Pathways In Systemic Lupus Erythematosus Research Articles

Transcriptome Profiling of Pediatric Myeloproliferative Neoplasms Demonstrates Dysregulation of Platelet-Relevant Genes and Enrichment of Inflammatory and JAK2 Mediated Complement Pathways

Introduction : Myeloproliferative neoplasms (MPNs) are rare clonal bone marrow disorders in children characterized by high blood counts, predisposition to clotting events, and the potential to transform to myelofibrosis or acute myeloid leukemia (AML). Children with MPNs have lower rates of the known driver mutations (in JAK2, MPL, and CALR) than adult patients, and the underlying pathways and molecular derangements in young patients remain unknown. Given the lack of knowledge about pediatric MPNs, it is critical that we gain a better understanding of the dysregulated pathways in these diseases, which is necessary for improving disease understanding and broadening treatment options in children. Therefore, the objective of this work was to identify differentially expressed genes and pathways between children with MPNs and healthy controls, as well as children with AML, to guide further study. Methods : Mononuclear cells were extracted from peripheral blood of pediatric MPN patients (n=20) and pediatric and young adult AML patients (n=1410), and bone marrow of normal controls (NC, n=68). AML patient samples were being evaluated as part of a Children's Oncology Group planned analysis. To identify an expression profile unique to MPNs, transcriptome data from MPN patients was contrasted against NC and AML patients. All samples were ribodepleted and underwent Illumina RNA-Seq to generate transcriptome expression data. All analyses were performed in R. Differentially expressed genes were identified using the voom function from the limma package (v. 3.38.3), and enriched pathways were identified using the pathfindR package (v. 1.3.1). Unsupervised hierarchical clustering and heatmap generation was performed using the ComplexHeatmap package (v. 1.20.0). Results : MPN patient samples showed a unique expression signature, distinct from both AML patients and normal controls. Unsupervised PCA plot (Figure 1A) and heatmaps (Figure 1B) show that MPN samples cluster together. There were 4,012 differentially expressed (DE) genes in MPNs compared to NC and 6,743 DE genes in MPNs compared to AML patients. There were 2,493 shared genes between the 2 groups (Figure 1C.) Significantly DE genes between MPNs and other groups included multiple platelet-relevant genes including PF4 (CXCL4), PF4V1, P2RY12, and PPBP (CXCL7). Interestingly, PF4V1 was the most DE gene in MPNs compared to AML, and third highest versus NC. Dysregulation of some of these genes has been seen in adult MPNs, as well as thrombosis. Further comparison of transcriptome profiles between children with (n=13) and without (n=7)JAK2 mutations showed upregulation of three genes, CFB, C2, and SERPING1, which are all known complement genes, implicating complement activation in JAK2-mutated MPN patients. Complement activation has previously been reported in adult MPNs. Pathway enrichment analysis shows a number of immune and inflammatory pathways as enriched in MPN patients compared to both AML and NC. There were 179 enriched pathways in MPNs compared to AML and 142 compared to NC, with 134 common pathways (Figure 1D.) The systemic lupus erythematosus pathway was the most heavily enriched pathway in MPNs compared to both AML and NC. Additional pathways with significant enrichment include hematopoietic cell lineage, cytokine-cytokine interactions, DNA replication, and various infection-relevant pathways. The JAK-STAT signaling pathway was also enriched in MPNs compared to both AML and NC, as was the platelet activation pathway. Conclusion: Transcriptome evaluation of childhood MPNs shows enrichment of numerous inflammatory and immune pathways, highlighting that, as in adult MPNs, inflammation is implicated in pediatric MPNs. Furthermore, specific complement genes were upregulated in JAK2-mutant MPN. Upregulation of platelet-specific genes implies potential insights into disease mechanisms and warrants more study. Variations in the cell populations may account for some of the differences seen, however all samples were largely mononuclear cells, making their comparisons reasonable. Further analysis of this early data is needed to better assess inflammatory changes and platelet activation in pediatric MPNs, as are larger sample sizes. Individual cells may have differential expression of various genes, and future experiments with single-cell RNA-seq would be helpful to further elucidate differences. Disclosures Levine: Novartis: Consultancy; Loxo: Membership on an entity's Board of Directors or advisory committees; Celgene: Consultancy, Research Funding; Gilead: Consultancy; Roche: Consultancy, Research Funding; Lilly: Honoraria; Amgen: Honoraria; Qiagen: Membership on an entity's Board of Directors or advisory committees; Imago Biosciences: Membership on an entity's Board of Directors or advisory committees; C4 Therapeutics: Membership on an entity's Board of Directors or advisory committees; Prelude Therapeutics: Research Funding; Isoplexis: Membership on an entity's Board of Directors or advisory committees.

