SLC22A4 and RUNX1: identification of RA susceptible genes

The biology of ergothioneine, an antioxidant nutraceutical

Ergothioneine (ERG) is an unusual thio-histidine betaine amino acid that has potent antioxidant activities. It is synthesised by a variety of microbes, especially fungi (including in mushroom fruiting bodies) and actinobacteria, but is not synthesised by plants and animals who acquire it via the soil and their diet, respectively. Animals have evolved a highly selective transporter for it, known as solute carrier family 22, member 4 (SLC22A4) in humans, signifying its importance, and ERG may even have the status of a vitamin. ERG accumulates differentially in various tissues, according to their expression of SLC22A4, favouring those such as erythrocytes that may be subject to oxidative stress. Mushroom or ERG consumption seems to provide significant prevention against oxidative stress in a large variety of systems. ERG seems to have strong cytoprotective status, and its concentration is lowered in a number of chronic inflammatory diseases. It has been passed as safe by regulatory agencies, and may have value as a nutraceutical and antioxidant more generally.

An Intergenic rs9275596 Polymorphism on Chr. 6p21 Is Associated with Multiple Sclerosis in Latvians

Background and objectives: Multiple sclerosis (MS) is a chronic inflammatory disease of the central nervous system, leading to demyelination of neurons and potentially debilitating physical and mental symptoms. The disease is more prevalent in women than in men. The major histocompatibility complex (MHC) region has been identified as a major genetic determinant for autoimmune diseases, and its role in some neurological disorders including MS was evaluated. An intergenic single-nucleotide polymorphism (SNP), rs9275596, located between the HLA-DQB1 and HLA-DQA2 genes, is in significant association with various autoimmune diseases according to genome-wide association studies (GWASs). A cumulative effect of this SNP with other polymorphisms from this region was revealed. The aim of the study was to verify the data on rs9275596 association in multiple sclerosis in a case/control study of the Latvian population and to evaluate eventual functional significance of allele substitutions. Materials and Methods: rs9275596 (chr6:32713854; GRCh38.p12) was genotyped in 273 MS patients and 208 controls on main and sex-specific associations. Eventual functional significance of allele substitutions was evaluated in silico using publicly available tools. Results: The rs9275596 rare alleles were identified as a disease susceptibility factor in association with the MS main group and in affected females (p < 0.001 and p < 0.01, respectively). Risk factor genotypes with rare alleles included were associated with the MS common cohort (p < 0.002) and female cohort (odds ratio, OR = 2.24) and were identified as disease susceptible in males (OR = 2.41). It was shown that structural changes of rs9275596 affect the secondary structure of DNA. Functional significance of allele substitutions was evaluated on the eventual sequence affinity to transcription factors (TFs) and splicing signals similarity. A possible impact of the particular polymorphisms on the transcription and splicing efficiency is discussed. Conclusions: Our results suggest susceptibility of rs9275596 to multiple sclerosis in Latvians.

Runt-Related Transcription Factor 1 (RUNX1) Promotes TGF-β-Induced Renal Tubular Epithelial-to-Mesenchymal Transition (EMT) and Renal Fibrosis through the PI3K Subunit p110δ

Renal fibrosis is widely considered a common mechanism leading to end-stage renal failure. Epithelial-to-mesenchymal transition (EMT) plays important roles in the pathogenesis of renal fibrosis. Runt-related transcription factor 1(RUNX1) plays a vital role in hematopoiesis via Endothelial-to-Hematopoietic Transition (EHT), a process that is conceptually similar to EMT, but its role in EMT and renal fibrosis is unclear. Here, we demonstrate that RUNX1 is overexpressed in the processes of TGF-β-induced partial EMT and renal fibrosis and that the expression level of RUNX1 is SMAD3-dependent. Knockdown of RUNX1 attenuated both TGF-β-induced phenotypic changes and the expression levels of EMT marker genes in renal tubular epithelial cells (RTECs). In addition, overexpression of RUNX1 promoted the expression of EMT marker genes in renal tubular epithelial cells. Moreover, RUNX1 promoted TGF-β-induced partial EMT by increasing transcription of the PI3K subunit p110δ, which mediated Akt activation. Specific deletion of Runx1 in mouse RTECs attenuated renal fibrosis, which was induced by both unilateral ureteral obstruction (UUO) and folic acid (FA) treatment. These findings suggest that RUNX1 is a potential target for preventing renal fibrosis.

