Potent HPIV3-neutralizing IGHV5-51 Antibodies Identified from Multiple Individuals Show L Chain and CDRH3 Promiscuity

Human parainfluenza virus 3 (HPIV3) is a widespread pathogen causing severe and lethal respiratory illness in at-risk populations. Effective countermeasures are in various stages of development; however, licensed therapeutic and prophylactic options are not available. The fusion glycoprotein (HPIV3 F), responsible for facilitating viral entry into host cells, is a major target of neutralizing Abs that inhibit infection. Although several neutralizing Abs against a small number of HPIV3 F epitopes have been identified to date, relatively little is known about the Ab response to HPIV3 compared with other pathogens, such as influenza virus and SARS-CoV-2. In this study, we aimed to characterize a set of HPIV3-specific Abs identified in multiple individuals for genetic signatures, epitope specificity, neutralization potential, and publicness. We identified 12 potently neutralizing Abs targeting three nonoverlapping epitopes on HPIV3 F. Among these, six Abs identified from two different individuals used Ig heavy variable gene IGHV 5-51, with five of the six Abs targeting the same epitope. However, despite the use of the same H chain variable (VH) gene, these Abs used multiple different L chain variable genes (VL) and diverse H chain CDR 3 (CDRH3) sequences. Together, these results provide further information about the genetic and functional characteristics of HPIV3-neutralizing Abs and suggest the existence of a reproducible VH-dependent Ab response associated with VL and CDRH3 promiscuity. Understanding sites of HPIV3 F vulnerability and the genetic and molecular characteristics of Abs targeting these sites will help guide efforts for effective vaccine and therapeutic development.

Lectin: A Molecular Tool in Cancer Diagnosis and Therapy with Special Reference to Reproductive Cancers

The prevalence of cancer deaths globally and domestically is higher especially due to the deferment of diagnosis and lack of facilities for women's reproductive cancers. The present review focussed to explore the application of lectins in cancer theranostics. Though there is cancer diagnostic and treatment available there is no promising early diagnostic tool and effective treatment available for the cancer which is the major concern. Lectins are cellulose-binding proteins that are strongly determined in saccharide groups of glycans, glycopeptides, or glycolipids. In the concomitance of events in cells, carbohydrates, and proteins, lectins play an important role. Lectins bind superiorly to the cancer cell membrane and their receptors induce the cytotoxic effect, which results in caspase-mediated cell death, and prohibits tumour development. Lectin snuffing also reveals polyamine stocks and impedes the growth of cancerous cells. They affect the cell cycle by non-apoptotic aggregation, seizure of the cell cycle phase G2, M, and the mediation of caspases. It can also adversely affect the action of telomerase and hinder vascularisation. They promote immunomodulation and adversely limit protein synthesis. Their easy availability and its characteristics support its use in cancer diagnosis and therapy, despite their small corollary effects. Future investigations recommend focussing more on the key applications of lectin by reducing its concurrent effects and carrying out more in-vitro investigations. However, the use of lectin formulations for cancer theranostics is a new area in cancer detection and treatment. In this review, plant lectin appears to be a potential target for cancer research in the fields of diagnosis and theranostics.

The CARD8 inflammasome dictates HIV/SIV pathogenesis and disease progression

While CD4+ T cell depletion is key to disease progression in people living with HIV and SIV-infected macaques, the mechanisms underlying this depletion remain incompletely understood, with most cell death involving uninfected cells. In contrast, SIV infection of "natural" hosts such as sooty mangabeys does not cause CD4+ depletion and AIDS despite high-level viremia. Here, we report that the CARD8 inflammasome is activated immediately after HIV entry by the viral protease encapsulated in incoming virions. Sensing of HIV protease activity by CARD8 leads to rapid pyroptosis of quiescent cells without productive infection, while T cell activation abolishes CARD8 function and increases permissiveness to infection. In humanized mice reconstituted with CARD8-deficient cells, CD4+ depletion is delayed despite high viremia. Finally, we discovered loss-of-function mutations in CARD8 from "natural hosts," which may explain the peculiarly non-pathogenic nature of these infections. Our study suggests that CARD8 drives CD4+ T cell depletion during pathogenic HIV/SIV infections.

