%) and combined immunodeficiencies (16.2%). Antibody deficiency disorders were identified in only 11.9% of the cohort. The putative causative gene was identified in 70 patients (43.8%), and an X-linked pattern was found in 45.7% of the genetically diagnosed patients. CONCLUSION: The current study provides the first collective study of PID phenotypes and genotypes in south China and provides a strong argument for the diagnostic application of targeted next-generation sequencing panels in patients with suspected PID.

Novel genetic loci associated HLA-B*08:01 positive myasthenia gravis.

OBJECTIVE: To identify potential causative markers involved in the development of early-onset myasthenia gravis (EOMG) in the MHC and non-MHC regions that may interact with the HLA-B*08:01 allele. METHODS: We analyzed 583 MG patients and identified 5 patients homozygous for the disease-associated ancestral haplotype 8.1 (HLA-A*01:01, B*08:01, DRB1*03:01, DQB1*02:01). We also analyzed more than 9000 controls and selected 24 for further investigation. We subsequently conducted a fine mapping analysis through high-throughput sequencing of the MHC region (from upstream of the GPα5 gene to downstream of the ZBTB9 gene). For the interaction analysis we analyzed a total of 150,090 SNPs equally distributed throughout the genome in the individuals that were homozygous for the main susceptibility HLA allele HLA-B*08:01 and investigated the expression of the genes located close to the observed susceptibility variants. RESULTS: The overall coverage of the 4.79 Mb MHC region ranged between 96.57% and 97.41%. We identified 705 new variants in the MHC region (673 SNPs and 32 InDels). However, no significant differences were found between patients and controls within the MHC region of the ancestral 8.1 haplotype. As the susceptibility gene is considered to be located close to the HLA-B locus, complete sequencing of the surrounding 200 kb was carried out in the 5 patients and 24 controls. No significant differences where observed, suggesting that the HLA-B molecule itself is the susceptibility factor for EOMG. We also observed two new susceptibility loci specific for MG HLA*08:01 patients (P < 3.33 × 10-7). These loci map to an intronic OVCH1 variant (rs10492374; P = 1.90 × 10-8) and a 5' downstream CNPY2 variant (rs10783780; P = 3.33 × 10-7) on chromosome 12. Individuals heterozygous for GA*rs10492374 showed an increased expression of the OVCH1 gene. The rs10783780 genotypes were not associated with CNPY2 mRNA levels, but the MG HLA*08:01 patients present a lower expression of this gene than the healthy controls. CONCLUSION: Our results showed that when we control for the influence of the ancestral haplotype 8.1, no polymorphism was demonstrated to be associated with EOMG development within the MHC region suggesting that the HLA-B*08:01 allele is the unique genetic factor within the HLA region responsible for EOMG development in patients who carry the ancestral haplotype 8.1. Our study also identified two novel polymorphisms as risk factors for MG HLA-B*08:01 positive patients which regulate the expression of the OVCH1 and CNYP2 genes.

Next Generation Sequencing Data Analysis in Primary Immunodeficiency Disorders - Future Directions.

Primary immunodeficiency diseases (PIDs) comprise a group of highly heterogeneous immune system diseases and around 300 forms of PID have been described to date. Next Generation Sequencing (NGS) has recently become an increasingly used approach for gene identification and molecular diagnosis of human diseases. Herein we summarize the practical considerations for the interpretation of NGS data and the techniques for searching disease-related PID genes, and suggest future directions for research in this field.

Human TYK2 deficiency: Mycobacterial and viral infections without hyper-IgE syndrome.

Autosomal recessive, complete TYK2 deficiency was previously described in a patient (P1) with intracellular bacterial and viral infections and features of hyper-IgE syndrome (HIES), including atopic dermatitis, high serum IgE levels, and staphylococcal abscesses. We identified seven other TYK2-deficient patients from five families and four different ethnic groups. These patients were homozygous for one of five null mutations, different from that seen in P1. They displayed mycobacterial and/or viral infections, but no HIES. All eight TYK2-deficient patients displayed impaired but not abolished cellular responses to (a) IL-12 and IFN-α/ß, accounting for mycobacterial and viral infections, respectively; (b) IL-23, with normal proportions of circulating IL-17(+) T cells, accounting for their apparent lack of mucocutaneous candidiasis; and (c) IL-10, with no overt clinical consequences, including a lack of inflammatory bowel disease. Cellular responses to IL-21, IL-27, IFN-γ, IL-28/29 (IFN-λ), and leukemia inhibitory factor (LIF) were normal. The leukocytes and fibroblasts of all seven newly identified TYK2-deficient patients, unlike those of P1, responded normally to IL-6, possibly accounting for the lack of HIES in these patients. The expression of exogenous wild-type TYK2 or the silencing of endogenous TYK2 did not rescue IL-6 hyporesponsiveness, suggesting that this phenotype was not a consequence of the TYK2 genotype. The core clinical phenotype of TYK2 deficiency is mycobacterial and/or viral infections, caused by impaired responses to IL-12 and IFN-α/ß. Moreover, impaired IL-6 responses and HIES do not appear to be intrinsic features of TYK2 deficiency in humans.