Энзимное профилирование плазмы крови и лимфоцитов при системной красной волчанке: фокус на ферменты пуринового и пиримидинового метаболизма

Изучение метаболизма пуриновых и пиримидиновых оснований при системной красной волчанке в настоящее время является актуальным направлением, как с позиций фундаментальной науки, так и в аспекте разработки инновационных средств лечения. Не менее важным является и энзимное профилирование, поскольку именно ферменты - перспективные предикторы ответа на терапию и удобные «мишени» для терапевтических воздействий. Цель исследования - описание профиля активности ключевых ферментов пуринового и пиримидинового метаболизма в плазме крови и в лизатах циркулирующих лимфоцитов у больных системной красной волчанкой. Методика. В плазме крови и лизатах лимфоцитов 50 больных системной красной волчанкой определяли активность комплекса из 10 ферментов пуринового и пиримидинового метаболизма. В качестве контроля использовали образцы 30 здоровых лиц. Оценка степени активности проводилась с использованием шкалы индексов ECLAM. Выделение лимфоцитов из венозной периферической крови проводили c помощью метода седиментации в градиенте плотности. Результаты. У больных системной красной волчанкой была установлена зависимость активности ферментов пуринового пиримидинового метаболизма от тяжести заболевания. Прямые корреляционные связи с индексом ECLAM выявлены в плазменной активности пуриннуклеозидфосфорилазы, аденозинкиназы, урацил/тимидиндегидрогеназы, ИМФ-дегидрогеназы, цитидиндезаминазы, тимидинкиназы, дигидрооротатдегидрогеназы, а также у активности аденозинкиназы, ИМФ-дегидрогеназы и тимидинкиназы в лизатах лимфоцитов. Обратные корреляционные связи с индексом ECLAM выявлены для аденозиндезаминазы, тимидинфосфорилазы в плазме и активности пуриннуклеозидфосфорилазы, аденозиндезаминазы, гуанилаткиназы, урацил/тимидиндегидрогеназы, цитидиндезаминазы, тимидинфосфорилазы, дигидрооротатдегидрогеназы в лизатах лимфоцитов. При системной красной волчанке в плазме наиболее информативными оказались показатели минимальной активности пуриннуклеозидфосфорилазы, аденозинкиназы и ИМФ-дегидрогеназы, в лимфоцитах - пуриннуклеозидфосфорилазы, аденозиндезаминазы и аденозинкиназы. Заключение. Изученные энзимные показатели можно использовать в качестве дополнительных маркеров активности системной красной волчанке. Purine and pyrimidine metabolic pathways are emerging topical areas of research from the perspective of both basic science and development of innovative therapies for systemic lupus erythematosus (SLE). It is particularly important, therefore, to disclose characteristic enzymatic patterns for further prediction of the response to treatment. Objective: to characterize activity patterns of the major enzymes of purine and pyrimidine metabolic pathways in SLE. Methods. Samples were obtained from 50 patients with verified SLE and 30 healthy controls. Disease activity was assessed using the ECLAM scale. Blood lymphocytes were isolated by a standard density gradient centrifugation procedure. Activities of 10 major purine and pyrimidine enzymes were measured in blood plasma and lysed lymphocytes. Results. For different enzyme groups, enzyme activities directly or inversely correlated with SLE severity. Plasma purine nucleoside phosphorylase, adenosine kinase, uracil/thymidine dehydrogenase, IMP dehydrogenase, cytidine deaminase, thymidine kinase, dihydroorotate dehydrogenase, and lymphocyte adenosine kinase, IMP dehydrogenase, and thymidine kinase activities positively correlated with the ECLAM score. Negative correlations with ECLAM score were found for plasma adenosine deaminase and thymidine phosphorylase, and for lymphocyte purine nucleoside phosphorylase, adenosine deaminase, guanylate kinase, uracil/thymidine dehydrogenase, cytidine deaminase, thymidine phosphorylase, and dihydroorotate dehydrogenase. Activities of plasma purine nucleoside phosphorylase, adenosine kinase, IMP dehydrogenase, and lymphocyte purine nucleoside phosphorylase, adenosine deaminase, and adenosine kinase activities had the highest correlations with minimal SLE activity and represented candidate markers for the disease severity. Conclusion. The studied enzymatic patterns can be used as auxiliary markers of SLE activity, with special emphasis on minimal disease activity.