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RUNX1 is required for TGF-β induced renal tubular EMT, which increases p110δ transcription for Akt activation.

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Ablation of RUNX1 in mouse RTECs inhibits renal fibrosis induced by unilateral ureteral obstruction or folic acid.

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These findings suggest that RUNX1 might be used as a potential target to prevent renal fibrosis.

Kidney fibrosis is a critical pathologic step during the development of renal failure, while epithelial-to-mesenchymal transition (EMT) contributes to the pathogenesis of renal fibrosis. Exploring the new effectors as potential targets to inhibit renal fibrosis is currently under extensive investigation. This manuscript has identified that RUNX1 is required for TGF-β induced renal tubular EMT via increasing expression levels of the PI3K subunit p110δ and Akt activation. Importantly, ablation of Runx1 in mouse renal tubular epithelial cells or the RUNX1 inhibitor could reduce renal fibrosis in response to unilateral ureteral obstruction or under the treatment of folic acid. These findings suggest that the RUNX1 inhibitor might be used to prevent renal fibrosis.

Messenger RNA delivery of a cartilage-anabolic transcription factor as a disease-modifying strategy for osteoarthritis treatment

Osteoarthritis (OA) is a chronic degenerative joint disease and a major health problem in the elderly population. No disease-modifying osteoarthritis drug (DMOAD) has been made available for clinical use. Here we present a disease-modifying strategy for OA, focusing on messenger RNA (mRNA) delivery of a therapeutic transcription factor using polyethylene glycol (PEG)-polyamino acid block copolymer-based polyplex nanomicelles. When polyplex nanomicelles carrying the cartilage-anabolic, runt-related transcription factor (RUNX) 1 mRNA were injected into mouse OA knee joints, OA progression was significantly suppressed compared with the non-treatment control. Expressions of cartilage-anabolic markers and proliferation were augmented in articular chondrocytes of the RUNX1-injected knees. Thus, this study provides a proof of concept of the treatment of degenerative diseases such as OA by the in situ mRNA delivery of therapeutic transcription factors; the presented approach will directly connect basic findings on disease-protective or tissue-regenerating factors to disease treatment.

Genetic variants in the JAK1 gene confer higher risk of Behcet's disease with ocular involvement in Han Chinese

Recent surveys have identified SLC22A4, SLC22A5, RUNX1, JAK1 as susceptibility genes for various immune-related diseases. An association study was performed in 738 Behcet's patients with ocular involvement and 1,873 controls using the iPLEX system method. The first-stage study for 30 SNPs showed that SNPs rs2780815, rs310241, rs3790532 in JAK1 were associated with Behcet's disease in Han Chinese (Pc(Bonferroni correction) = 0.022-7.7 × 10(-3)). The G allele and AA genotype of SNP rs2834643 in RUNX1 (Pc = 0.041-1.75 × 10(-3)), but none of the other SNPs, were associated with Behcet's disease. Haplotype analysis for the SLC22A4, SLC22A5 genes showed an increased tendency for AGTCTGCCGC frequency in patients compared with controls; however, the significance was lost after Bonferroni correction (P = 0.004, Pc > 0.05). Subsequently, we further replicated the significantly associated SNPs using another independent cohort. Replication and combining studies showed that three SNPs rs2780815, rs310241, rs3790532 in JAK1, but not SNP rs2834643 in RUNX1, were consistently associated with Behcet's disease (replication: Pc = 0.012-9.60 × 10(-4); combining: Pc = 0.030-1.90 × 10(-4)). SNPs rs2780815, rs310241, rs3790532 were estimated to confer a population attributable risk of 35.0, 28.0, 27.0 %, respectively. We found a strong association between HLA-B51 with Behcet's disease in Chinese Han population (P = 1.35 × 10(-73); OR = 5.15; 95 % CI 4.28-6.19). GMDR analysis showed that no gene-gene interaction was detectable between JAK1 and HLA-B51. Logistic analysis indicated that the JAK1 gene was an independent risk factor for Behcet's disease (P > 0.05). Real-time PCR analysis showed that no difference on the expression of JAK1 in PBMCs or LPS-stimulated PBMCs between individuals with the different rs1762780815 genotypes studied (P > 0.05). In conclusion, this study suggests that JAK1, but not SLC22A4, SLC22A5 and RUNX1, contributes to the genetic susceptibility to Behcet's disease with ocular involvement.