Development of LIBRA-seq for the guinea pig model system as a tool for the evaluation of antibody responses to multivalent HIV-1 vaccines

Consistent elicitation of serum antibody responses that neutralize diverse clades of HIV-1 remains a primary goal of HIV-1 vaccine research. Prior work has defined key features of soluble HIV-1 Envelope (Env) immunogen cocktails that influence the neutralization breadth and potency of multivalent vaccine-elicited antibody responses including the number of Env strains in the regimen. We designed immunization groups that consisted of different numbers of SOSIP Env strains to be used in a cocktail immunization strategy: the smallest cocktail (group 2) consisted of a set of two Env strains, which were a subset of the three Env strains that made up group 3, which, in turn, were a subset of the six Env strains that made up group 4. Serum neutralizing titers were modestly broader in guinea pigs that were immunized with a cocktail of three Envs compared to cocktails of two and six, suggesting that multivalent Env immunization could provide a benefit but may be detrimental when the cocktail size is too large. We then adapted the LIBRA-seq platform for antibody discovery to be compatible with guinea pigs, and isolated several tier 2 neutralizing monoclonal antibodies. Three antibodies isolated from two separate guinea pigs were similar in their gene usage and CDR3s, establishing evidence for a guinea pig public clonotype elicited through vaccination. Taken together, this work investigated multivalent HIV-1 Env immunization strategies and provides a novel methodology for screening guinea pig B cell receptor antigen specificity at a high-throughput level using LIBRA-seq.IMPORTANCEMultivalent vaccination with soluble Env immunogens is at the forefront of HIV-1 vaccination strategies but little is known about the influence of the number of Env strains included in vaccine cocktails. Our results suggest that adding more strains is sometimes beneficial but may be detrimental when the number of strains is too high. In addition, we adapted the LIBRA-seq platform to be compatible with guinea pig samples and isolated several tier 2 neutralizing monoclonal antibodies, some of which share V and J gene usage and >70% CDR3 identity, thus establishing the existence of public clonotypes in guinea pigs elicited through vaccination.

Assessment of inspiration and technical quality in anteroposterior thoracic radiographs using machine learning

INTRODUCTION

Chest radiographs are the most performed radiographic procedure, but suboptimal technical factors can impact clinical interpretation. A deep learning model was developed to assess technical and inspiratory adequacy of anteroposterior chest radiographs.

METHODS

Adult anteroposterior chest radiographs (n = 2375) were assessed for technical adequacy, and if otherwise technically adequate, for adequacy of inspiration. Images were labelled by an experienced radiologist with one of three ground truth labels: inadequate technique (n = 605, 25.5 %), adequate inspiration (n = 900, 37.9 %), and inadequate inspiration (n = 870, 36.6 %). A convolutional neural network was then iteratively trained to predict these labels and evaluated using recall, precision, F1 and micro-F1, and Gradient-weighted Class Activation Mapping analysis on a hold-out test set. Impact of kyphosis on model accuracy was assessed.

RESULTS

The model performed best for radiographs with adequate technique, and worst for images with inadequate technique. Recall was highest (89 %) for radiographs with both adequate technique and inspiration, with recall of 81 % for images with adequate technique and inadequate inspiration, and 60 % for images with inadequate technique, although precision was highest (85 %) for this category. Per-class F1 was 80 %, 81 % and 70 % for adequate inspiration, inadequate inspiration, and inadequate technique respectively. Weighted F1 and Micro F1 scores were 78 %. Presence or absence of kyphosis had no significant impact on model accuracy in images with adequate technique.

CONCLUSION

This study explores the promising performance of a machine learning algorithm for assessment of inspiratory adequacy and overall technical adequacy for anteroposterior chest radiograph acquisition.

IMPLICATIONS FOR PRACTICE

With further refinement, machine learning can contribute to education and quality improvement in radiology departments.

Dynamics and durability of HIV-1 neutralization are determined by viral replication

Human immunodeficiency virus type 1 (HIV-1)-neutralizing antibodies (nAbs) that prevent infection are the main goal of HIV vaccine discovery. But as no nAb-eliciting vaccines are yet available, only data from HIV-1 neutralizers-persons with HIV-1 who naturally develop broad and potent nAbs-can inform about the dynamics and durability of nAb responses in humans, knowledge which is crucial for the design of future HIV-1 vaccine regimens. To address this, we assessed HIV-1-neutralizing immunoglobulin G (IgG) from 2,354 persons with HIV-1 on or off antiretroviral therapy (ART). Infection with non-clade B viruses, CD4+ T cell counts <200 µl-1, being off ART and a longer time off ART were independent predictors of a more potent and broad neutralization. In longitudinal analyses, we found nAb half-lives of 9.3 and 16.9 years in individuals with no- or low-level viremia, respectively, and 4.0 years in persons who newly initiated ART. Finally, in a potent HIV-1 neutralizer, we identified lower fractions of serum nAbs and of nAb-encoding memory B cells after ART initiation, suggesting that a decreasing neutralizing serum activity after antigen withdrawal is due to lower levels of nAbs. These results collectively show that HIV-1-neutralizing responses can persist for several years, even at low antigen levels, suggesting that an HIV-1 vaccine may elicit a durable nAb response.