Novel Autoantibodies Related to Cell Death and DNA Repair Pathways in Systemic Lupus Erythematosus

Systemic lupus erythematosus (SLE) is a complex autoimmune syndrome characterized by various co-existing autoantibodies (autoAbs) in patients’ blood. However, the full spectrum of autoAbs in SLE has not been comprehensively elucidated. In this study, a commercial platform bearing 9400 antigens (ProtoArray) was used to identify autoAbs that were significantly elevated in the sera of SLE patients. By comparing the autoAb profiles of SLE patients with those of healthy controls, we identified 437 IgG and 1213 IgM autoAbs that the expression levels were significantly increased in SLE (P < 0.05). Use of the ProtoArray platform uncovered over 300 novel autoAbs targeting a broad range of nuclear, cytoplasmic, and membrane antigens. Molecular interaction network analysis revealed that the antigens targeted by the autoAbs were most significantly enriched in cell death, cell cycle, and DNA repair pathways. A group of autoAbs associated with cell apoptosis and DNA repair function, including those targeting APEX1, AURKA, POLB, AGO1, HMGB1, IFIT5, MAPKAPK3, PADI4, RGS3, SRP19, UBE2S, and VRK1, were further validated by ELISA and Western blot in a larger cohort. In addition, the levels of autoAbs against APEX1, HMGB1, VRK1, AURKA, PADI4, and SRP19 were positively correlated with the level of anti-dsDNA in SLE patients. Comprehensive autoAb screening has identified novel autoAbs, which may shed light on potential pathogenic pathways leading to lupus.

A promising approach to targeting type 1 IFN in systemic lupus erythematosus.

Despite advances in understanding systemic lupus erythematosus (SLE) pathogenesis, most clinical trials of new targeted therapies have been met with disappointment. The type I IFN pathway is believed to play an important role in SLE, and the proposed involvement of this pathway helps explain the frustration behind the failure at targeting either IFN-α or the type 1 IFN receptor itself. In this issue of the JCI, Furie et al. report on an intriguing phase 1b study that demonstrates an approach for inhibiting this pathway in the skin using an mAB (BIIB059) that targets the blood DC antigen 2 (BDCA-2) receptor on plasmacytoid DCs (pDCs). BIIB059 decreased IFN expression and improved cutaneous lupus disease activity, with a favorable safety profile. Whether or not this strategy will be effective in managing SLE in other organs remains unanswered. However, these results suggest that closing the door on targeting the type 1 IFN pathway in SLE may be premature and highlight the emerging question of whether an organ-specific approach toward lupus trials and treatment should be the wave of the future.

IL-12 and IL-23/Th17 axis in systemic lupus erythematosus.

Our article is focused on emerging pathogenetic pathways in systemic lupus erythematosus (SLE). Notably, IL-12 and IL-23 have been described as emerging cytokines in SLE pathogenesis. We know that IL-23 stimulates Th17 cells to produce IL-17. We try to point out the importance of IL-23/Th17 axis in SLE and to focus on the interaction between this axis and IL-12. Ustekinumab, a fully human IgG1κ monoclonal antibody directed towards the p40 shared subunit of IL-12 and IL-23, has been recently investigated in SLE, suggesting a potential novel therapeutic strategy in SLE. To our knowledge, there are no reviews which simultaneously focus on IL-12 an IL-23/Th17 axis in SLE. Thus, we believe our work will be of interest to the readers.

Gene microarray analysis of expression profiles in Suberoyllanilide hyroxamic acid-treated Dendritic cells

ObjectiveThe purpose of this study is to provide a further theoretical basis for the role of Suberoyllanilide hyroxamic acid (SAHA) affect on Dendritic cells (DCs). MethodsWe first downloaded the GSE74306 microarray data, which was about the effect of SAHA act on DCs, from the Gene Expression Omnibus database. Then we analyzed the differential expression genes (DEGs) between SAHA-treated DCs and SAHA-untreated DCs by limma package of R software; The Database for Annotation, Visualization and Integrated Discovery was used to analyze the Gene Ontology and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways for these DEGs. The protein protein interaction (PPI) network was constructed by using STRING database, Cytoscape 3.6.1 software was used to dispose the PPI network for visualization. Finally, we determine the Hub genes in the PPI network according by the degree centrality and betweenness centrality, which were calculated by the CentScaPe 2.2 plug-in of Cytoscape 3.6.1 software. ResultThere were 551 DEGs between SAHA-treated DC cells and SAHA-untreated DC cells, including 357 upregulated genes and 194 downregulated genes. These DEGs genes were enriched in 115 Go terms (Biological Process, 51; Cellular Component, 35 and Molecular Function, 29) and a total of 16 pathways. Glutathione metabolic process, Glutathione metabolism pathway, Rheumatoid arthritis pathway and Systemic lupus erythematosus pathway were most significant function clusters. In the PPI network, Rad51, Src, and Eno2 were Hub genes. ConclusionThe biological function and KEGG pathway enriched by DEGs may reveal the molecular mechanism of SAHA acting on DC cells. Its Hub genes, Src, Rad51 and Eno2, were expected to be new targets for SAHA therapeutic effects. However, it still need to be confirmed by the next more rigorous molecular biological experiments research.