Causal modeling using network ensemble simulations of genetic and gene expression data predicts genes involved in rheumatoid arthritis

Tumor necrosis factor α (TNF-α) is a key regulator of inflammation and rheumatoid arthritis (RA). TNF-α blocker therapies can be very effective for a substantial number of patients, but fail to work in one third of patients who show no or minimal response. It is therefore necessary to discover new molecular intervention points involved in TNF-α blocker treatment of rheumatoid arthritis patients. We describe a data analysis strategy for predicting gene expression measures that are critical for rheumatoid arthritis using a combination of comprehensive genotyping, whole blood gene expression profiles and the component clinical measures of the arthritis Disease Activity Score 28 (DAS28) score. Two separate network ensembles, each comprised of 1024 networks, were built from molecular measures from subjects before and 14 weeks after treatment with TNF-α blocker. The network ensemble built from pre-treated data captures TNF-α dependent mechanistic information, while the ensemble built from data collected under TNF-α blocker treatment captures TNF-α independent mechanisms. In silico simulations of targeted, personalized perturbations of gene expression measures from both network ensembles identify transcripts in three broad categories. Firstly, 22 transcripts are identified to have new roles in modulating the DAS28 score; secondly, there are 6 transcripts that could be alternative targets to TNF-α blocker therapies, including CD86 - a component of the signaling axis targeted by Abatacept (CTLA4-Ig), and finally, 59 transcripts that are predicted to modulate the count of tender or swollen joints but not sufficiently enough to have a significant impact on DAS28.

The collection and analysis of clinical data has played a key role in providing insights into the diagnosis, prognosis and treatment of disease. However, it is imperative that molecular and genetic data also be collected and integrated into the creation of network models, which capture underlying mechanisms of disease and can be interrogated to elucidate previously unknown biology. Bringing data from the clinic to the bench completes the cycle of translational research, which we demonstrate with this work. We built disease models from genetics, whole blood gene expression profiles and the component clinical measures of rheumatoid arthritis using a data-driven approach that leverages supercomputing. Genetic factors can be utilized as a source of perturbation to the system such that causal connections between genetics, molecular entities and clinical outcomes can be inferred. The existing TNF-α blocker treatments for rheumatoid arthritis are only effective for approximately 2/3 of the affected population. We identified novel therapeutic intervention points that may lead to the development of alternatives to TNF-α blocker treatments. We believe this approach will provide improved drug discovery programs, new insights into disease progression, increased drug efficacy and novel biomarkers for chronic and complex diseases.

A two-stage search strategy for detecting multiple loci associated with rheumatoid arthritis

Gene x gene interactions play important roles in the etiology of complex multi-factorial diseases like rheumatoid arthritis (RA). In this paper, we describe our use of a two-stage search strategy consisting of information theoretic methods and logistic regression to detect gene x gene interactions associated with RA using the data in Problem 1 of Genetic Analysis Workshop 16. Our method detected interactions of several SNPs (single-SNP and SNP x SNP) that are located on chromosomal regions linked to RA and related diseases in previous studies.

A genetic basis of susceptibility to acute pyelonephritis

Background

For unknown reasons, urinary tract infections (UTIs) are clustered in certain individuals. Here we propose a novel, genetically determined cause of susceptibility to acute pyelonephritis, which is the most severe form of UTI. The IL-8 receptor, CXCR1, was identified as a candidate gene when mIL-8Rh mutant mice developed acute pyelonephritis (APN) with severe tissue damage.

