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Recent advances indicate that bone and energy metabolism are closely related. However, little direct evidence on causality has been provided in humans. We aimed to assess the association of three bone-related biomarkers-25 hydroxyvitamin D (25OHD), parathyroid hormone (PTH), and osteocalcin (OCN)-with several metabolic phenotypes and investigate any causal relevance to the associations using a Mendelian randomization (MR) study. Serum 25OHD, PTH, and total OCN were measured at baseline in 5169 eligible Chinese participants in Changfeng study. Partial correlation and bivariate GREML analysis were used to estimate phenotypic and genetic correlations, respectively. Multiple linear regression and logistic regression were used to assess linear associations. Genomewide association analysis (GWAS) was performed. Bidirectional two-sample MR analyses were conducted to examine causal relationships between OCN and body mass index (BMI), diastolic blood pressure (DBP), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C), glycated hemoglobin A1c (HbA1c), and type 2 diabetes (T2DM), using our GWAS result of OCN and GWAS statistics from Biobank Japan project (BBJ) and the largest meta-analysis of T2DM GWAS in East Asian population. Circulating OCN was significantly associated with higher DBP and HDL-C and decreased TG, blood glucose level, insulin resistance, liver fat content, bone mineral density, BMI, and a favorable body fat distribution pattern. GWAS identified one novel serum PTH locus and two novel serum OCN loci, explaining 0.81% and 1.98% of variances of PTH and OCN levels, respectively. MR analysis suggested a causal effect of T2DM on lower circulating OCN concentration (causal effect: -0.03; -0.05 to -0.01; p = 0.006 for T2DM_BBJ and -0.03; -0.05 to -0.01; p = 0.001 for T2DM_EAS). These findings indicate that T2DM might impact bone remodeling and provide a resource for understanding complex relationships between osteocalcin and metabolic (and related) traits in humans. © 2021 American Society for Bone and Mineral Research (ASBMR).

Osteocalcin regulates energy metabolism in an active undercarboxylated/uncarboxylated form. However, its role on the development of non-alcoholic fatty liver disease (NAFLD) is still controversial. In the current study, we investigated the causal relationship of circulating osteocalcin with NAFLD in two human cohorts and studied the effect of uncarboxylated osteocalcin on liver lipid metabolism through animal models. We analyzed the correlations of serum total/uncarboxylated osteocalcin with liver steatosis/fibrosis in a liver biopsy cohort of 196 participants, and the causal relationship between serum osteocalcin and the incidence/remission of NAFLD in a prospective community cohort of 2055 subjects from Shanghai Changfeng Study. Serum total osteocalcin was positively correlated with uncarboxylated osteocalcin (r = 0.528, p < .001). Total and uncarboxylated osteocalcin quartiles were inversely associated with liver steatosis, inflammation, ballooning, and fibrosis grades in both male and female participants (all p for trend

Objective To explore the effect of berberine (BBR) on skeletal muscle mass and metabolism and the possible mechanism. Methods Eight-week-old male C57BL/6 mice were fed with a high-fat diet (HFD) for 8 weeks to establish the insulin resistance obesity model. Then, mice were randomly divided into two groups (normal chow diet (NCD) and HFD), while NCD and HFD were further classified into two groups respectively, which were NCD+CS (Carmellose Sodium), NCD+BBR, HFD+CS and HFD+BBR. After the BBR intervention, insulin tolerance test (ITT) and glucose tolerance test (GTT) were carried out. Metabolic parameters and inflammatory biomarkers were detected. Various parts of adipose tissue and gastrocnemius were separated and measured. The gastrocnemius muscle was selected for tissue staining. The mRNA expression of myostatin (Mstn) was tested by quantitative real-time PCR (RT-PCR). Western blotting was performed to detect the expression of Mstn, phosphatidylinositol 3-kinase (PI3K), protein kinase B (Akt), small ribonucleoprotein particle protein 2 (Smd2), small ribonucleoprotein particle protein 3 (Smd3), and small ribonucleoprotein particle protein 4 (Smd4). Results Both body weights (P

