Genome-wide DNA methylation analysis in primary antiphospholipid syndrome neutrophils.

Antiphospholipid syndrome (APS) is a systemic autoimmune disease characterized by thromboembolic events and pregnancy loss. We sought to characterize the DNA methylation profile of primary APS in comparison to healthy controls and individuals with SLE. In primary APS neutrophils compared to controls, 17 hypomethylated and 25 hypermethylated CpG sites were identified. Notable hypomethylated genes included ETS1, a genetic risk locus for SLE, and PTPN2, a genetic risk locus for other autoimmune diseases. Gene ontology analysis of hypomethylated genes revealed enrichment of genes involved in pregnancy. None of the differentially methylated sites in primary APS were differentially methylated in SLE neutrophils, and there was no demethylation of interferon signature genes in primary APS as is seen in SLE. Hypomethylation within a single probe in the IFI44L promoter (cg06872964) was able to distinguish SLE from primary APS with a sensitivity of 93.3% and specificity of 80.0% at a methylation fraction of 0.329.

SynBioSS designer: a web-based tool for the automated generation of kinetic models for synthetic biological constructs.

Modeling tools can play an important role in synthetic biology the same way modeling helps in other engineering disciplines: simulations can quickly probe mechanisms and provide a clear picture of how different components influence the behavior of the whole. We present a brief review of available tools and present SynBioSS Designer. The Synthetic Biology Software Suite (SynBioSS) is used for the generation, storing, retrieval and quantitative simulation of synthetic biological networks. SynBioSS consists of three distinct components: the Desktop Simulator, the Wiki, and the Designer. SynBioSS Designer takes as input molecular parts involved in gene expression and regulation (e.g. promoters, transcription factors, ribosome binding sites, etc.), and automatically generates complete networks of reactions that represent transcription, translation, regulation, induction and degradation of those parts. Effectively, Designer uses DNA sequences as input and generates networks of biomolecular reactions as output. In this paper we describe how Designer uses universal principles of molecular biology to generate models of any arbitrary synthetic biological system. These models are useful as they explain biological phenotypic complexity in mechanistic terms. In turn, such mechanistic explanations can assist in designing synthetic biological systems. We also discuss, giving practical guidance to users, how Designer interfaces with the Registry of Standard Biological Parts, the de facto compendium of parts used in synthetic biology applications.

One-third of patients with lupus nephritis classified as complete responders continue to accrue progressive renal damage despite resolution of proteinuria.

OBJECTIVE: Treatment response in lupus nephritis (LN) is defined based on proteinuria, yet protocol kidney biopsy studies have shown that patients with lupus can have active nephritis in the absence of proteinuria. Using estimated glomerular filtration rate (eGFR) trajectories, we characterised early chronic kidney disease in LN and examined whether certain patients continue to accrue renal damage despite proteinuric response. METHODS: We conducted a single-centre study of patients diagnosed with their first episode of biopsy-proven class III, IV, and/or V LN (n=37). For each patient, eGFR trajectory was graphed over 5 years following renal biopsy. Participants were divided into those with progressive eGFR loss (eGFR slope <-5 mL/min/1.73 m2/year) versus those with stable eGFR. Participant demographics, renal biopsy features and response status at 1 year (urine protein to creatinine ratio <500 mg/g) were compared between eGFR trajectory groups. RESULTS: Overall, 30% (n=11) of participants accrued progressive eGFR loss despite standard of care therapy over the first 5 years following renal biopsy. There were no significant differences in baseline renal biopsy features, medication regimens or comorbidities between eGFR trajectory groups. Resolution of proteinuria at 1 year did not differentiate between groups: 6 of 18 (33%) of complete responders continued to accrue renal damage compared with 5 of 17 (29%) of non-responders. Response status could not be assigned for two participants in the stable eGFR group due to missing clinical information at 1 year. CONCLUSIONS: We identified an understudied category of patients with LN who accrue progressive renal damage despite apparent response to standard of care therapy. Better definitions and biomarkers of response are needed to improve renal outcomes and trial design.

Urine proteomic insights from the belimumab in lupus nephritis trial.