Knowledge-Based Genetic Association Study of Hepatitis B Virus Related Hepatocellular Carcinoma in Chinese Populations

Background: Recent genome-wide association studies (GWASs) have suggested several susceptibility loci of hepatitis B virus (HBV)-related hepatocellular carcinoma (HCC) by statistical analysis at individual single-nucleotide polymorphisms (SNPs). However, these loci only explain a small fraction of HBV-related HCC heritability. Methods: In the present study, we aimed to identify additional susceptibility loci in two existing HBV-related HCC GWAS datasets using advanced gene- and gene-set-based association tests. Findings: The gene-based association analysis suggested that five genes are associated with HBV-related HCC risk: RNY4, GOLGA8M, LINC01207, WHAMMP2 and SLC39A8 with statistical significance. Through gene-set-based association analysis, we found that the genes in systemic lupus erythematosus pathway may be relevant to development of HBV-related HCC. Three previously reported genes, NAT2, GSTA1 and GSTA2, were also highlighted when genes were stratified in a liver-specific expression set. Furthermore, our analyses suggested that susceptibility loci of HBV-related HCC are unlikely to be enriched in several functional gene sets of HCC defined by our current knowledge. However, our failure to replicate significance at individual SNPs selected from the knowledge-based association analyses in independent cohorts calls for larger replication studies. Interpretation: This comprehensive knowledge-based association mining study suggested several promising genes significantly associated with HBV-related HCC risk, which may shed insights into the pathogenic mechanism of this fatal disorder. Funding Statement: This study was supported by Hong Kong Health and the Medical Research Fund (01121436 and 02132236 to M.X.L.), the National Natural Science Foundation of China (31100895, 81472618 and 81670535 to D.K.J., 81402297 to Q.L.X.), the National Science and Technology Major Project (No. 2018ZX10301202 to D.K.J. and J.H.), the Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program (No. 2017BT01S131 to D.K.J. and J.H.), the Grant for Recruited Talents to Start Scientific Research from Nanfang Hospital (to D.K.J.), and the Distinguished Youth Scholars Incubation Project of Nanfang Hospital (No. 2017J001 to D.K.J.) Declaration of Interests: The authors declare that they have no conflict of interest. Ethics Approval Statement: The study was performed in accordance with guidelines approved by the local ethical committees from all participating centers involved in both the GWAS stage and the replication stage. An informed consent to participate in the study was obtained from each subject in accordance with the declaration of Helsinki principles. All study participants approved the storage of their frozen DNA specimens, for research purposes, in our laboratory.

Emerging areas for therapeutic discovery in SLE.

Recent advances in the field of autoimmunity have identified numerous dysfunctional pathways in Systemic Lupus Erythematosus (SLE), including aberrant clearance of nucleic-acid-containing debris and immune complexes, excessive innate immune activation leading to overactive type I IFN signalling, and abnormal B and T cell activation. On the background of genetic polymorphisms that reset thresholds for immune responses, multiple immune cells contribute to inflammatory amplification circuits. Neutrophils activated by immune complexes are a rich source of immunogenic nucleic acids. Identification of new B subsets suggests several mechanisms for induction of autoantibody producing effector cells. Disordered T cell regulation involves both CD4 and CD8 cells. An imbalance in immunometabolism in immune cells amplifies autoimmunity and inflammation. These new advances in understanding of disease pathogenesis provide fertile ground for therapeutic development.

Transposable element dysregulation in systemic lupus erythematosus and regulation by histone conformation and Hsp90

Systemic lupus erythematosus (SLE) represents an autoimmune disease in which activation of the type I interferon pathway leads to dysregulation of tolerance and the generation of autoantibodies directed against nuclear constituents. The mechanisms driving the activation of the interferon pathway in SLE have been the subject of intense investigation but are still incompletely understood. Transposable elements represent an enormous source of RNA that could potentially stimulate the cell intrinsic RNA-recognition pathway, leading to upregulation of interferons. We used RNA-seq to define transposable element families and subfamilies in three cell types in SLE and found diverse effects on transposable element expression in the three cell types and even within a given family of transposable elements. When potential mechanisms were examined, we found that Hsp90 inhibition could drive increased expression of multiple type of transposable elements. Both direct inhibition and the delivery of a heat shock itself, which redirects heat shock regulators (including Hsp90) off of basal expression promoters and onto heat shock-responsive promoters, led to increased transposable element expression. This effect was amplified by the concurrent delivery of a histone deacetylase inhibitor. We conclude that transposable elements are dysregulated in SLE and there are tissue-specific effects and locus-specific effects. The magnitude of RNAs attributable to transposable elements makes their dysregulation of critical interest in SLE where transposable element RNA complexed with proteins has been shown to drive interferon expression.