Functional HIV-1/HCV cross-reactive antibodies isolated from a chronically co-infected donor

Despite prolific efforts to characterize the antibody response to human immunodeficiency virus type 1 (HIV-1) and hepatitis C virus (HCV) mono-infections, the response to chronic co-infection with these two ever-evolving viruses is poorly understood. Here, we investigate the antibody repertoire of a chronically HIV-1/HCV co-infected individual using linking B cell receptor to antigen specificity through sequencing (LIBRA-seq). We identify five HIV-1/HCV cross-reactive antibodies demonstrating binding and functional cross-reactivity between HIV-1 and HCV envelope glycoproteins. All five antibodies show exceptional HCV neutralization breadth and effector functions against both HIV-1 and HCV. One antibody, mAb688, also cross-reacts with influenza and coronaviruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We examine the development of these antibodies using next-generation sequencing analysis and lineage tracing and find that somatic hypermutation established and enhanced this reactivity. These antibodies provide a potential future direction for therapeutic and vaccine development against current and emerging infectious diseases. More broadly, chronic co-infection represents a complex immunological challenge that can provide insights into the fundamental rules that underly antibody-antigen specificity.

Neutralization fingerprinting technology for characterizing polyclonal antibody responses to dengue vaccines

Dengue is a major public health threat. There are four dengue virus (DENV) serotypes; therefore, efforts are focused on developing safe and effective tetravalent DENV vaccines. While neutralizing antibodies contribute to protective immunity, there are still important gaps in understanding of immune responses elicited by dengue infection and vaccination. To that end, here, we develop a computational modeling framework based on the concept of antibody-virus neutralization fingerprints in order to characterize samples from clinical studies of TAK-003, a tetravalent vaccine candidate currently in phase 3 trials. Our results suggest a similarity of neutralizing antibody specificities in baseline-seronegative individuals. In contrast, amplification of pre-existing neutralizing antibody specificities is predicted for baseline-seropositive individuals, thus quantifying the role of immunologic imprinting in driving antibody responses to DENV vaccines. The neutralization fingerprinting analysis framework presented here can contribute to understanding dengue immune correlates of protection and help guide further vaccine development and optimization.

Single-cell profiling of the antigen-specific response to BNT162b2 SARS-CoV-2 RNA vaccine

RNA-based vaccines against SARS-CoV-2 have proven critical to limiting COVID-19 disease severity and spread. Cellular mechanisms driving antigen-specific responses to these vaccines, however, remain uncertain. Here we identify and characterize antigen-specific cells and antibody responses to the RNA vaccine BNT162b2 using multiple single-cell technologies for in depth analysis of longitudinal samples from a cohort of healthy participants. Mass cytometry and unbiased machine learning pinpoint an expanding, population of antigen-specific memory CD4+ and CD8+ T cells with characteristics of follicular or peripheral helper cells. B cell receptor sequencing suggest progression from IgM, with apparent cross-reactivity to endemic coronaviruses, to SARS-CoV-2-specific IgA and IgG memory B cells and plasmablasts. Responding lymphocyte populations correlate with eventual SARS-CoV-2 IgG, and a participant lacking these cell populations failed to sustain SARS-CoV-2-specific antibodies and experienced breakthrough infection. These integrated proteomic and genomic platforms identify an antigen-specific cellular basis of RNA vaccine-based immunity.

High-Throughput B Cell Epitope Determination by Next-Generation Sequencing

Development of novel technologies for the discovery of human monoclonal antibodies has proven invaluable in the fight against infectious diseases. Among the diverse antibody repertoires elicited by infection or vaccination, often only rare antibodies targeting specific epitopes of interest are of potential therapeutic value. Current antibody discovery efforts are capable of identifying B cells specific for a given antigen; however, epitope specificity information is usually only obtained after subsequent monoclonal antibody production and characterization. Here we describe LIBRA-seq with epitope mapping, a next-generation sequencing technology that enables residue-level epitope determination for thousands of single B cells simultaneously. By utilizing an antigen panel of point mutants within the HIV-1 Env glycoprotein, we identified and confirmed antibodies targeting multiple sites of vulnerability on Env, including the CD4-binding site and the V3-glycan site. LIBRA-seq with epitope mapping is an efficient tool for high-throughput identification of antibodies against epitopes of interest on a given antigen target.

