Serum bile acid change correlates with improvement in pruritus in patients with primary biliary cholangitis receiving linerixibat.

BACKGROUND & AIMS: Total serum bile acid (TSBA) levels are elevated in patients with primary biliary cholangitis (PBC) and may mediate cholestatic pruritus. Linerixibat, an ileal bile acid transporter inhibitor, improved pruritus in patients with PBC. We explored the relationship between linerixibat dose, TSBA concentration, and pruritus. METHODS: Data from Phase 1/2 trials were used to develop a population kinetic-pharmacodynamic model to characterize the linerixibat dose-TSBA relationship. Individual Bayesian parameter estimates for participants in the GLIMMER study were used to derive the area under the TSBA concentration curve over 24 h (AUC0-24). Time-matched post hoc estimates of AUC0-24 were correlated with pruritus reported on a 0-10 numerical rating scale. Baseline TSBA concentration was correlated with change from baseline (ΔBL) in monthly itch score (MIS). ΔBL in model-estimated TSBA AUC0-24 was correlated with time-matched ΔBL in weekly itch score (WIS) or MIS. RESULTS: Linerixibat dose dependently reduced TSBA AUC0-24, reaching steady state after 5 days. Baseline TSBA levels in GLIMMER did not correlate with ΔBL in MIS. ΔBL in TSBA AUC0-24 correlated with improved WIS over 12 weeks of treatment (r = 0.52, p < 0.0001). Of participants with a ≥30% decrease in TSBA AUC0-24, 60% were pruritus responders (≥2-point improvement in WIS from baseline). CONCLUSIONS: Linerixibat treatment leads to rapid, dose-dependent TSBA reductions. Baseline TSBA levels do not correlate with on-treatment pruritus change, suggesting they do not predict linerixibat response. Change in TSBA AUC0-24 correlates significantly with, and can be predictive of, pruritus improvement in patients with PBC.

In-Situ-Generated Fluoride-Assisted Rapid Dissolution of Uranium Oxides by Ionic Liquids.

A quantitative, rapid, endothermic dissolution of U3O8 in C4mim·PF6 (1-alkyl-3-methyl imidazolium hexafluorophosphate) has been achieved within 2 h at 65 °C by in situ generated fluoride ions by pre-equilibrating the ionic liquid with suitable concentrations of nitric acid. The efficiency of the dissolution followed the trend: UO3 > UO2 > U3O8. The fluoride generation was found to increase with the concentration of nitric acid being equilibrated, the water content of the ionic liquid, and also the time of equilibration. The rate of dissolution of U3O8 followed the trend: C4mim·PF6> C6mim·PF6 > C8mim·PF6. The maximum loading observed for the present case was 200 mg mL-1 which is considered to be quite high with an ionic liquid. The effects of different acid pre-equilibration (HClO4, HCl) on F- generation and subsequent dissolution characteristics have also been investigated. The in situ F- generation, as well as U3O8 dissolution, were found to predominantly follow a pseudo-second-order rate kinetics, while the rate constants for U3O8 dissolution were found to be higher than that of F- generation. The dissolved uranium was successfully electrodeposited on a Cu plate, as confirmed by EDXRF, while the formation of UO2 was revealed from the XRD pattern of the deposit.

Anti-GM-CSF otilimab versus tofacitinib or placebo in patients with active rheumatoid arthritis and an inadequate response to conventional or biologic DMARDs: two phase 3 randomised trials (contRAst 1 and contRAst 2).