Context: The relationship between resveratrol and histone acetylation in renal cell carcinoma (RCC) has not yet been reported. Objective: To explore the functional role of resveratrol in RCC. Materials and methods: Functional experiments were performed to determine proliferatio n of ACHN cells with treatment of resveratrol (0, 7.8125, 15.625, 31.25 and 62.5 μg/mL, for 12, 24 and 48 h of culture) or 0.1 μM SAHA. The enzyme activities of MMP-2/-9 were measured by gelatine zymography and histone acetylation by Western blot. Results: When the cells were treated with 15.625, 31.25 and 62.5 μg/mL resveratrol, ACHN cells viability was 73.2 ± 3.5%, 61.4 ± 3.1%, 50.2 ± 4.7% for 12 h, 62.7 ± 4.5%, 52.4 ± 5.5%, 40.2 ± 3.8% for 24 h, and 60.8 ± 3.7%, 39.4 ± 5.1%, 37.6 ± 2.7% for 48 h, and the wound closure (%) of migration was increased from 0.6 to 0.7, 0.85, 0.9 for 12 h and from 0.23 to 0.3, 0.48, 0.59 for 24 h. The invasion rate was 8.5 ± 0.9%, 7.4 ± 0.3% and 5.8 ± 0.6%, and cell cycle was arrested at G1 from 42.5 ± 2.9% to 55.3 ± 5.7%, 59.8 ± 3.4%, 68.7 ± 4.6%. MMP-2/-9 expression (p

Soil fungi play a vital role in soil nutrient dynamics, but knowledge of their diversity and community composition in response to biochar addition into red soil is either limited or inconsistent. Therefore, we determined the impact of bamboo biochar (BB) with increasing concentrations (0, 5, 20, and 80 g kg−1 of soil, referred to as B0, BB5, BB20, and BB80, respectively) on soil physicochemical properties and fungal communities (Illumina high-throughput sequencing) in red soil under Fokenia hodginsii (Fujian cypress). We found that increasing BB levels effectively raised the soil pH and soil nutrients, particularly under BB80. BB addition significantly increased the relative abundance of important genera, i.e., Basidiomycota, Mucoromycota, and Chytridiomycota that could play a key role in ecological functioning, e.g., wood degradation and litter decomposition, improvement in plant nutrients uptake, and resistance to several abiotic stress factors. Soil amended with BB exhibited a substantial ability to increase the fungal richness and diversity; BB80 > BB20 > BB5 > B0. Basidiomycota, Mucoromycota, Glomeromycota, Rozellomycota, Aphelidiomycota, Kickxellomycota, and Planctomycetes were positively associated with soil pH, total nitrogen, phosphorous, and carbon, and available potassium and phosphorous. Besides, the correlation analysis between the soil fungal communities and soil properties also showed that soil pH was the most influential factor in shaping the soil fungal communities in the red soil. These findings have significant implications for a comprehensive understanding of how to ameliorate acidic soils with BB addition, as well as for future research on sustainable forest management, which might increase soil fungi richness, diversity, and functionality in acidic soils.

Branch patterns play a key role in assessing plant architecture and are adapted to forest ecosystems. The study aimed to reveal the pattern of branch traits at various distances and orientations from the seashore. For that reason, four sites with various distances from the seashore (SP1: 50–60 m, SP2: 60–100 m, SP3: 100–200 m, and SP4: 200–800 m) were selected and branch traits of Dendrocalamus minor var. amoenus were determined in Dongshan Island, China. The results showed that there were differences in the branch traits between both the 1st-order and 2nd-order branches, and distance from seashore had a significant impact on branch angle, length, diameter, and the number of leaves of 1st-order branches, whereas branch diameter, length, and the number of leaves of 2nd-order branches. In different orientations, the branch angle, length, number, and diameters of the 1st-order and 2nd-order branches showed no significant differences. Nonetheless, the number of leaves of the 1st-order branches were significantly influenced by different orientations. D. minor var. amoenus exhibited strong phenotypic plasticity with longer branches and formed a sparse crown shape. It adjusted the fractal dimension of the crown and branches by modulating the allometric growth relationships among branching traits to adapt to harsh coastal pressure. This study would provide valuable recommendations for D. minor var. amoenus as windbreaks in the coastal climate.