Sequence and functional characterization of a public HIV-specific antibody clonotype

Public antibody clonotypes shared among multiple individuals have been identified for several pathogens. However, little is known about the determinants of antibody "publicness". Here, we characterize the sequence and functional properties of antibodies from a public clonotype targeting the CD4 binding site on HIV-1 Env. Our results showed that HIV-1 specificity for the public antibodies studied here, comprising sequences from three individuals, was modulated by the VH, but not VL, germline gene. Non-native pairing of public heavy and light chains from different individuals suggested functional complementation of sequences within this public antibody clonotype. The strength of antigen recognition appeared to be dependent on the specific antibody light chain used, but not on other sequence features such as native-antibody or germline sequence identity. Understanding the determinants of antibody clonotype "publicness" can provide insights into the fundamental rules of host-pathogen interactions at the population level, with implications for clonotype-specific vaccine development.

Potent neutralization of SARS-CoV-2 variants of concern by an antibody with an uncommon genetic signature and structural mode of spike recognition

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) lineages that are more transmissible and resistant to currently approved antibody therapies poses a considerable challenge to the clinical treatment of coronavirus disease (COVID-19). Therefore, the need for ongoing discovery efforts to identify broadly reactive monoclonal antibodies to SARS-CoV-2 is of utmost importance. Here, we report a panel of SARS-CoV-2 antibodies isolated using the linking B cell receptor to antigen specificity through sequencing (LIBRA-seq) technology from an individual who recovered from COVID-19. Of these antibodies, 54042-4 shows potent neutralization against authentic SARS-CoV-2 viruses, including variants of concern (VOCs). A cryoelectron microscopy (cryo-EM) structure of 54042-4 in complex with the SARS-CoV-2 spike reveals an epitope composed of residues that are highly conserved in currently circulating SARS-CoV-2 lineages. Further, 54042-4 possesses uncommon genetic and structural characteristics that distinguish it from other potently neutralizing SARS-CoV-2 antibodies. Together, these findings provide motivation for the development of 54042-4 as a lead candidate to counteract current and future SARS-CoV-2 VOCs.

Efficient discovery of potently neutralizing SARS-CoV-2 antibodies using LIBRA-seq with ligand blocking

SARS-CoV-2 therapeutic antibody discovery efforts have met with notable success but have been associated with a generally inefficient process, requiring the production and characterization of exceptionally large numbers of candidates for the identification of a small set of leads. Here, we show that incorporating antibody-ligand blocking as part of LIBRA-seq, the high-throughput sequencing platform for antibody discovery, results in efficient identification of ultra-potent neutralizing antibodies against SARS-CoV-2. LIBRA-seq with ligand blocking is a general platform for functional antibody discovery targeting the disruption of antigen-ligand interactions.

Cross-reactive coronavirus antibodies with diverse epitope specificities and Fc effector functions

The continual emergence of novel coronaviruses (CoV), such as severe acute respiratory syndrome-(SARS)-CoV-2, highlights the critical need for broadly reactive therapeutics and vaccines against this family of viruses. From a recovered SARS-CoV donor sample, we identify and characterize a panel of six monoclonal antibodies that cross-react with CoV spike (S) proteins from the highly pathogenic SARS-CoV and SARS-CoV-2, and demonstrate a spectrum of reactivity against other CoVs. Epitope mapping reveals that these antibodies recognize multiple epitopes on SARS-CoV-2 S, including the receptor-binding domain, the N-terminal domain, and the S2 subunit. Functional characterization demonstrates that the antibodies mediate phagocytosis-and in some cases trogocytosis-but not neutralization in vitro. When tested in vivo in murine models, two of the antibodies demonstrate a reduction in hemorrhagic pathology in the lungs. The identification of cross-reactive epitopes recognized by functional antibodies expands the repertoire of targets for pan-coronavirus vaccine design strategies.