OBJECTIVES: To investigate the efficacy and safety of otilimab, an antigranulocyte-macrophage colony-stimulating factor antibody, in patients with active rheumatoid arthritis. METHODS: Two phase 3, double-blind randomised controlled trials including patients with inadequate responses to methotrexate (contRAst 1) or conventional synthetic/biologic disease-modifying antirheumatic drugs (cs/bDMARDs; contRAst 2). Patients received background csDMARDs. Through a testing hierarchy, subcutaneous otilimab (90/150 mg once weekly) was compared with placebo for week 12 endpoints (after which, patients receiving placebo switched to active interventions) or oral tofacitinib (5 mg two times per day) for week 24 endpoints. PRIMARY ENDPOINT: proportion of patients achieving an American College of Rheumatology response ≥20% (ACR20) at week 12. RESULTS: The intention-to-treat populations comprised 1537 (contRAst 1) and 1625 (contRAst 2) patients. PRIMARY ENDPOINT: proportions of ACR20 responders were statistically significantly greater with otilimab 90 mg and 150 mg vs placebo in contRAst 1 (54.7% (p=0.0023) and 50.9% (p=0.0362) vs 41.7%) and contRAst 2 (54.9% (p<0.0001) and 54.5% (p<0.0001) vs 32.5%). Secondary endpoints: in both trials, compared with placebo, otilimab increased the proportion of Clinical Disease Activity Index (CDAI) low disease activity (LDA) responders (not significant for otilimab 150 mg in contRAst 1), and reduced Health Assessment Questionnaire-Disability Index (HAQ-DI) scores. Benefits with tofacitinib were consistently greater than with otilimab across multiple endpoints. Safety outcomes were similar across treatment groups. CONCLUSIONS: Although otilimab demonstrated superiority to placebo in ACR20, CDAI LDA and HAQ-DI, improved symptoms, and had an acceptable safety profile, it was inferior to tofacitinib. TRIAL REGISTRATION NUMBERS: NCT03980483, NCT03970837.

Anti-GM-CSF otilimab versus sarilumab or placebo in patients with rheumatoid arthritis and inadequate response to targeted therapies: a phase III randomised trial (contRAst 3).

OBJECTIVES: To investigate the efficacy and safety of otilimab, an anti-granulocyte-macrophage colony-stimulating factor antibody, in patients with active rheumatoid arthritis and an inadequate response to conventional synthetic (cs) and biologic disease-modifying antirheumatic drugs (DMARDs) and/or Janus kinase inhibitors. METHODS: ContRAst 3 was a 24-week, phase III, multicentre, randomised controlled trial. Patients received subcutaneous otilimab (90/150 mg once weekly), subcutaneous sarilumab (200 mg every 2 weeks) or placebo for 12 weeks, in addition to csDMARDs. Patients receiving placebo were switched to active interventions at week 12 and treatment continued to week 24. The primary end point was the proportion of patients achieving an American College of Rheumatology ≥20% response (ACR20) at week 12. RESULTS: Overall, 549 patients received treatment. At week 12, there was no significant difference in the proportion of ACR20 responders with otilimab 90 mg and 150 mg versus placebo (45% (p=0.2868) and 51% (p=0.0596) vs 38%, respectively). There were no significant differences in Clinical Disease Activity Index, Health Assessment Questionnaire-Disability Index, pain Visual Analogue Scale or Functional Assessment of Chronic Illness Therapy-Fatigue scores with otilimab versus placebo at week 12. Sarilumab demonstrated superiority to otilimab in ACR20 response and secondary end points. The incidence of adverse or serious adverse events was similar across treatment groups. CONCLUSIONS: Otilimab demonstrated an acceptable safety profile but failed to achieve the primary end point of ACR20 and improve secondary end points versus placebo or demonstrate non-inferiority to sarilumab in this patient population. TRIAL REGISTRATION NUMBER: NCT04134728.

Capra cartilage-derived peptide delivery via carbon nano-dots for cartilage regeneration.