Investigation of MicroRNA in Mitochondrial Apoptotic Pathway in Systemic Lupus Erythematosus

Background Accumulating evidence indicates that microRNAs play a pivotal role in the pathogenesis of systemic lupus erythematosus (SLE). This study tested the hypothesis that microRNA is associated with the mitochondrial apoptotic pathway in patients with SLE. Methods Thirteen patients were in the clinical comparison study and microRNA study and overall 19 patients in the study of intracellular protein. Levels of microRNAs were determined by miRNeasy kit in 13 patients with SLE and 29 volunteer normal controls. Intracellular levels of caspase-9, caspase-10, MAVS, MDA5, and pIRF7 in mononuclear cells from 19 patiens and the SLE disease activity index (SLEDAI) were determined in all SLE patients. Correlation analyses were performed among microRNAs, intracellular adaptor proteins, and caspase levels and mean SLEDAI. Results The ΔCT, defined by test reading difference between the target and the internal control microRNA (miR-451a), of miR-21-5p, miR-150-5p, and miR221-3p were significantly higher in plasma from SLE patients than in normal controls. miR-150-5pΔCT was positively correlated with both CRP and SLEDAI value. miR-150-5pΔCT was negatively associated with MAVS 70 kD. Caspase-10 protein levels were negatively associated with plasma miR-22-3pΔCT and miR-21-5pΔCT levels. Conclusions Our study confirmed the hypothesis that these microRNAs were associated with the mitochondrial apoptotic pathway in SLE. miR-150-5pΔCT was positively associated with SLE disease activity and it was negatively correlated with MAVS 70 kD, which may facilitate viral survival and further enhance inflammation. On the other hand, miR-22-3pΔCT and miR-21-5pΔCT, were negatively correlated with caspase-10 levels, which may repress extrinsic apoptosis and increase cell survival.

Disruption of microglia histone acetylation and protein pathways in mice exhibiting inflammation-associated depression-like symptoms

BackgroundPeripheral immune challenge can elicit microglia activation and depression-related symptoms. The balance of inflammatory signals in the tryptophan pathway can skew the activity of indoleamine-pyrrole 2,3 dioxygenase (IDO1) towards the metabolization of tryptophan into kynurenine (rather than serotonin), and towards neuroprotective or neurotoxic metabolites. The proteome changes that accompany inflammation-associated depression-related behaviors are incompletely understood. MethodsThe changes in microglia protein abundance and post-translational modifications in wild type (WT) mice that exhibit depression-like symptoms after recovery from peripheral Bacille Calmette-Guerin (BCG) challenge were studied. This WT_BGG group was compared to mice that do not express depression-like symptoms after BCG challenge due to IDO1 deficiency by means of genetic knockout (BCG_KO group), and to WT Saline-treated (Sal) mice (WT_Sal group) using a mass spectrometry-based label-free approach. ResultsThe comparison of WT_BCG relative to WT_Sal and KO_BCG mice uncovered patterns of protein abundance and acetylation among the histone families that could influence microglia signaling and transcriptional rates. Members of the histone clusters 1, 2 and 3 families were less abundant in WT_BCG relative to WT_Sal whereas members in the H2A family exhibited the opposite pattern. Irrespective of family, the majority of the histones were less abundant in WT_BCG relative to KO_BCG microglia. Homeostatic mechanisms may temper the potentially toxic effects of high histone levels after BCG challenge to levels lower than Sal. Histone acetylation was highest in WT_BCG and the similar levels observed in WT_Sal and KO_BCG. This result suggest that histone acetylation levels are similar between IDO1 deficient mice after immune challenge and unchallenged WT mice. The over-abundance of tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation proteins (14-3-3 series) in WT_BCG relative to KO_BCG is particularly interesting because these proteins activate another rate-limiting enzyme in the tryptophan pathway. The over-representation of alcoholism and systemic lupus erythematosus pathways among the proteins exhibiting differential abundance between the groups suggest that these disorders share microglia activation pathways with BCG challenge. The over-representation of phagosome pathway among proteins differentially abundant between WT_BCG and KO_BCG microglia suggest an association between IDO1 deficiency and phagocytosis. Likewise, the over-representation of the gap junction pathway among the differentially abundant proteins between KO_BCG and WT_Sal suggest a multifactorial effect of BCG and IDO1 deficiency on cell communication. ConclusionsThe present study of histone acetylation and differential protein abundance furthers the understanding of the long lasting effects of peripheral immune challenges. Our findings offer insights into target proteins and mechanisms that provide clues for therapies to ameliorate inflammation-associated depression-related behaviors.