Background Sarcandra glabra is an evergreen and traditional Chinese herb with anti-oxidant, anti-bacterial, anti-inflammatory, and anti-tumor effects. Light is one of the most influential factor affecting the growth and quality of herbs. In recent times, the introduction of Light Emission Diode (LED) technology has been widely used for plants in greenhouse. However, the impact of such lights on plant growth and the regulatory mechanism of phenylpropanoid-derived compounds in S. glabra remain unclear. Results The red LED light (RL) substantially increased the plant height and decreased the stem diameter and leaf area relative to the white LED light (WL), while the blue LED light (BL) significantly reduced the height and leaf area of S. glabra. According to transcriptomic profiling, 861, 378, 47, 10,033, 7917, and 6379 differentially expressed genes (DEGs) were identified among the groups of leaf tissue under BL (BY) vs. leaf tissue under RL (RY), BY vs. leaf tissue under WL (WY), RY vs. WY, root tissue under WL (WG) vs. WY, stem tissue under WL (WJ) vs. WG, and WJ vs. WY, respectively. We identified 46 genes encoding for almost all known enzymes involved in phenylpropanoid biosynthesis, e.g., phenylalanine ammonia lyase (PAL), chalcone synthase (CHS), and flavonol synthase (FLS). We found 53 genes encoding R2R3-MYB proteins and bHLH proteins, respectively, where several were related to flavonoids biosynthesis. A total of 454 metabolites were identified based on metabolomic profiling, of which 44, 87, and 296 compounds were differentially produced in WY vs. RY, WY vs. BY, and WY vs. WG. In BY there was a substantial reduction in the production of esculetin, caffeic acid, isofraxidin, and fraxidin, while the yields of quercitrin and kaempferol were significantly up-regulated. In RY, the contents of cryptochlorogenic acid, cinnamic acid, and kaempferol decreased significantly. Besides, in WG, the production of metabolites (e.g. chlorogenic acid, cryptochlorogenic acid, and scopolin) declined, while their yields increased significantly (e.g. esculetin, fraxetin, isofraxidin, and fraxidin). Conclusion These results provide further insight into the regulatory mechanism of accumulation patterns of phenylpropanoid-derived compounds in S. glabra under various light conditions, allowing optimum breeding conditions to be developed for this plant.

Genome-wide association studies have identified many individual genetic loci associated with multiple complex traits and common diseases. There are, however, few examples where the molecular basis of such pleiotropy has been elucidated. To address this challenge, we describe an integrative approach, focusing on the p.Ser219Gly (rs867186 A>G) variant in thePROCRgene (encoding the endothelial protein C receptor, EPCR), which has been associated with lower coronary artery disease (CAD) risk but higher venous thromboembolism (VTE) risk. In a phenome scan of 12 cardiometabolic diseases and 24 molecular factors, we found thatPROCR-219Gly associated with higher plasma levels of zymogenic and activated protein C as well as coagulation factor VII. Using statistical colocalization and Mendelian randomization analyses, we uncovered shared genetic etiology across activated protein C, factor VII, CAD and VTE, identifying p.S219G as the likely causal variant at the locus. In a recall-by-genotype study of 52 healthy volunteers stratified by p.S219G, we detected 2.5-fold higher soluble EPCR levels and 1.2-fold higher protein C levels in plasma per effect allele, suggesting the allele induces EPCR shedding from the membrane of endothelial cells. Finally, in cell adhesion assays, we found that increasing concentrations of activated protein C, but not soluble EPCR, reduced leukocyte–endothelial cell adhesion, a marker for vascular inflammation. These results support a role for protein C as a causal factor in arterial and venous diseases, suggesting thatPROCR-219Gly protects against CAD through anti-inflammatory mechanisms while it promotes VTE risk through pro-thrombotic mechanisms. Overall, our study illustrates a multi-modal approach that can help reveal molecular underpinnings of cross-disease associations.