Cross-reactive coronavirus antibodies with diverse epitope specificities and extra-neutralization functions

The continual emergence of novel coronavirus (CoV) strains, like SARS-CoV-2, highlights the critical need for broadly reactive therapeutics and vaccines against this family of viruses. Coronavirus spike (S) proteins share common structural motifs that could be vulnerable to cross-reactive antibody responses. To study this phenomenon in human coronavirus infection, we applied a high-throughput sequencing method called LIBRA-seq (Linking B cell receptor to antigen specificity through sequencing) to a SARS-CoV-1 convalescent donor sample. We identified and characterized a panel of six monoclonal antibodies that cross-reacted with S proteins from the highly pathogenic SARS-CoV-1 and SARS-CoV-2 and demonstrated a spectrum of reactivity against other coronaviruses. Epitope mapping revealed that these antibodies recognized multiple epitopes on SARS-CoV-2 S, including the receptor binding domain (RBD), N-terminal domain (NTD), and S2 subunit. Functional characterization demonstrated that the antibodies mediated a variety of Fc effector functions in vitro and mitigated pathological burden in vivo . The identification of cross-reactive epitopes recognized by functional antibodies expands the repertoire of targets for pan-coronavirus vaccine design strategies that may be useful for preventing potential future coronavirus outbreaks.

Longitudinal Antibody Responses in People Who Inject Drugs Infected With Similar Human Immunodeficiency Virus Strains

BACKGROUND

Multiple factors influence the human immunodeficiency virus (HIV) antibody response produced during natural infection, leading to responses that can vary in specificity, strength, and breadth.

METHODS

People who inject drugs identified as recently infected with HIV (n = 23) were analyzed for clustering of their viral sequences (genetic distance, <2%). Longitudinal antibody responses were identified for neutralizing antibody (Nab) potential, and differences in antibody subclass, specificity, and Fc receptor ligation using pseudovirus entry and multiplexed Fc array assays, respectively. Responses were analyzed for differences between subject groups, defined by similarity in the sequence of the infecting virus.

RESULTS

Viral sequences from infected individuals were grouped into 3 distinct clusters with 7 unclustered individuals. Subjects in cluster 1 generally had lower antibody response magnitudes, except for antibodies targeting the V1/V2 region. Subjects in clusters 2 and 3 typically had higher antibody response magnitudes, with the Fv specificity of cluster 2 favoring gp140 recognition. NAb responses differed significantly between clusters for 3 of 18 pseudoviruses examined (P < .05), but there were no differences in overall NAb breadth (P = .62).

DISCUSSION

These data demonstrate that individuals infected with similar viral strains can generate partially similar antibody responses, but these do not drastically differ from those in individuals infected with relatively unrelated strains.

NFPws: a web server for delineating broadly neutralizing antibody specificities from serum HIV-1 neutralization data

MOTIVATION

A better understanding of antibody responses to HIV-1 infection in humans can provide novel insights for the development of an effective HIV-1 vaccine. Neutralization fingerprinting (NFP) is an efficient and accurate algorithm for delineating the epitope specificities found in polyclonal antibody responses to HIV-1 infection. Here, we report the development of NFPws, a web server implementation of the NFP algorithm. The server takes as input serum neutralization data for a set of diverse viral strains, and uses a mathematical model to identify similarities between the serum neutralization pattern and the patterns for known broadly neutralizing monoclonal antibodies (bNAbs), in order to predict the prevalence of bNAb epitope specificities in the given serum. In addition, NFPws also computes and displays a number of estimates related to prediction confidence, as well as the likelihood of presence of novel, previously uncharacterized, antibody specificities in a given serum. NFPws also implements a JSmol viewer for molecular structure visualization of the prediction results. Overall, the NFPws server will be an important tool for the identification and analysis of epitope specificities of bNAb responses against HIV-1.

AVAILABILITY AND IMPLEMENTATION

NFPws is freely available to access at (http://iglab.accre.vanderbilt.edu/NFPws). The webserver is developed using html, CSS, javascript and perl CGI scripts. The NFP algorithm is implemented with scripts written in octave, linux shell and perl. JSmol is implemented to visualize the prediction results on a representative 3D structure of an HIV-1 antigen.

Envelope characteristics in individuals who developed neutralizing antibodies targeting different epitopes in HIV-1 subtype C infection

Broadly neutralizing antibodies (bNAbs) may constitute an essential component of a protective vaccine against HIV-1, yet no immunogen has been able to elicit them. To characterize the development of bNAbs in HIV-1 subtype C infected individuals, a panel of 18 Env-pseudotyped viruses was used to screen 18 study participants. The specificity of plasma neutralization was mapped against Env mutants and MPER chimeras. Envelope (env) gene sequence evolution was characterized by single genome amplification and sequencing. Three out of eighteen individuals developed broad plasma neutralizing activity (>60% breadth). Two of the three participants may target epitopes comprising glycans at position 276 of the D loop in the CD4 binding site and 332 glycan supersite, respectively. Deletion of these glycans was associated with neutralization resistance. Our study describes the kinetics of the development of plasma neutralizing activity and identified amino acid residue changes suggestive of immune pressure on putative epitopes. The study enhances our understanding of how neutralization breadth develops in the course of HIV-1 subtype C infection.