DIFFICULTIES OF DIAGNOSTICS OF «COMPETITIVE» PROCESSES: THE SYSTEMIC LUPUS ERYTHEMATOSUS AT THE PATIENT WITH THE MODERN COMORBIDITY. THE CLINICAL CASE

The paper deals with the problem of recognizing systemic lupus erythematosus, which is getting a rather common disease. It present a clinical case of a female patient with type 2-diabetes mellitus, arterial hypertension, hyperuricemia, who developed systemic lupus erythematosus at the age of 52. The onset of a new disease in a patient with comorbidity is often concealed by the symptoms of the new disease. It troubles the well-timed diagnostics of the new disease. The diagnosis of systemic lupus erythematosus was established according to the accepted criteria in Federal clinical recommendations. The author emphasize that according the Federal clinical recommendations a long-course we of Hydroxychloroquine adder to the basic therapy proved to be effective in relieving clinical manifestations of systemic lupus erythematosus and preventing its exacerbations. Detailed differential diagnostics in the presented case is given in discussion. The considerable attention is paid to diagnosing and treatment of the fastprogressing lupoid nephrite. The example of standard pulse-therapy is given at the fast-progressing lyupus-nephrite for an induction of remission and its effectiveness for knocking over of a nephrotic syndrome on a concrete example is shown. The authors considered pathological processes which lead to fast progression of secondary nephrotic syndrome. Recently opened pathophysiological mechanisms of development of anemia of chronic disease are presented for it contributes to more complete of systemic lupus erythematosus path ways. Search of the reason of not expressed joint syndrome with systemic manifestations was run among probable autoimmune and exchange diseases for people of the senior age group. Specific laboratory indicators of function of a liver indicated the diagnosis of lupoid hepatitis. Probable mechanisms of injury of a liver to a concrete clinical case are described. Work of authors has cross-disciplinary character and it can be useful to experts of theoretical and applied medicine.

Decreased T cell expression of H/ACA box small nucleolar RNA 12 promotes lupus pathogenesis in patients with systemic lupus erythematosus.

Objective To investigate whether the aberrant expression of non-coding RNAs (ncRNAs) in T cells from patients with systemic lupus erythematosus (SLE) could contribute to the pathogenesis of lupus. Methods Expression profiles of RNA transcripts in T cells from three patients with SLE and three controls were analyzed by microarray analysis. Potentially aberrant-expressed ncRNAs were validated using T cell samples from 23 patients with SLE and 17 controls. Transfection studies and microarray analyses were conducted to search for any gene expression that is regulated by specific ncRNAs. Results Initial analysis revealed differential expression of 18 ncRNAs in SLE T cells. After validation, decreased expression of H/ACA box small nucleolar RNA 12 (SNORA12) was confirmed in SLE T cells (0.69-fold, P = 0.007) compared with normal T cells, and its expression level was inversely associated with higher SLE disease activity scores. Jurkat cells transfected with a plasmid encoding SNORA12 showed increased expression of two genes and decreased expression of 15 genes in Jurkat cells. These changes of gene expression were significantly associated with the SLE pathway in the Kyoto Encyclopedia of Genes and Genomes map using microarray analysis. Overexpression of SNORA12 altered the expression of CD69, decreased the expression of histone cluster 1 H4 family member k (HIST1H4K), inhibited the secretion of interferon gamma and the expression of HIST1H4K was increased in SLE T cells. Conclusion Among the ncRNAs, we found that the expression level of SNORA12, which belongs to the family of small nucleolar RNAs, was lower in SLE T cells and affected T cell function. This novel finding suggests that aberrant-expressed snoRNAs lead to dysfunction of T cells and may be involved in the immunopathogenesis of SLE.