OBJECTIVE: Urine proteomic approaches have shown promise in identifying biological pathways in lupus nephritis (LN) which are not captured on renal histopathology or by measurement of proteinuria alone. We investigated how the urine proteome changes with treatment response and with belimumab therapy. METHODS: Urine samples from 54 Belimumab International Systemic Lupus Erythematosus-Lupus Nephritis trial participants (all with biopsy-proven LN) were collected at weeks 0, 24 and 52. At each time point, 1000 urinary proteins were quantified using antibody microarrays (Raybiotech Kiloplex), and their abundance was compared in responders (n=31) versus non-responders (n=22) and with belimumab treatment (n=28) versus standard of care therapy (n=26). Response was defined as proteinuria <500 mg/gcreatinine (cr), serum creatinine ≤1.25 times the week 0 value and prednisone ≤10 mg/day at week 52. RESULTS: By week 52, CD163 was the urine protein with the most significant difference in abundance between complete responders (median 1.8 pg/mgcr) versus non-responders (median 8.2 pg/mgcr, p=4e-7) regardless of treatment arm. At week 24, five urinary proteins were present at a significantly lower (CD23 and Siglec-5) or higher (AIF, CRELD2 and ROR2) level in the belimumab group. Belimumab therapy was particularly associated with reduction in CD23 between week 0 and week 24 (p=0.0001). CONCLUSIONS: Reduction in urinary CD163 was strongly associated with complete renal response, confirming the results of multiple prior studies. Treatment with belimumab can be detected in the urine proteome, and further study is needed to determine whether modulation of CD23-mediated immune enhancement pathways might be implicated in LN treatment response.

Therapeutic management of immune-mediated necrotizing myositis.

PURPOSE OF REVIEW: The idiopathic inflammatory myopathies are a heterogeneous group of autoimmune disorders characterized by skeletal muscle inflammation leading to chronic muscle weakness. Immune-mediated necrotizing myopathy (IMNM) is a distinct subgroup of inflammatory myopathy typically characterized by myofiber necrosis with minimal inflammatory infiltrates on muscle biopsy, highly elevated creatine kinase levels, and infrequent extra-muscular involvement. This review provides an overview of currently recommended treatment strategies for IMNM, including discussion of disease activity monitoring and recommended first-line immunomodulatory agents depending on clinical phenotype and autoantibody status. RECENT FINDINGS: IMNM can be divided into three subtypes based on autoantibody positivity: anti-3-hydroxy-3-methylglutaryl-CoA reductase (HMGCR) IMNM, anti-signal recognition particle (SRP) IMNM, and antibody negative IMNM. Autoantibody status in IMNM has considerable correlation with clinical phenotype, prognosis, and recommended choice of immunosuppressive agent. Patients with anti-HMGCR IMNM tend to respond well to intravenous immunoglobulin (IVIG), and IVIG monotherapy may be sufficient treatment for certain patients. In anti-SRP IMNM, early rituximab is commonly favored. More generally, prompt initiation of aggressive immunosuppression is often indicated, as both anti-SRP and anti-HMGCR IMNM can potentially cause debilitating weakness, and muscle atrophy and irreversible fatty replacement happen early in the disease course. Patients with IMNM frequently require combination therapy to achieve disease control, and have a high rate of relapse when tapering immunosuppression. Young age of onset is a poor prognostic factor. SUMMARY: IMNM can be severely disabling and often requires aggressive immunosuppression. For any given patient, the treatment strategy should be informed by the severity of their presenting features and autoantibody status. While our ability to treat IMNM has certainly improved, there remains a need for more prospective trials to inform optimal treatment strategies.

Cancer and Scleroderma.

Individuals with scleroderma have an increased risk of cancer compared with the general population. This heightened risk may be from chronic inflammation and tissue damage, malignant transformation provoked by immunosuppressive therapies, or a common inciting factor. In unique subsets of patients with scleroderma, there is a close temporal relationship between the onset of cancer and scleroderma, suggesting cancer-induced autoimmunity. This article discusses the potential mechanistic links between cancer and scleroderma, the serologic and clinical risk factors associated with increased cancer risk in patients with scleroderma, and implications for cancer screening.

SynBioSS: the synthetic biology modeling suite.

UNLABELLED: SynBioSS (Synthetic Biology Software Suite) is a suite of software for the modeling and simulation of synthetic genetic constructs. SynBioSS utilizes the registry of standard biological parts, a database of kinetic parameters, and both graphical and command-line interfaces to multiscale simulation algorithms. AVAILABILITY: SynBioSS is available under the GNU General Public License at http://synbioss.sourceforge.net.

Deoxyribonucleic Acid Methylation in Systemic Lupus Erythematosus: Implications for Future Clinical Practice.