High-Throughput Mapping of B Cell Receptor Sequences to Antigen Specificity

B cell receptor (BCR) sequencing is a powerful tool for interrogating immune responses to infection and vaccination, but it provides limited information about the antigen specificity of the sequenced BCRs. Here, we present LIBRA-seq (linking B cell receptor to antigen specificity through sequencing), a technology for high-throughput mapping of paired heavy- and light-chain BCR sequences to their cognate antigen specificities. B cells are mixed with a panel of DNA-barcoded antigens so that both the antigen barcode(s) and BCR sequence are recovered via single-cell next-generation sequencing. Using LIBRA-seq, we mapped the antigen specificity of thousands of B cells from two HIV-infected subjects. The predicted specificities were confirmed for a number of HIV- and influenza-specific antibodies, including known and novel broadly neutralizing antibodies. LIBRA-seq will be an integral tool for antibody discovery and vaccine development efforts against a wide range of antigen targets.

Therapeutic antibody discovery in lung tumors by B-cell receptor sequencing

Malignancies of the lung are expected to be responsible for over 25% of all cancer-associated mortalities in the United States in 2019. Clinical treatment of lung cancer is complicated by both poor detection of early disease activity and relapse or unresponsiveness to administered therapy. Taken together, these realities of patient outcome underscore the need for alternative therapeutic strategies. Research efforts in the cancer immunology field focus primarily on T cells in the tumor microenvironment, however, there is evidence that B cells may impart a clinical benefit in patients. The formation of tertiary lymphoid structures and antibody secretion in lung tumors associate with positive clinical outcomes yet remain understudied and poorly characterized. In an effort to expand upon these observations, we isolated B cells from cryopreserved human lung cancer tissue and recovered B-cell receptor (BCR) sequences by paired heavy and light chain single cell RNA sequencing. From these experiments, we identified clonally expanded B-cell populations and convergent BCR sequences shared between different patients. We further demonstrated that recombinant antibodies derived from lung cancer patients bind cultured lung cancer cell lines in a dose-dependent manner. This preliminary data supports the notion that tumor-resident B-cells secrete functional antibodies that may additionally be tumor-reactive. Future characterization of these antibodies includes antigen identification and the measurement of in vitro and in vivo cytotoxic activity. Human patient-derived antibodies not only could serve as a novel source for therapeutic and diagnostic agents but may also help inform vaccine design in lung cancer indications.

Coronary Angiography Profile at the Time of Hemodialysis Initiation in End-Stage Renal Disease Population: A Retrospective Analysis

Cardiovascular disease is associated with increased mortality in dialysis population. However, there are very few studies that assessed the prevalence of coronary artery disease (CAD) at the time of initiation of hemodialysis (HD). The present study was aimed to assess the prevalence of CAD in end-stage renal disease (ESRD) patients at the time of initiation of HD and the risk factors for CAD in this population. This was a single-center retrospective study and included ESRD patients who underwent coronary angiography (CAG) at the time of initiation of HD. Inclusion criteria were age >18 years and those who were subjected to CAG within 2 weeks of initiation of HD. According to the findings on CAG, patients were divided into no CAD and CAD groups. CAD was diagnosed if there was >50% stenosis of vessel. Clinical and laboratory parameters between these two groups were analyzed. Ninety-seven patients were included in the study based on the inclusion criteria. Forty-four (45%) patients were diagnosed with CAD. Patients who had CAD were younger compared to no CAD group (50.7 + 10 vs. 55.8 + 9.3 years; P = 0.01). Majority of them were males. Diabetic nephropathy (DN) was associated with increased risk of CAD (60% vs. 40%, P = 0.007). History of smoking, high high-sensitivity C-reactive protein (hs-CRP), low total cholesterol, and low high-density lipoprotein (HDL) were associated with significantly increased risk of CAD. Gender, symptoms of CAD, serum low-density lipoprotein (LDL), very LDL, and triglycerides were not associated with increased risk of CAD. Neither calcium (Ca), phosphorus (PO₄), nor Ca × PO₄products were associated with an increased risk of CAD. Resting electrocardiogram abnormalities had no significance in predicting CAD (32% in CAD and 19% in no CAD group). Echocardiography showed regional wall motion abnormalities/global hypokinesia in 18% patients of CAD group and 3.8% patients of no CAD group (P = 0.03). Single-, double-, and triple-vessel disease was documented in 17 (38%), 13 (29.5%), and 14 (32.5%) patients, respectively, and the most common vessel involved was the left anterior descending artery. At the initiation of HD in ESRD patients, CAD was seen in almost half of the patients. DN was a significant risk factor for CAD. Other risk factors for CAD include smoking, low cholesterol, low HDL, and high hs-CRP levels.