Methods and Findings

We have obtained CXCR1 sequences from two, highly selected APN prone patient groups, and detected three unique mutations and two known polymorphisms with a genotype frequency of 23% and 25% compared to 7% in controls (p<0.001 and p<0.0001, respectively). When reflux was excluded, 54% of the patients had CXCR1 sequence variants. The UTI prone children expressed less CXCR1 protein than the pediatric controls (p<0.0001) and two sequence variants were shown to impair transcription.

Conclusions

The results identify a genetic innate immune deficiency, with a strong link to APN and renal scarring.

Further development of multiplex single nucleotide polymorphism typing method, the DigiTag2 assay

A number of single nucleotide polymorphisms (SNPs) are considered to be candidate susceptibility or resistance genetic factors for multifactorial disease. Genome-wide searches for disease susceptibility regions followed by high-resolution mapping of primary genes require cost-effective and highly reliable technology. To accomplish successful and low-cost typing for candidate SNPs, new technologies must be developed. We previously reported a multiplex SNP typing method, designated the DigiTag assay, that has the potential to analyze nearly any SNP with high accuracy and reproducibility. However, the DigiTag assay requires multiple washing steps in manipulation and uses genotyping probes modified with biotin for each target SNP. Here we describe the next version of the assay, DigiTag2, which works with simple protocols and uses unmodified genotyping probes. We investigated the feasibility of the DigiTag2 assay by genotyping 96 target SNPs spanning a 610-kb region of human chromosome 5. The DigiTag2 assay is suitable for genotyping an intermediate number of SNPs (tens to hundreds of sites) with a high conversion rate (>90%), high accuracy, and low cost.

DigiTag assay for multiplex single nucleotide polymorphism typing with high success rate

As a consequence of Human Genome Project and single nucleotide polymorphism (SNP) discovery projects, several millions of SNPs, which include possible susceptibility SNPs for multifactorial diseases, have been revealed. Accordingly, there has been a strong drive to perform the investigation with all candidate SNPs for a certain disease without decreasing the number of analyzed SNPs. We developed DigiTag assay, which uses well-designed oligonucleotides called DNA coded numbers (DCNs) in multiplex SNP genotype analysis. During the analysis, the information of a genotype is converted to one of the DCNs in a one to one manner using oligonucleotide ligation assay (encoding). After the encoding reaction, only the DCNs regions and not the SNP specific regions are amplified using the universal primers and then SNP genotype is read out using DNA capillary arrays. DigiTag assay was found to be successful in SNP genotyping, giving a high success rate (24 of 27 SNPs) for randomly chosen SNPs. Moreover, this assay has the potential to analyze almost all kinds of the target SNPs by applying mismatch-induced probes and redesigned primer pairs at a low-cost.

The genetics of shared autoimmunity

Researchers have long suspected that genetic susceptibility is shared among autoimmune diseases. With the increased understanding of genetic risks and disease etiology, we are beginning to comprehend the nature of shared autoimmunity. This article briefly describes the most recent advances in the genetics of autoimmunity and the novel genes discovered.

Genome-wide single nucleotide polymorphism analyses of rheumatoid arthritis

Because of the limitations of candidate gene studies and linkage analyses for common diseases, genome-wide association studies are now recognized as a powerful approach to mapping responsible genes with modest effects on various diseases. We performed whole genome case-control linkage disequilibrium (LD) mapping for rheumatoid arthritis (RA)-associated genes in Japanese subjects using single nucleotide polymorphisms (SNPs) mainly discovered in gene-containing regions. We identified RA-associated polymorphisms in two genes/loci, PADI4 and SLC22A4/A5 cluster. PADI4 catalyzes the conversion of arginine residues to citrulline in proteins. Recent reports on the high specificity of autoantibodies against citrullinated proteins to RA and the results of our study suggest that citrullination by PADI4 is a fundamental phenomenon of RA. On the other hand, the functions of SLC22A4/A5 have not been studied in detail, but SLC22A4/A5 have been reported to have multiple polymorphisms associated with several autoimmune diseases. Thus, large-scale LD mapping appears to be effective for identifying RA-associated polymorphisms.