Targeted delivery of site-specific therapeutic agents is an effective strategy for osteoarthritis treatment. The lack of blood vessels in cartilage makes it difficult to deliver therapeutic agents like peptides to the defect area. Therefore, nucleus-targeting zwitterionic carbon nano-dots (CDs) have immense potential as a delivery vehicle for effective peptide delivery to the cytoplasm as well as nucleus. In the present study, nucleus-targeting zwitterionic CDs have been synthesized as delivery vehicle for peptides while also working as nano-agents towards optical monitoring of cartilage healing. The functional groups of zwitterion CDs were introduced by a single-step microwave assisted oxidation procedure followed by COL II peptide conjugation derived from Capra auricular cartilage through NHS/EDC coupling. The peptide-conjugated CDs (PCDs) allows cytoplasmic uptake within a short period of time (∼30 m) followed by translocation to nucleus after ∼24 h. Moreover, multicolor fluorescence of PCDs improves (blue, green, and read channel) its sensitivity as an optical code providing a compelling solution towards enhanced non-invasive tracking system with multifunctional properties. The PCDs-based delivery system developed in this study has exhibited superior ability to induce ex-vivo chondrogenic differentiation of ADMSCs as compared to bare CDs. For assessment of cartilage regeneration potential, pluronic F-127 based PCDs hydrogel was injected to rabbit auricular cartilage defects and potential healing was observed after 60 days. Therefore, the results confirm that PCDs could be an ideal alternate for multimodal therapeutic agents.

Design and Additive Manufacturing of Acetabular Implant with Continuously Graded Porosity.

Porous structured metallic implants are preferable as bone graft substitutes due to their faster tissue integration mediated by bone in-growth and vascularization. The porous scaffolds/implants should also mimic the graded structure of natural bone to ensure a match of mechanical properties. This article presents a method for designing a graded porous structured acetabular implant and identifies suitable parameters for manufacturing the model through additive manufacturing. The design method is based on slice-wise modification to ensure continuity of gradation. Modification of the slices was achieved through the binary image processing route. A geodesic dome-type design was adopted for developing the acetabular cup model from the graded porous structure. The model had a solid shell with the target porosity and pore size gradually changing from 65% and 950 µm, respectively, in the inner side to 75% and 650 µm, respectively, towards the periphery. The required dimensions of the unit structures and the combinations of pore structure and strut diameter necessary to obtain the target porosity and pore size were determined analytically. Suitable process parameters were identified to manufacture the model by Direct Metal Laser Sintering (DMLS) using Ti6Al4V powder after carrying out a detailed experimental study to minimize the variation of surface roughness and warping over different build angles of the strut structures. Dual-contour scanning was implemented to simplify the scan strategy. The minimum diameter of struts that could be manufactured using the selected scanning strategy and scanning parameters was found to be 375 µm. Finally, the model was built and from the micro-CT data, the porosities and pore sizes were found to be closely conforming to the designed values. The stiffness of the structures, as found from compression testing, was also found to match with that of human trabecular bone well. Further, the structure exhibited compliant bending-dominated behaviour under compressive loading.

A randomised trial of anti-GM-CSF otilimab in severe COVID-19 pneumonia (OSCAR).

BACKGROUND: Granulocyte-macrophage colony-stimulating factor (GM-CSF) and dysregulated myeloid cell responses are implicated in the pathophysiology and severity of COVID-19. METHODS: In this randomised, sequential, multicentre, placebo-controlled, double-blind study, adults aged 18-79 years (Part 1) or ≥70 years (Part 2) with severe COVID-19, respiratory failure and systemic inflammation (elevated C-reactive protein/ferritin) received a single intravenous infusion of otilimab 90 mg (human anti-GM-CSF monoclonal antibody) plus standard care (NCT04376684). The primary outcome was the proportion of patients alive and free of respiratory failure at Day 28. RESULTS: In Part 1 (n=806 randomised 1:1 otilimab:placebo), 71% of otilimab-treated patients were alive and free of respiratory failure at Day 28 versus 67% who received placebo; the model-adjusted difference of 5.3% was not statistically significant (95% CI -0.8-11.4%, p=0.09). A nominally significant model-adjusted difference of 19.1% (95% CI 5.2-33.1%, p=0.009) was observed in the predefined 70-79 years subgroup, but this was not confirmed in Part 2 (n=350 randomised) where the model-adjusted difference was 0.9% (95% CI -9.3-11.2%, p=0.86). Compared with placebo, otilimab resulted in lower serum concentrations of key inflammatory markers, including the putative pharmacodynamic biomarker CC chemokine ligand 17, indicative of GM-CSF pathway blockade. Adverse events were comparable between groups and consistent with severe COVID-19. CONCLUSIONS: There was no significant difference in the proportion of patients alive and free of respiratory failure at Day 28. However, despite the lack of clinical benefit, a reduction in inflammatory markers was observed with otilimab, in addition to an acceptable safety profile.