Clinical Profile and Outcome of Posterior Reversible Encephalopathy Syndrome in Hemodialysis Patients

Posterior reversible encephalopathy syndrome (PRES) is a clinico-radiologic entity characterized by headache, altered level of consciousness, seizures, visual disturbances, and reversible vasogenic subcortical edema. Hypertension and renal failure are well known principal risk factors for the development of PRES. However, risk factors and outcome of PRES has not been studied in patients on maintenance hemodialysis (MHD). The objective of this study is to characterize the factors predisposing to the development of PRES in patients on MHD. We performed a retrospective analysis in patients of MHD who were diagnosed with PRES between August 1, 2013, and July 31, 2015. Those with a history of cerebrovascular accidents/stroke, and epilepsy were excluded. We analyzed the clinical details, course, and laboratory data. One year follow-up data were noted in recurrence of PRES and mortality. A total of 18 patients were included for the final analysis. Of these, 13 (72%) patients were males. Majority of these patients were young and mean age was 21.1 years (6–50 years). Most of the PRES episodes developed shortly after initiation of MHD with mean duration of 2 months after initiation of MHD (1 month–3 years). All 18 patients had resistant hypertension. Eight (45%) patients had infection at the time of PRES episodes. Four patients had catheter-related bloodstream infection, 1 had pneumonia and 3 patients were recently diagnosed with pulmonary tuberculosis. Four (22%) patients developed recurrence of PRES and all these episodes developed within 2 months of index event. Seven (39%) patients underwent renal transplantation, and all received triple immune suppression and had uncontrolled hypertension in the perioperative period. However, none of these patients developed PRES after transplantation. All these patients had been maintaining stable graft function in the follow-up. All episodes of PRES were of generalized tonic–clonic seizure type and 6 of them presented as status epilepticus. None of them had any neurological sequel and no mortality at the end of 1 year. PRES is not uncommon in patients on MHD. Uncontrolled hypertension and infection are common predisposing factors. Renal transplantation is safe and not adversely affected by prior episodes of PRES in MHD.

Multi-Donor Longitudinal Antibody Repertoire Sequencing Reveals the Existence of Public Antibody Clonotypes in HIV-1 Infection

Characterization of single antibody lineages within infected individuals has provided insights into the development of Env-specific antibodies. However, a systems-level understanding of the humoral response against HIV-1 is limited. Here, we interrogated the antibody repertoires of multiple HIV-infected donors from an infection-naive state through acute and chronic infection using next-generation sequencing. This analysis revealed the existence of "public" antibody clonotypes that were shared among multiple HIV-infected individuals. The HIV-1 reactivity for representative antibodies from an identified public clonotype shared by three donors was confirmed. Furthermore, a meta-analysis of publicly available antibody repertoire sequencing datasets revealed antibodies with high sequence identity to known HIV-reactive antibodies, even in repertoires that were reported to be HIV naive. The discovery of public antibody clonotypes in HIV-infected individuals represents an avenue of significant potential for better understanding antibody responses to HIV-1 infection, as well as for clonotype-specific vaccine development.

Association of CD14 and macrophage migration inhibitory factor gene polymorphisms with inflammatory microRNAs expression levels in ankylosing spondylitis and polyarthralgia

This study aimed to investigate the genetic basis of ankylosing spondylitis (AS) and polyarthralgia (PA) conditions among Indian subjects through genotyping two immune regulatory genes CD14 (-159C>T) and MIF (-173G>C) and find their association with the expression levels of three circulating inflammatory miRNAs. This investigation may provide early genetic cause of these two forms of arthritis and more optimal biological targets to predict early therapeutic outcomes. A total of 140 patients (AS: 70 and PA: 70) and 156 controls were recruited from Indian population. CD14 and MIF genotyping was performed using ARMS-PCR. Expression level of three inflammatory miRNAs (miRNA-146a, miRNA-155 and miRNA-181) was quantified using RT-qPCR. C/T genotype of CD14 gene was found to cause 2.06-fold risk of developing AS (CI 1.06-5.98, p = .04) as compared to others and G/C genotype in MIF also shown significant variation between AS and control subjects. In PA subjects, CD14 genotypes (C/T) was found to be associated with disease susceptibility and G/C genotype of MIF gene polymorphism showed 4.71-fold risk of developing PA (CI 2.58-8.62, p = .0001). The study also revealed significant upregulation of miRNA-155 expression in AS subjects (p = .0001) with more than 1.3-fold difference between AS and PA as compared to the control subjects. miRNA-155 had strong association with AS patients with CD14 genotypes (p < .05) than PA and control subjects. This study provides better understanding of the mechanisms and disease susceptibility for MIF and CD14 genetic variants and inflammatory miRNAs networks involved in AS and PA.