Global Proteomics Deciphered Novel-Function of Osthole Against Pulmonary Arterial Hypertension

Pulmonary arterial hypertension (PAH) is a progressive cardiovascular-disease with high mortality lacking high-efficiency drug. Our efforts attempted to delineate therapeutic action of osthole produced by Angelica Pubescens Maxim, which has the capacity to treat PAH by exploiting an iTRAQ-based proteomic method. Excitingly, osthole was observed to significantly restore 98 of 315 differential proteins significantly modified by PAH progression. They were primarily annotated into 24 signaling pathways. Four mostly affected proteins (RPL15, Cathepsin S, Histone H3.3 and HMGB1) were experimentially validated which belonged to ribosome pathway, oxidative phosphorylation pathway, systemic lupus erythematosus pathway, complement and coagulation cascades pathway, whose modifications and modulations mostly accounted for therapeutic capacity of this compound against PAH. Altogether, our findings demonstrated that global proteomics is a promising systems-biology approach for deciphering therapeutic actions and associated mechanisms of natural products derived from traditional Chinese medicine. Importantly, osthole is supposed to be a candidate compound for new drug development to treat PAH.

Recent developments in systemic lupus erythematosus pathogenesis and applications for therapy.

Systemic lupus erythematosus (SLE) pathogenesis is complex. Aberrancies of immune function that previously were described but not well understood are now becoming better characterized, in part through recognition of monogenic cases of lupus-like disease. We highlight here recent descriptions of metabolic dysfunction, cytokine dysregulation, signaling defects, and DNA damage pathways in SLE. Specifically, we review the effects of signaling abnormalities in mammalian target of rapamycin, Rho kinase, Bruton's tyrosine kinase, and Ras pathways. The importance of DNA damage sensing and repair pathways, and their influence on the overproduction of type I interferon in SLE are also reviewed. Recent findings in SLE pathogenesis expand on previous understandings of broad immune dysfunction. These findings have clinical applications, as the dysregulated pathways described here can be targeted by existing and preclinical therapies.

Bioinformatics analysis of the CDK2 functions in neuroblastoma.

The present study aimed to elucidate the potential mechanism of cyclin-dependent kinase 2 (CDK2) in neuroblastoma progression and to identify the candidate genes associated with neuroblastoma with CDK2 silencing. The microarray data of GSE16480 were obtained from the gene expression omnibus database. This dataset contained 15samples: Neuroblastoma cell line IMR32 transfected with CDK2 shRNA at 0, 8, 24, 48 and 72h (n=3 per group; total=15). Significant clusters associated with differentially expressed genes (DEGs) were identified using fuzzy C‑Means algorithm in the Mfuzz package. Gene ontology and pathway enrichment analysis of DEGs in each cluster were performed, and a protein‑protein interaction (PPI) network was constructed. Additionally, functional annotation of DEGs in clusters was performed for the detection of transcription factors and tumor‑associated genes. A total of 4 clusters with significant change tendency and 1,683 DEGs were identified. The hub nodes of the PPI network constructed by DEGs in Cluster 1, Cluster 2, Cluster 3 and Cluster 4 were MDM2 oncogene, E3 ubiquitin protein ligase (MDM2), cyclin‑dependent kinase 1 (CDK1), proteasome (prosome, macropain) 26S subunit, non‑ATPase, 14 (PSMD14) and translocator protein (18kDa) (TSPO) respectively. These genes were significantly enriched in the p53 signaling pathway, cell cycle, proteasome and systemic lupus erythematosus pathways. MDM2, CDK1, PSMD14 and TSPO may be key target genes of CDK2. CDK2 may have key functions in neuroblastoma progression by regulating the expression of these genes.

Bioinformatics analysis of differentially expressed gene profiles associated with systemic lupus erythematosus.

DNA microarray and high-throughput sequencing have been widely used to identify the differentially expressed genes (DEGs) in systemic lupus erythematosus (SLE). However, the big data from gene microarrays are also challenging to work with in terms of analysis and processing. The presents study combined data from the microarray expression profile (GSE65391) and bioinformatics analysis to identify the key genes and cellular pathways in SLE. Gene ontology (GO) and cellular pathway enrichment analyses of DEGs were performed to investigate significantly enriched pathways. A protein-protein interaction network was constructed to determine the key genes in the occurrence and development of SLE. A total of 310 DEGs were identified in SLE, including 193 upregulated genes and 117 downregulated genes. GO analysis revealed that the most significant biological process of DEGs was immune system process. Kyoto Encyclopedia of Genes and Genome pathway analysis showed that these DEGs were enriched in signaling pathways associated with the immune system, including the RIG-I-like receptor signaling pathway, intestinal immune network for IgA production, antigen processing and presentation and the toll-like receptor signaling pathway. The current study screened the top 10 genes with higher degrees as hub genes, which included 2′-5′-oligoadenylate synthetase 1, MX dynamin like GTPase 2, interferon induced protein with tetratricopeptide repeats 1, interferon regulatory factor 7, interferon induced with helicase C domain 1, signal transducer and activator of transcription 1, ISG15 ubiquitin-like modifier, DExD/H-box helicase 58, interferon induced protein with tetratricopeptide repeats 3 and 2′-5′-oligoadenylate synthetase 2. Module analysis revealed that these hub genes were also involved in the RIG-I-like receptor signaling, cytosolic DNA-sensing, toll-like receptor signaling and ribosome biogenesis pathways. In addition, these hub genes, from different probe sets, exhibited significant co-expressed tendency in multi-experiment microarray datasets (P<0.01). In conclusion, these key genes and cellular pathways may improve the current understanding of the underlying mechanism of development of SLE. These key genes may be potential biomarkers of diagnosis, therapy and prognosis for SLE.