Tailoring defect structure and dopant composition and the generation of various color characteristics in Eu3+ and Tb3+ doped MgF2 phosphors.

A novel approach to generate a wide range of color characteristics such as near white, yellow, orange and red in MgF2, by proper tailoring of the defect structure and varying the composition of Eu3+ and Tb3+ dopant ions have been presented here. It has been observed from positron annihilation lifetime spectroscopy (PALS) study that various defect centers such as mono vacancies and their cluster forms exist in the system, whose amount varies upon varying the dopant ion's composition. The experimentally observed positron lifetime values of the defect centers also matched well with the theoretically calculated lifetime values using the MIKA-DOPPLER package. It has been found that a few vacancies or defect centers act as color centers, while the cluster vacancies change the local symmetry of the rare earth ion by inducing more distortion surrounding them thereby resulting in different emission characteristics in the photoluminescence (PL) study. The defect-related host emission in combination with the green and red emission from Tb3+ and Eu3+ ions generated near-white-light in some of the compounds, while other compounds showed a variety of other color characteristics due to the Tb3+ → Eu3+energy transfer dynamics. The various defect-related emissions, the role of the defect-related trap state in the decay kinetics and the energy-transfer dynamics were also understood by analyzing the electronic structure using HSE06 hybrid functional calculation.

The Transcriptome of Paired Major and Minor Salivary Gland Tissue in Patients With Primary Sjögren's Syndrome.

Background: While all salivary glands (SGs) can be involved in primary Sjögren's syndrome (pSS), their respective role in pathogenesis remains unclear. Our objective was to assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pSS and non-SS sicca patients. Methods: Paraffin-embedded, paired parotid and labial salivary gland tissue and peripheral blood mononuclear cells were obtained from 39 pSS and 20 non-SS sicca patients. RNA was extracted, complementary DNA libraries were prepared and sequenced. For analysis of differentially expressed genes (DEGs), patients were subdivided based on fulfillment of ACR-EULAR criteria and histopathology. Results: With principal component analysis, only biopsy-positive pSS could be separated from non-SS sicca patients based on SG gene expression. When comparing the transcriptome of biopsy-positive pSS and biopsy-negative non-SS sicca patients, 1235 and 624 DEGs (FDR<0.05, log2FC<-1 or >1) were identified for parotid and labial glands, respectively. The number of DEGs between biopsy-negative pSS and non-SS sicca patients was scarce. Overall, transcript expression levels correlated strongly between parotid and labial glands (R2 = 0.86, p-value<0.0001). Gene signatures present in both glands of biopsy-positive pSS patients included IFN-α signaling, IL-12/IL-18 signaling, CD3/CD28 T-cell activation, CD40 signaling in B-cells, DN2 B-cells, and FcRL4+ B-cells. Signature scores varied considerably amongst pSS patients. Conclusion: Transcriptomes of paired major and minor SGs in pSS were overall comparable, although significant inter-individual heterogeneity in immunopathway activation existed. The SG transcriptome of biopsy-negative pSS was indistinguishable from non-SS sicca patients. Different patterns of SG immunopathway activation in pSS argue for personalized treatment approaches.

Engineering defect clusters in distorted NaMgF3 perovskite and their important roles in tuning the emission characteristics of Eu3+ dopant ion.