Reversal of Immunoglobulin A Deficiency in Children.

PURPOSE: Immunoglobulin A deficiency (IgAD) is the most common primary immunodeficiency in the general population. It is defined as a serum IgA level below or equal to 0.07 g/l with normal IgM and IgG levels in children over the age of 4. However, a few cases of reversal of IgAD at later ages have been observed previously, especially in pediatric patients. This study aimed at investigating the frequency of reversal in a large cohort of children and young adults in order to evaluate the present definition of IgAD. METHODS: Clinical laboratory records from 654 pediatric IgA deficient patients, 4-13 years of age, were retrieved from five university hospitals in Sweden. Follow up in the children where IgA serum levels had been routinely measured was subsequently performed. In addition, follow up of the IgA-levels was also performed at 4, 8 and 16 years of age in children who were IgA deficient at the age of 4 years in a Swedish population-based birth cohort study in Stockholm (BAMSE). RESULTS: Nine out of 39 (23.1%) children who were identified as IgAD at 4 years of age subsequently increased their serum IgA level above 0.07 g/L. The average age of reversal was 9.53 ± 2.91 years. In addition, 30 out of the 131 (22.9%) children with serum IgAD when sampled between 5 and 9.99 years of age reversed their serum IgA level with time. The BAMSE follow up study showed a reversal of IgAD noted at 4 years of age in 8 out of 14 IgAD children at 16 years of age (5 at 8 years of age) where 4 were normalized their serum IgA levels while 4 still showed low serum levels of IgA, yet above the level defining IgAD. The results indicate that using 4 years of age, as a cut off for a diagnosis of IgAD may not be appropriate. CONCLUSIONS: Our findings suggest that a diagnosis of IgAD should not be made before the early teens using 0.07 g/L of IgA in serum as a cut off.

Serum methylation levels of TAC1. SEPT9 and EYA4 as diagnostic markers for early colorectal cancers: a pilot study.

OBJECTIVE: To identify methylated genes in serum with diagnostic potentials for early colorectal cancer (CRC). METHODS: Serum methylation levels of up to 12 genes were measured in two sets of serum samples with the second set from 26 stage I CRC patients and 26 age/gender-matched controls. RESULTS: Serum methylation levels of TAC1, SEPT9, and EYA4 were significant discriminants between stage I CRC and healthy controls. Combination of TAC1 and SEPT9 rendered 73.1% sensitivity with 92.3% specificity. CONCLUSION: Serum methylation levels of TAC1. SEPT9 and EYA4 may be useful biomarkers for early detection of CRC though a validation study is necessary.

Keloid fibroblasts are more sensitive to Wnt3a treatment in terms of elevated cellular growth and fibronectin expression.