Differential deoxyribonucleic acid (DNA) methylation has emerged as a critical feature of systemic lupus erythematosus (SLE). Genome-wide DNA methylation studies have revealed methylation patterns characteristic of SLE-in particular, robust hypomethylation of interferon-regulated genes is a prominent finding in all cells of the immune system studied to date. These patterns reliably distinguish individuals with SLE from healthy controls and from individuals with other autoimmune diseases. For example, hypomethylation within IFI44L is both highly sensitive and highly specific for SLE, superior to currently available biomarkers. Furthermore, methylation status of other genetic loci has been associated with clinically relevant features of SLE including disease severity and organ-specific manifestations. Finally, DNA methylation studies have provided important insights into the pathophysiology of SLE. Most recently, there is a growing body of evidence that the transcription factor enhancer of zeste homolog 2 (EZH2) plays an important role in triggering SLE disease activity via epigenetic mechanisms, and that EZH2 blockade may be a future treatment option in SLE. In this short review, we discuss the DNA methylation patterns associated with SLE, their relationship to clinically significant features of SLE, and their implications in the development of novel diagnostic and therapeutic approaches to this complex disease.

Outcome of patients with primary sclerosing cholangitis and ulcerative colitis undergoing colectomy.

AIM: To study the outcomes of primary sclerosing cholangitis (PSC) patients with ulcerative colitis (UC) undergoing colectomy. METHODS: We identified 193 patients with PSC and UC undergoing colectomy at the Mayo Clinic (Rochester, MN, United States), between January 1, 1995 and December 31, 2008 using a computerized record system. Eighty-nine patients were excluded due to unclear diagnosis, liver transplantation prior to colectomy, age less than 18 years, inadequate follow-up data or known cases of cholangiocarcinoma. We retrospectively reviewed data from patient medical records. Clinical information, date of colectomy, preoperative and follow-up liver tests and pathological findings of the colon were reviewed. The Mayo risk score at baseline was calculated to obtain survival estimates for up to 4 years of follow-up. The primary endpoint was defined by the presence of all-cause mortality and/or liver decompensation requiring liver transplantation. All patients who did not have a clinical note on December 31, 2008 were considered as patients with an incomplete follow-up unless they reached a study endpoint (death or underwent liver transplantation) prior to that date. The study was approved by the Institutional Review Boards of the Mayo Clinic. RESULTS: Of the 2441 patients with PSC observed in this period, 104 patients (4.3%) had UC and underwent colectomy and were included. The median age was 43.2 years, and 67% were male. The leading indications for colectomy were severe colonic inflammation (49%), the presence of colonic dysplasia during routine surveillance (42%) and bowel perforation (3%). Twenty-six patients were lost to follow-up after a median duration of 3.9 years. The remaining 78 patients included 52 patients (66.7%) who were followed for a median duration of 5.5 years and 26 patients (33.3%) who developed primary endpoints including death (n = 13) or underwent liver transplantation (n = 13) with a median follow up of 2.6 years. For the secondary endpoint, the liver complications within 1 mo following the colectomy were found in 9 patients (8.6%) and included worsening liver tests (n = 3), liver failure requiring liver transplantation (n = 2), acute cholangitis (n = 3) and right hepatic vein thrombosis with hepatic infarct (n = 1). A multivariate logistic analysis demonstrated that only lower platelet count and lower albumin level preoperatively were significantly associated with more primary endpoints (OR = 0.99 and 0.05 respectively). CONCLUSION: One third of patients with PSC and UC undergoing colectomy died or underwent liver transplantation within 2.6 years. PSC patients with lower platelet counts and lower albumin levels were significantly more likely to have a poorer outcome.

Recent developments in the management of idiopathic cholestatic liver disease.

In recent years, the clinical management of patients with idiopathic cholestatic liver disease has shown significant progress. Advancement of diagnostic and therapeutic approaches and better understanding of the pathophysiology underlying these diseases have all contributed considerably to this progress. In this review, we aim to touch briefly on several developments that have occurred in this regard and to discuss novel findings and interventions valuable to clinical practice.

Eugene--a domain specific language for specifying and constraining synthetic biological parts, devices, and systems.

BACKGROUND: Synthetic biological systems are currently created by an ad-hoc, iterative process of specification, design, and assembly. These systems would greatly benefit from a more formalized and rigorous specification of the desired system components as well as constraints on their composition. Therefore, the creation of robust and efficient design flows and tools is imperative. We present a human readable language (Eugene) that allows for the specification of synthetic biological designs based on biological parts, as well as provides a very expressive constraint system to drive the automatic creation of composite Parts (Devices) from a collection of individual Parts. RESULTS: We illustrate Eugene's capabilities in three different areas: Device specification, design space exploration, and assembly and simulation integration. These results highlight Eugene's ability to create combinatorial design spaces and prune these spaces for simulation or physical assembly. Eugene creates functional designs quickly and cost-effectively. CONCLUSIONS: Eugene is intended for forward engineering of DNA-based devices, and through its data types and execution semantics, reflects the desired abstraction hierarchy in synthetic biology. Eugene provides a powerful constraint system which can be used to drive the creation of new devices at runtime. It accomplishes all of this while being part of a larger tool chain which includes support for design, simulation, and physical device assembly.