An attempt has been made to explore various new defect clusters in distorted NaMgF3 perovskite and their important role in tuning optical properties. We have tried to tailor the defect clusters and to understand the impact on the luminescence of the lanthanide, for example the Eu3+ ion. Defect engineering has been carried out by doping aliovalent dopant ions to create a charge imbalance in the matrix, which in turn led to the creation of various mono-, di- and new cluster vacancies. Such vacancies have been characterized by Electron Para-magnetic Resonance (EPR), Positron Annihilation Lifetime Spectroscopy (PALS) and Photoluminescence (PL) studies. The PALS data of both undoped and Eu3+ doped compounds confirmed that in addition to Mg mono vacancies, cluster vacancies with different configurations comprising Mg, Na and F atom vacancies also exist in the matrix. The PL study revealed that depending on the surrounding defect structure, three different types of Eu3+ components can be created. The position of the Eu3+ ion with respect to these cluster vacancies determines the respective emission profiles and the decay kinetics. It has been found that when Li+ ions are co-doped with Eu3+, there is a sudden change in the decay kinetics and the emission profiles. The PALS study revealed that Li+ co-doping modified the configuration of the vacancy clusters, which in turn changes the emission characteristics. The EPR study confirmed the presence of different types of F-centers (F, F2, etc.) which are responsible for the host emission. Overall, this new study will be very helpful for a detailed understanding of the defect structures, in particular the cluster vacancies in distorted NaMgF3 perovskite, which have a direct or indirect impact on many physical properties.

Efficacy and safety of abatacept in active primary Sjögren's syndrome: results of a phase III, randomised, placebo-controlled trial.

OBJECTIVES: To evaluate efficacy and safety of abatacept in adults with active primary Sjögren's syndrome (pSS) in a phase III, randomised, double-blind, placebo-controlled trial. METHODS: Eligible patients (moderate-to-severe pSS [2016 ACR/European League Against Rheumatism (EULAR) criteria], EULAR Sjögren's Syndrome Disease Activity Index [ESSDAI] ≥5, anti-SS-related antigen A/anti-Ro antibody positive) received weekly subcutaneous abatacept 125 mg or placebo for 169 days followed by an open-label extension to day 365. Primary endpoint was mean change from baseline in ESSDAI at day 169. Key secondary endpoints were mean change from baseline in EULAR Sjögren's Syndrome Patient Reported Index (ESSPRI) and stimulated whole salivary flow (SWSF) at day 169. Other secondary clinical endpoints included glandular functions and patient-reported outcomes. Selected biomarkers and immune cell phenotypes were examined. Safety was monitored. RESULTS: Of 187 patients randomised, 168 completed double-blind period and 165 continued into open-label period. Mean (SD) baseline ESSDAI and ESSPRI total scores were 9.4 (4.3) and 6.5 (2.0), respectively. Statistical significance was not reached for primary (ESSDAI -3.2 abatacept vs -3.7 placebo, p=0.442) or key secondary endpoints (ESSPRI, p=0.337; SWSF, p=0.584). No clinical benefit of abatacept over placebo at day 169 was seen with other clinical and PRO endpoints. Relative to baseline, abatacept was associated with significant differences vs placebo in some disease-relevant biomarkers (including IgG, IgA, IgM-rheumatoid factor) and pathogenic cell subpopulations (post hoc analyses). No new safety signals were identified. CONCLUSIONS: Abatacept treatment did not result in significant clinical efficacy compared with placebo in patients with moderate-to-severe pSS, despite evidence of biological activity.

Simultaneous tuning of optical and electrical properties in a multifunctional LiNbO3 matrix upon doping with Eu3+ ions.

Combined photoluminescence (PL) and dielectric studies have been carried out on both undoped and Eu3+ doped LiNbO3 compounds for their potential application in optical-electrical integration for the first time. Special focus has been given to simultaneously tuning both these physical properties. A PL study reveals that the blank compound is a blue emitting material, while upon doping with Eu3+ ions, the emitting color can be tuned from blue to red upon changing the excitation wavelength. Interestingly, the electrical property measurement of this ferroelectric compound showed that upon doping with Eu3+ ions, the remnant polarization was increased significantly. Density Functional Theory (DFT) based calculations were carried out to explain both the optical and electrical properties. It has been found that different defect centers are responsible for the bluish host emission while Eu3+ ions are energetically preferred to occupy the Nb site and gives rise to red emission. The DFT based results also showed that Eu3+ ions induced more distortion into the nearby Nb-site, which is responsible for enhancement of the remnant polarization. Stark-splitting patterns in the PL study also showed that the point symmetry of LiNbO3 upon Eu3+ doping changes from C 6v to D 3, which indicates that the structure becomes less symmetric. Overall, the study presents a novel approach to designing multifunctional materials for optical-electrical integration application and to tuning their physical properties simultaneously in the desired range.