ObjectiveUsing three European and two Chinese genome-wide association studies (GWAS), we investigated the performance of genetic risk scores (GRS) for predicting the susceptibility and severity of Systemic lupus erythematosus (SLE), using renal disease as a proxy for severity.MethodsWe used four GWASs to test the performance of GRS both cross validating within the European population and between European and Chinese populations. The performance of GRS in SLE risk prediction was evaluated by Receiver Operating Characteristic (ROC) curves. We then analyzed the polygenic nature of SLE statistically. We also partitioned patients according to their age-of-onset and evaluated the predictability of GRS in disease severity in each age group.ResultsWe found consistently that the best GRS in the prediction of SLE used SNPs associated at the level of PP-values above 0.2 were inflated for SLE true positive signals. The GRS results in an area under the ROC curve ranging between 0.64 and 0.72, within European and between the European and Chinese populations. We further showed a significant positive correlation between a GRS and renal disease in two independent European GWAS (Pcohort1=2.44e-08; Pcohort2=0.00205) and a significant negative correlation with age of SLE onset (Pcohort1=1.76e-12; Pcohort2=0.00384). We found that the GRS performed better in prediction of renal disease in the ‘later onset’ compared to the ‘earlier onset’ group.ConclusionThe GRS predicts SLE in both European and Chinese populations and correlates with poorer prognostic factors: young age of onset and lupus nephritis.

Variegated temple bamboo (Sinobambusa tootsik f. luteoloalbostriata) is a species of ornamental bamboo (Bambusoideae) that has gained popularity because of its striped or variegated leaves. In this study, a series of experiments was conducted to determine the factors contributing to the leaf color of this species, which included the content of the photosynthetic pigments and the chlorophyll biosynthetic precursors, the photosynthetic parameters, and the microstructure and ultrastructure of the different phenotypes. Discoloration in the leaves of variegated temple bamboo plants is attributed to two possible pathways. One was a block in chlorophyll biosynthesis, which led to the failure in biosynthesis of the thylakoid membrane. The other one was a disruption in chloroplast development. The lack of thylakoid membrane may have inhibited the conversion of coproporphyrinogen III (Coprogen III) to protoporphyrin IX (Proto IX) during the chlorophyll biosynthesis because the enzyme responsible for this conversion, protogen oxidase, is bound to the thylakoid membrane. The abnormalities in chloroplasts and a low concentration of chlorophyll in the variegated leaves led to a significantly lower photosynthetic rate than in the entirely green leaves, as demonstrated in the light-response curve.

Plant structure and architecture have a significant influence on how people interpret them. Bamboo plants have highly ornamental attributes, but the traits that attract people the most are still unknown. Therefore, to assess the people's preference for ornamental features of bamboo plants, eye-tracking measures (fixation count, percent of dwell time, pupil size, and saccade amplitude) and a questionnaire survey about subjective preference were conducted by ninety college students as the participants. The result showed that subjective ratings of stem color, leaf stripes, and stem stripes showed a significant positive correlation with the fixation count. The pupil size and saccade amplitude of different ornamental features were not correlated with the subjective ratings. According to random forest model, fixation count was the most influential aspect affecting subjective ratings. Based on integrated eye-tracking measures and subjective ratings, we conclude that people prefer the ornamental features like green stem, green stem with irregular yellow stripes or yellow stem with narrow green stripes, leaves with less number of stripes, normal stem, and tree. In addition, people prefer natural traits, for instance, green stem, normal stem, and tree, related to latent conscious belief and evolutionary adaptation. Abnormal traits, such as leaf stripes and stem stripes attract people’s visual attention and interests, making the fixation count and increasing the percentage of dwell time. This study has significant implications for landscape experts in the design and maintenance of ornamental bamboo plantations in China as well as in other areas of the world.

Background: Canine parvovirus (CPV) emerged in 1970s as a highly infectious disease. CPV modified live vaccines have been widely used to control the disease. It is urgent to develop specific monoclonal antibodies to differentiate field virus from vaccine virus in vaccinated dogs.