BACKGROUND: Current evidence suggests the potential role of Wnt signalling in keloids pathogenesis but such literature remains scanty. We hypothesize that Wnt signalling is upregulated in keloid fibroblasts (KFs) and this promotes cellular growth, migration and extracellular matrix (ECM) production in such fibroblasts. OBJECTIVES: To verify the downregulation of secreted frizzled-related protein 1 (SFRP1), a Wnt inhibitor and test KFs sensitivity to Wnt3a treatment compared to NFs in terms of activation of Wnt/ß-catenin, cellular growth, migration and ECM expressions. Next, to investigate if ectopic expression of SFRP1 and treatment of quercetin in KFs can reverse their phenotypes. METHODS: Quantitative Real-time PCR and western blotting were used to verify SFRP1 expression in NFs and KFs. The fibroblasts were tested with Wnt3a conditioned media and its effects were tested for (1) the cells' sensitivity to direct Wnt signalling via the activation of TCF reporter assay and protein expression of ß-catenin, (2) cellular growth, (3) cell migration and (4) expressions of ECM components. Finally KFs were stably transduced with SFRP1 and treated with 2 doses of quercetin. RESULTS: Lower levels of SFRP1 were confirmed at mRNA and protein levels in KFs which partly explained their sensitivity to Wnt3a treatment in terms of higher Wnt activation, cellular growth and fibronectin expression. Interestingly, Wnt3a did not promote higher cell migration rate and increase in collagen I expression. Ectopic expression of SFRP1 and quercetin treatment was able to mitigate Wnt3a-mediated phenotype of KFs. CONCLUSIONS: Using SFRP1 or inhibitors of Wnt signalling might be one of the therapeutic solutions to treat keloid scarring.

Study of gene expression profile during cord blood-associated megakaryopoiesis.

AIMS: To study the gene profile in cord blood (CB)-associated megakaryopoiesis. METHODS: In vitro differentiation of megakaryocytes (Mks) was carried out using human CB CD34(+) cells under the stimulation of recombinant human interleukin-3, stem cell factor and thrombopoietin for 7 d, followed by thrombopoietin only for further 3 d. Lineage-specific differentiation of Mk was examined by the expression of CD41 using flow cytometry and confocal microscopy. Total cellular RNA was extracted from day-0 CD34(+), day-10 CD41(+) and CD41(-) populations were isolated by immunomagnetic sorting respectively. Microarray was performed, and the data were analyzed using the GeneChip Operating System, Spotfire software and Genomatix BiblioSphere. RESULTS: Flow cytometric analysis showed 19.44 +/- 3.05% CD41(+) cells at day 10 of culture. The purity of CD41(+) population was enriched to 95.70 +/- 4.19% after sorting. Gene expression profiling revealed an upregulation of 285 and downregulation of 53 unique genes in the CD41(+) cells compared with CD41(-) and CD34(+) cells. Platelet-associated genes, such as thrombospondin 1, platelet glycoprotein IIIa, etc., were highly expressed in CD41(+) cells but not in CD41(-) cells and CD34(+) cells. Moreover, some genes that have not been reported to be associated with CB-derived megakaryopoiesis, such as Cbl-interacting proteins Sts-1, protocadherin 21, etc., are found to be highly expressed in the CD41(+) cells from this study. CONCLUSIONS: This study reveals a global gene expression profile of in vitro human CB-derived megakaryopoiesis at day 10. Some of these genes may play regulatory roles during the development of CB-derived megakaryopoiesis.

Studies of Wilms' Tumor (WT1) Gene Expression in Adult Acute Leukemias in Singapore.

UNLABELLED: Biomarkers provide certain values for diagnosis, monitor treatment efficacy, or for the development of novel therapeutic approach for particular diseases. Thus, the identification of specific of biomarkers for specific medical problems, including malignant diseases may be valuable in medical practice. In the study, we have used the Wilms' tumor gene (WT1) as a biomarker to evaluate its expression in local adult patients with newly diagnosed acute leukemia, including both acute myeloid and lymphoid leukemias (AML and ALL). AIM: To investigate WT1 gene expression in adult patients with acute leukemia at diagnosis. METHODS: Eighteen patients with acute leukemia diagnosed at Singapore General Hospital, Singapore, between September, 2004 and July, 2005 were included in this study. There were fifteen AML and three ALL cases aged from 18 to 71 years old. Total RNA and DNA was extracted from peripheral blood mononuclear cells (PBMCs). Expression of WT1 was detected by nested reverse-transcription polymerase chain reaction (Nested RT-PCR). K562, and 3T3 cells were used as positive- and negative-controls. The results were revalidated using real-time PCR. HLA-A genotyping was performed using sequence specific oligonucleotide polymorphism (SSOP) analysis. RESULTS: WT1 gene was exclusively expressed in all eighteen, including three ALL and fifteen AML, patients. In contrast with WT1 gene, the HLA-A genotyping was remarkably heterogeneous in these patients. CONCLUSIONS: WT1 gene expression was observed in local patients with acute leukemia at diagnosis. It may be used as a potential molecular marker for diagnosis, clinical progression of the diseases or monitoring the response to treatment, as well as a target for the development of novel therapeutic approaches.