Development and validation of an in vitro 3D model of NASH with severe fibrotic phenotype.

Nonalcoholic steatohepatitis represents a significant and rapidly growing unmet medical need. The development of novel therapies has been hindered in part, by the limitations of existing preclinical models. There is a strong need for physiologically relevant in vivo and in vitro liver fibrosis models that are characterized by better translational predictability. In this study, we used the InSphero 3D InSightTM three-dimensional (3D) human liver microtissue (3D-hLMT) system prepared by co-culturing primary human hepatocytes with hepatic stellate cells, Kupffer cells and endothelial cells to develop a model of NASH with a severe fibrotic phenotype. In our model, palmitic acid (PA) induced a robust proinflammatory and profibrogenic phenotype in the 3D-hLMT. PA significantly increased several markers of the inflammatory and profibrotic process including gene expression of collagens, α-sma, tissue inhibitor of matrix metalloprotease 1 (timp1) and the stellate cell activation marker pdgfrß as well as secreted CXCL8 (IL8) levels. We also observed TGFß pathway activation, increase in active collagen synthesis and significant overall increase in tissue damage in the 3D-hLMTs. Immunohistochemistry analysis demonstrated the upregulation of collagen, cleaved caspase 3 as well as of the PDGFRß protein. We further validated the model using a phase 3 clinical compound, GS-4997, an apoptosis signal-regulating kinase 1 (ASK-1) inhibitor and showed that GS-4997 significantly decreased PA induced profibrotic and proinflammatory response in the 3D-hLMTs with decreases in apoptosis and stellate cell activation in the microtissues. Taken together we have established and validated an in vitro 3D-hLMT NASH model with severe fibrotic phenotype that can be a powerful tool to investigate experimental compounds for the treatment of NASH.

Role of genetic heterogeneity in determining the epidemiological severity of H1N1 influenza.

Genetic differences contribute to variations in the immune response mounted by different individuals to a pathogen. Such differential response can influence the spread of infectious disease, indicating why such diseases impact some populations more than others. Here, we study the impact of population-level genetic heterogeneity on the epidemic spread of different strains of H1N1 influenza. For a population with known HLA class-I allele frequency and for a given H1N1 viral strain, we classify individuals into sub-populations according to their level of susceptibility to infection. Our core hypothesis is that the susceptibility of a given individual to a disease such as H1N1 influenza is inversely proportional to the number of high affinity viral epitopes the individual can present. This number can be extracted from the HLA genetic profile of the individual. We use ethnicity-specific HLA class-I allele frequency data, together with genome sequences of various H1N1 viral strains, to obtain susceptibility sub-populations for 61 ethnicities and 81 viral strains isolated in 2009, as well as 85 strains isolated in other years. We incorporate these data into a multi-compartment SIR model to analyse the epidemic dynamics for these (ethnicity, viral strain) epidemic pairs. Our results show that HLA allele profiles which lead to a large spread in individual susceptibility values can act as a protective barrier against the spread of influenza. We predict that populations skewed such that a small number of highly susceptible individuals coexist with a large number of less susceptible ones, should exhibit smaller outbreaks than populations with the same average susceptibility but distributed more uniformly across individuals. Our model tracks some well-known qualitative trends of influenza spread worldwide, suggesting that HLA genetic diversity plays a crucial role in determining the spreading potential of different influenza viral strains across populations.

A novel encystation specific protein kinase regulates chitin synthesis in Entamoeba invadens.