To investigate the impact of cytochrome P450 (CYP) genetic polymorphisms CYP2B6, CYP2C19, and CYP3A5 on mRNA expression, cyclophosphamide/4-hydroxycyclophosphamide pharmacokinetics, and treatment outcomes of the R-CHOP regimen (rituximab, cyclophosphamide, doxorubicin, vincristine, and prednisone) in Chinese patients with non-Hodgkin's lymphoma, 567 cases were investigated. Plasma concentrations of cyclophosphamide/4-hydroxycyclophosphamide were determined using liquid chromatography-tandem mass spectrometry and pharmacokinetic parameters calculated. The frequencies of CYP2B6*1/*29 and CYP2B6*1/*30 were 18 (3.2%) and 30 (5.3%), respectively. Liver samples with CYP2B6*29/*30, CYP2C19*2, CYP2B6*6, or CYP3A5*3 had significantly lower target mRNA expression. Samples with CYP2B6*6 and/or CYP2C19*2 had lower exposure to 4-hydroxycyclophosphamide, whereas those with CYP2B6*1G/*1H had higher exposure. Multivariate model showed that samples with CYP2C19*2 or CYP2B6 785A>raG had worse treatment response than samples with CYP3A5*3. CYP2C19*2, CYP2B6*6, CYP2B6*29, and CYP2B6*30 were protective factors for toxicity in the multivariate model. The best model for gene-gene interactions for treatment response contained CYP2C19*2, CYP2B6 785A>G, and CYP3A5*3 (cross-validation consistency [CVC], 8/10; P = .0035). The best prediction model for grade 2-4 toxicities had CYP2C19*2, CYP2B6 785A>G, and 516 G>T (CVC, 10/10; P T, or CYP2B6 785A>G had higher tolerance to treatment.

Bambusa beecheyana var. pubescens is mainly distributed in South China to Southwest China, growing on hillsides or river banks. In the current study, we sequenced the complete chloroplast genome of B.beecheyana var. pubescens and reported for the first time. The genome is 139,402 bp in total length, include a large single-copy (LSC) region of 82,936 bp, small single-copy (SSC) region of 12,868 bp, a pair of invert repeats (IR) regions of 21,799 bp. Plastid genome contains 132 genes, 85 protein-coding genes, 39 tRNA genes, and 8 rRNA genes. Phylogenetic analysis based on 25 chloroplast genomes indicates that B. beecheyana var. pubescens is closely related to Bambusa oldhamii, Bambusa ventricosa and Bambusa ventricosa multiplex in Bambusodae.

Dendrocalamus is an economically important woody bamboo genus. In this study, the complete chloroplast genome of D. yunnanicus was determined from Illumina HiSeq pair-end sequencing data. T...

Dendrocalamus brandisii is high bamboo with branches several, dominant branches well developed. In this study, the complete plastid genome of D. brandisii was assembled and annotated. The total pla...

Bambusa pervariabilis is mostly produced in south China; usually cultivated on the banks of the rivers and near villages. We determined the complete chloroplast (cp) genome sequence of B. pervariab...

Zinc finger 644 (Zfp644 in mouse, ZNF644 in human) gene is a transcription factor whose mutation S672G is considered a potential genetic factor of inherited high myopia. ZNF644 interacts with G9a/GLP complex, which functions as a H3K9 methyltransferase to silence transcription. In this study, we generated mouse models to unravel the mechanisms leading to symptoms associated with high myopia. Employing TALEN technology, two mice mutants were generated, either with the disease-carrying mutation (Zfp644S673G) or with a truncated form of Zfp644 (Zfp644Δ8). Eye morphology and visual functions were analysed in both mutants, revealing a significant difference in a vitreous chamber depth and lens diameter, however the physiological function of retina was preserved as found under the high-myopia conditions. Our findings prove that ZNF644/Zfp644 is involved in the development of high-myopia, indicating that mutations such as, Zfp644S673G and Zfp644Δ8 are causative for changes connected with the disease. The developed models represent a valuable tool to investigate the molecular basis of myopia pathogenesis and its potential treatment. Electronic supplementary material The online version of this article (10.1186/s13578-019-0280-4) contains supplementary material, which is available to authorized users.