Targeting interferons and their pathways in systemic lupus erythematosus.

Significant advances in the understanding of the molecular basis of innate immunity have led to the identification of interferons (IFNs), particularly IFN-α, as central mediators in the pathogenesis of Systemic Lupus Erythematosus. Therefore, targeting of IFNs and of their downstream pathways has emerged as important developments for novel drug research in SLE. Based on this, several specific interferon blocking strategies using anti-IFN-α antibodies, anti-type I interferon receptor antibodies, Interferon-α-kinoid, or anti-IFN-γ antibodies have all been assessed in recent clinical trials. Alternative strategies targeting the plasmacytoid dendritic cells (pDCs), Toll-Like Receptors (TLRs)-7/9 or their downstream pathways such as the myeloid differentiation primary-response protein 88 (MYD88), spleen tyrosine kinase (Syk), Janus-kinases (JAKs), interleukin-1 receptor-associated kinase 4 (IRAK4), or the Tyrosine Kinase 2 (TYK2) are also investigated actively in SLE, at more preliminary clinical development stages, except for JAK inhibitors which have reached phase 2 studies. In a near future, in-depth and personalized functional characterization of IFN pathways may provide further guidance for the selection of the most relevant therapeutic strategy in SLE, tailored at the patient-level.

Identification of key genes for diabetic kidney disease using biological informatics methods.

Diabetic kidney disease (DKD) is a common complication of diabetes, which is characterized by albuminuria, impaired glomerular filtration rate or a combination of the two. The aim of the present study was to identify the potential key genes involved in DKD progression and to subsequently investigate the underlying mechanism involved in DKD development. The array data of GSE30528 including 9 DKD and 13 control samples was downloaded from the Gene Expression Omnibus database. The differentially expressed genes (DEGs) in DKD glomerular and tubular kidney biopsy tissues were compared with normal tissues, and were analyzed using the limma package. Gene Ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses were performed for DEGs using the GO Function software in Bioconductor. The protein-protein interaction (PPI) network was then constructed using Cytoscape software. A total of 426 genes (115 up- and 311 downregulated) were differentially expressed between the DKD and normal tissue samples. The PPI network was constructed with 184 nodes and 335 edges. Vascular endothelial growth factor A (VEGFA), α-actinin-4 (ACTN4), proto-oncogene, Src family tyrosine kinase (FYN), collagen, type 1, α2 (COL1A2) and insulin-like growth factor 1 (IGF1) were hub proteins. Major histocompatibility complex, class II, DP α1 (HLA-DPA1) was the common gene enriched in the rheumatoid arthritis and systemic lupus erythematosus pathways, and the immune response was a GO term enriched in module A. VEGFA, ACTN4, FYN, COL1A2, IGF1 and HLA-DPA1 may be potential key genes associated with the progression of DKD, and immune mechanisms may serve a part in DKD development.

MicroRNA-302d targets IRF9 to regulate the IFN-induced gene expression in SLE

Systemic lupus erythematosus (SLE) is a complex disease targeting multiple organs as a result of overactivation of the type I interferon (IFN) system, a feature currently being targeted by multiple biologic therapies against IFN-α. We have identified an estrogen-regulated microRNA, miR-302d, whose expression is decreased in SLE patient monocytes and identify its target as interferon regulatory factor (IRF)-9, a critical component of the transcriptional complex that regulates expression of interferon-stimulated genes (ISGs). In keeping with the reduced expression of miR-302d in SLE patient monocytes, IRF9 levels were increased, as was expression of a number of ISGs including MX1 and OAS1. In vivo evaluation revealed that miR-302d protects against pristane-induced inflammation in mice by targeting IRF9 and hence ISG expression. Importantly, patients with enhanced disease activity have markedly reduced expression of miR-302d and enhanced IRF9 and ISG expression, with miR-302d negatively correlating with IFN score. Together these findings identify miR-302d as a key regulator of type I IFN driven gene expression via its ability to target IRF9 and regulate ISG expression, underscoring the importance of non-coding RNA in regulating the IFN pathway in SLE.