Phosphorylation is an important post-translational modification of proteins and is involved in the regulation of a variety of cellular events. The proteome of Entamoeba invadens, the reptilian counterpart of Entamoeba histolytica consists of an overwhelming number of putative protein kinases, and some may have a role to play in Entamoeba encystation. In this study, we have identified a novel protein kinase named as EiCSpk (Entamoeba invadenscyst specific protein kinase) which expressed almost exclusively during encystation. It is an active Protein kinase C with a characteristic substrate phosphorylation and auto-phosphorylation property. Gene silencing study has unveiled its role as a regulator of chitin synthesis through transcriptional activation of the chitin synthesis pathway genes along with glycogen phosphorylases that are involved in the influx of glucose from glycogen breakdown for chitin synthesis.

HLaffy: estimating peptide affinities for Class-1 HLA molecules by learning position-specific pair potentials.

MOTIVATION: T-cell epitopes serve as molecular keys to initiate adaptive immune responses. Identification of T-cell epitopes is also a key step in rational vaccine design. Most available methods are driven by informatics and are critically dependent on experimentally obtained training data. Analysis of a training set from Immune Epitope Database (IEDB) for several alleles indicates that the sampling of the peptide space is extremely sparse covering a tiny fraction of the possible nonamer space, and also heavily skewed, thus restricting the range of epitope prediction. RESULTS: We present a new epitope prediction method that has four distinct computational modules: (i) structural modelling, estimating statistical pair-potentials and constraint derivation, (ii) implicit modelling and interaction profiling, (iii) feature representation and binding affinity prediction and (iv) use of graphical models to extract peptide sequence signatures to predict epitopes for HLA class I alleles. CONCLUSIONS: HLaffy is a novel and efficient epitope prediction method that predicts epitopes for any Class-1 HLA allele, by estimating the binding strengths of peptide-HLA complexes which is achieved through learning pair-potentials important for peptide binding. It relies on the strength of the mechanistic understanding of peptide-HLA recognition and provides an estimate of the total ligand space for each allele. The performance of HLaffy is seen to be superior to the currently available methods. AVAILABILITY AND IMPLEMENTATION: The method is made accessible through a webserver http://proline.biochem.iisc.ernet.in/HLaffy CONTACT: : nchandra@biochem.iisc.ernet.in SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

RSV-Induced H3K4 Demethylase KDM5B Leads to Regulation of Dendritic Cell-Derived Innate Cytokines and Exacerbates Pathogenesis In Vivo.

Respiratory syncytial virus (RSV) infection can result in severe disease partially due to its ability to interfere with the initiation of Th1 responses targeting the production of type I interferons (IFN) and promoting a Th2 immune environment. Epigenetic modulation of gene transcription has been shown to be important in regulating inflammatory pathways. RSV-infected bone marrow-derived DCs (BMDCs) upregulated expression of Kdm5b/Jarid1b H3K4 demethylase. Kdm5b-specific siRNA inhibition in BMDC led to a 10-fold increase in IFN-ß as well as increases in IL-6 and TNF-α compared to control-transfected cells. The generation of Kdm5bfl/fl-CD11c-Cre+ mice recapitulated the latter results during in vitro DC activation showing innate cytokine modulation. In vivo, infection of Kdm5bfl/fl-CD11c-Cre+ mice with RSV resulted in higher production of IFN-γ and reduced IL-4 and IL-5 compared to littermate controls, with significantly decreased inflammation, IL-13, and mucus production in the lungs. Sensitization with RSV-infected DCs into the airways of naïve mice led to an exacerbated response when mice were challenged with live RSV infection. When Kdm5b was blocked in DCs with siRNA or DCs from Kdm5bfl/fl-CD11c-CRE mice were used, the exacerbated response was abrogated. Importantly, human monocyte-derived DCs treated with a chemical inhibitor for KDM5B resulted in increased innate cytokine levels as well as elicited decreased Th2 cytokines when co-cultured with RSV reactivated CD4+ T cells. These results suggest that KDM5B acts to repress type I IFN and other innate cytokines to promote an altered immune response following RSV infection that contributes to development of chronic disease.

Deciphering complex patterns of class-I HLA-peptide cross-reactivity via hierarchical grouping.