Single nucleotide polymorphisms (SNPs) of p53 rs1042522, MDM2 rs2279744 and p21 rs1801270, all in the p53 pathway, which plays a crucial role in DNA damage and genomic instability, were reported to be associated with cancer risk and pathologic characteristics. This case-control study was designed to analyse the association between these SNPs and retinoblastoma (RB) in a Chinese Han population. These SNPs in 168 RB patients and 185 adult controls were genotyped using genomic DNA from venous blood. No significant difference was observed in allele or genotypic frequencies of these SNPs between Chinese RB patients and controls (all P > 0.05). However, the rs1042522 GC genotype showed a protective effect against RB invasion, as demonstrated by event-free survival (HR = 0.53, P = 0.007 for GC versus GG/CC). This effect was significant for patients with a lag time >1 month and no pre-enucleation treatment (P = 0.007 and P = 0.010, respectively), indicating an interaction between p53 rs1042522 and clinical characteristics, including lag time and pre-enucleation treatment status. Thus, the rs1042522 SNP may be associated with RB invasion in the Han Chinese population; however, further large and functional studies are needed to assess the validity of this association.

Light is an essential energy source for plant photosynthesis, although it can also be a stress-causing element. Therefore, the current research was aimed to compare photosynthetic responses of Anthurium × ‘Red’ leaves at different positions (bottom old leaf, 1, center mature leaf, 2, top expanded leaf, 3) established under three photosynthetic photon flux densities (PPFDs): 550 μmol·m−2·s−1 as high (H), 350 μmol·m−2·s−1 as medium (M), and 255 μmol·m−2·s−1 as low (L). After six months, all the replicates were relocated to interior rooms with a PPFD of 30 μmol·m−2·s−1. There were no significant differences in chlorophyll concentration of the old leaf among treatments, before (Day 0) and after shifting the plants to interior rooms (Day 30). The total chlorophyll concentrations of the mature and top leaves increased significantly. In greenhouse conditions, H and M treatments did not show any significant change for net photosynthetic rate (Pn) at various leaf positions. However, M2 exhibited an improved Pn in the interior conditions. Plants grown under M treatment were greener and had bigger leaves compared to other treatments. Our study reveals that Anthurium × ‘Red’ photosynthesis responses to different light conditions varied distinctly. However, M treatment can keep the plants looking green by accumulating enough energy for indoor conditions, and middle and lower leaves may be triggered to restore photosynthetic activity under low light or indoor conditions.

The molecular mechanisms underlying cold-resistance in Prunus campanulata Maxim. (P. campanulata) are not fully understood. This study aimed to establish a full-length library and analyze expressed sequence tags (ESTs) to provide tools to investigate the mechanisms of P. campanulata growth at low temperatures. Based on the switching mechanism at 5’end of RNA transcript technology, a full-length cDNA library was generated from young leaves of P. campanulata after 72 h treatment at 1 °C, and a preliminary EST analysis was carried out. Quantitative reverse transcription polymerase chain reaction was used to assess the expression of selected cold-related genes. The cDNA library titer was 1.2 × 106 cfu/mL−1, with a recombinant rate of 96%. The average size of inserted cDNA fragments was 1.3 Kb. EST data revealed the existence of 834 clones representing a total of 667 unigenes, including 574 singletons and 93 contigs. Blast analysis identified 475 unigenes with known and putative functions. Based on similarity search and GO annotation, 84 unigenes were associated with “response to stimuli”, suggesting that cold stress induced significant alterations in gene expression in P. campanulata cultivated at 1°C for 72 h. Interestingly, DRP, MYB, HSP, GPX and GA20-ox gene expression was significantly up-regulated in plants cultivated at low temperature, while transcript levels of TIL, CDPK were decreased. P. campanulata cultivating at low temperature express genes associated with “response to stimuli”, and in particular DRP, MYB, HSP, GPX and GA20-ox gene are up-regulated while TIL, CDPK are downregulated in response to low temperature-stress.