T-cell responses in humans are initiated by the binding of a peptide antigen to a human leukocyte antigen (HLA) molecule. The peptide-HLA complex then recruits an appropriate T cell, leading to cell-mediated immunity. More than 2000 HLA class-I alleles are known in humans, and they vary only in their peptide-binding grooves. The polymorphism they exhibit enables them to bind a wide range of peptide antigens from diverse sources. HLA molecules and peptides present a complex molecular recognition pattern, as many peptides bind to a given allele and a given peptide can be recognized by many alleles. A powerful grouping scheme that not only provides an insightful classification, but is also capable of dissecting the physicochemical basis of recognition specificity is necessary to address this complexity. We present a hierarchical classification of 2010 class-I alleles by using a systematic divisive clustering method. All-pair distances of alleles were obtained by comparing binding pockets in the structural models. By varying the similarity thresholds, a multilevel classification was obtained, with 7 supergroups, each further subclassifying to yield 72 groups. An independent clustering performed based only on similarities in their epitope pools correlated highly with pocket-based clustering. Physicochemical feature combinations that best explain the basis of clustering are identified. Mutual information calculated for the set of peptide ligands enables identification of binding site residues contributing to peptide specificity. The grouping of HLA molecules achieved here will be useful for rational vaccine design, understanding disease susceptibilities and predicting risk of organ transplants.

Grouping of large populations into few CTL immune 'response-types' from influenza H1N1 genome analysis.

Despite extensive work on influenza, a number of questions still remain open about why individuals are differently susceptible to the disease and why only some strains lead to epidemics. Here we study the effect of human leukocyte antigen (HLA) genotype heterogeneity on possible cytotoxic T-lymphocyte (CTL) response to 186 influenza H1N1 genomes. To enable such analysis, we reconstruct HLA genotypes in different populations using a probabilistic method. We find that epidemic strains in general correlate with poor CTL response in populations. Our analysis shows that large populations can be classified into a small number of groups called response-types, specific to a given viral strain. Individuals of a response-type are expected to exhibit similar CTL responses. Extent of CTL responses varies significantly across different populations and increases with increase in genetic heterogeneity. Overall, our analysis presents a conceptual advance towards understanding how genetic heterogeneity influences disease susceptibility in individuals and in populations. We also obtain lists of top-ranking epitopes and proteins, ranked on the basis of conservation, antigenic cross-reactivity and population coverage, which provide ready short-lists for rational vaccine design. Our method is fairly generic and has the potential to be applied for studying other viruses.

PLIC: protein-ligand interaction clusters.

Most of the biological processes are governed through specific protein-ligand interactions. Discerning different components that contribute toward a favorable protein- ligand interaction could contribute significantly toward better understanding protein function, rationalizing drug design and obtaining design principles for protein engineering. The Protein Data Bank (PDB) currently hosts the structure of ∼68 000 protein-ligand complexes. Although several databases exist that classify proteins according to sequence and structure, a mere handful of them annotate and classify protein-ligand interactions and provide information on different attributes of molecular recognition. In this study, an exhaustive comparison of all the biologically relevant ligand-binding sites (84 846 sites) has been conducted using PocketMatch: a rapid, parallel, in-house algorithm. PocketMatch quantifies the similarity between binding sites based on structural descriptors and residue attributes. A similarity network was constructed using binding sites whose PocketMatch scores exceeded a high similarity threshold (0.80). The binding site similarity network was clustered into discrete sets of similar sites using the Markov clustering (MCL) algorithm. Furthermore, various computational tools have been used to study different attributes of interactions within the individual clusters. The attributes can be roughly divided into (i) binding site characteristics including pocket shape, nature of residues and interaction profiles with different kinds of atomic probes, (ii) atomic contacts consisting of various types of polar, hydrophobic and aromatic contacts along with binding site water molecules that could play crucial roles in protein-ligand interactions and (iii) binding energetics involved in interactions derived from scoring functions developed for docking. For each ligand-binding site in each protein in the PDB, site similarity information, clusters they belong to and description of site attributes are provided as a relational database-protein-ligand interaction clusters (PLIC). Database URL: http://proline.biochem.iisc.ernet.in/PLIC.