Porcine circovirus type 3 (PCV3) was initially reported in 2016 in the United States of America. Since then, the virus has been detected on swine farms in Poland, South Korea, and China using PCR. However, a serological survey of PCV3 in pig populations has never been conducted. In this study, for the first time, we established an indirect enzyme-linked immunosorbent (ELISA) assay and performed a national retrospective serological survey for PCV3. Our results showed that the PCV3-postive rate increased from 22.35% to 51.88% between 2015 and 2017. The above results suggest PCV3 has spread widely in China with increased positive rates since 2015.

Studies attempting to functionally interpret complex-disease susceptibility loci by GWAS and eQTL integration have predominantly employed microarrays to quantify gene-expression. RNA-Seq has the potential to discover a more comprehensive set of eQTLs and illuminate the underlying molecular consequence. We examine the functional outcome of 39 variants associated with Systemic Lupus Erythematosus (SLE) through integration of GWAS and eQTL data from the TwinsUK microarray and RNA-Seq cohort in lymphoblastoid cell lines. We use conditional analysis and a Bayesian colocalisation method to provide evidence of a shared causal-variant, then compare the ability of each quantification type to detect disease relevant eQTLs and eGenes. We discovered a greater frequency of candidate-causal eQTLs using RNA-Seq, and identified novel SLE susceptibility genes that were concealed using microarrays (e.g. NADSYN1, SKP1, and TCF7). Many of these eQTLs were found to influence the expression of several genes, suggesting risk haplotypes may harbour multiple functional effects. We pinpointed eQTLs modulating expression of four non-coding RNAs; three of which were replicated in whole-blood. Novel SLE associated splicing events were identified in the T-reg restricted transcription factor, IKZF2, the autophagy-related gene WDFY4, and the redox coenzyme NADSYN1, through asQTL mapping using the Geuvadis cohort. We have significantly increased our understanding of the genetic control of gene-expression in SLE by maximising the leverage of RNA-Seq and performing integrative GWAS-eQTL analysis against gene, exon, and splice-junction quantifications. In doing so, we have identified novel SLE candidate genes and specific molecular mechanisms that will serve as the basis for targeted follow-up studies.

© 2016 Nature Publishing Group, a division of Macmillan Publishers Limited. All Rights Reserved.Systemic lupus erythematosus (SLE; OMIM 152700) is a genetically complex autoimmune disease. Genome-wide association studies (GWASs) have identified more than 50 loci as robustly associated with the disease in single ancestries, but genome-wide transancestral studies have not been conducted. We combined three GWAS data sets from Chinese (1,659 cases and 3,398 controls) and European (4,036 cases and 6,959 controls) populations. A meta-analysis of these studies showed that over half of the published SLE genetic associations are present in both populations. A replication study in Chinese (3,043 cases and 5,074 controls) and European (2,643 cases and 9,032 controls) subjects found ten previously unreported SLE loci. Our study provides further evidence that the majority of genetic risk polymorphisms for SLE are contained within the same regions across both populations. Furthermore, a comparison of risk allele frequencies and genetic risk scores suggested that the increased prevalence of SLE in non-Europeans (including Asians) has a genetic basis.

© 2015 Nature America, Inc. All rights reserved.Systemic lupus erythematosus (SLE) is a genetically complex autoimmune disease characterized by loss of immune tolerance to nuclear and cell surface antigens. Previous genome-wide association studies (GWAS) had modest sample sizes, reducing their scope and reliability. Our study comprised 7,219 cases and 15,991 controls of European ancestry, constituting a new GWAS, a meta-analysis with a published GWAS and a replication study. We have mapped 43 susceptibility loci, including ten new associations. Assisted by dense genome coverage, imputation provided evidence for missense variants underpinning associations in eight genes. Other likely causal genes were established by examining associated alleles for cis-acting eQTL effects in a range of ex vivo immune cells. We found an over-representation (n = 16) of transcription factors among SLE susceptibility genes. This finding supports the view that aberrantly regulated gene expression networks in multiple cell types in both the innate and adaptive immune response contribute to the risk of developing SLE.