Use of Biocompatible Sorafenib-gold Nanoconjugates for Reversal of Drug Resistance in Human Hepatoblatoma Cells

The present study identifies the potential of highly biocompatible SF-GNP nano-conjugate to enhance the chemotherapeutic response to combat drug resistance in cancer cells. We developed a stable colloidal suspension of sorafenib-gold nanoconjugate (SF-GNP) of <10 nm size in aqueous medium for reverting the cancer drug resistance in SF-resistant HepG2 cells in a 3D ex-vivo model system. In-vivo biocompatibility assay of SF-GNPs showed absence of systemic toxicological effects including hematological, biochemical and histological parameters. More importantly, the histopathological analysis of vital organs such as liver, brain, lung, kidney and heart showed very least or no sign of inflammation, cell infiltration, necrosis, tissue disorganization or fibrotic reactions after intra-peritoneal administration of SF-GNP nanoconjugates in animals. However, SF-GNP nanoconjugates significantly reduced (>80%) the percentage cell survival and the size and number of SF resistant solid tumor colonies of HepG2 cells in 3D model system. The exposure of SF-GNP nanoconjugate to SF resistant HepG2 cell colonies also provided evidence for anti-proliferative effect and reversal of drug resistance by elucidating the molecular regulatory mechanisms of extracellular matrix factor (CD147), tumor growth factor (TGF-β), hepatoma upregulated protein (hURP) and drug transporter (ABCG-2).

Highlights from the 11th ISCB Student Council Symposium 2015. Dublin, Ireland. 10 July 2015

A1 Highlights from the eleventh ISCB Student Council Symposium 2015

Katie Wilkins, Mehedi Hassan, Margherita Francescatto, Jakob Jespersen, R. Gonzalo Parra, Bart Cuypers, Dan DeBlasio, Alexander Junge, Anupama Jigisha, Farzana Rahman

O1 Prioritizing a drug’s targets using both gene expression and structural similarity

Griet Laenen, Sander Willems, Lieven Thorrez, Yves Moreau

O2 Organism specific protein-RNA recognition: A computational analysis of protein-RNA complex structures from different organisms

Nagarajan Raju, Sonia Pankaj Chothani, C. Ramakrishnan, Masakazu Sekijima; M. Michael Gromiha

O3 Detection of Heterogeneity in Single Particle Tracking Trajectories

Paddy J Slator, Nigel J Burroughs

O4 3D-NOME: 3D NucleOme Multiscale Engine for data-driven modeling of three-dimensional genome architecture

Przemysław Szałaj, Zhonghui Tang, Paul Michalski, Oskar Luo, Xingwang Li, Yijun Ruan, Dariusz Plewczynski

O5 A novel feature selection method to extract multiple adjacent solutions for viral genomic sequences classification

Giulia Fiscon, Emanuel Weitschek, Massimo Ciccozzi, Paola Bertolazzi, Giovanni Felici

O6 A Systems Biology Compendium for Leishmania donovani

Bart Cuypers, Pieter Meysman, Manu Vanaerschot, Maya Berg, Hideo Imamura, Jean-Claude Dujardin, Kris Laukens

O7 Unravelling signal coordination from large scale phosphorylation kinetic data

Westa Domanova, James R. Krycer, Rima Chaudhuri, Pengyi Yang, Fatemeh Vafaee, Daniel J. Fazakerley, Sean J. Humphrey, David E. James, Zdenka Kuncic

Rituximab in the treatment of refractory late acute antibody-mediated rejection: Our initial experience

Antibody-mediated rejection (AMR) is not uncommon after renal transplantation and is harder to handle compared to cell-mediated rejection. When refractory to conventional therapies, rituximab is an attractive option. This study aims to examine the effectiveness of rituximab in refractory late acute AMR. This is a retrospective study involving nine renal transplant recipients. Four doses of rituximab were administered at weekly interval for 4 weeks, at a dose of 375 mg/m². The mean age of patients was 35.3 ± 7.38 years. The median period between transplantation and graft dysfunction was 30 ± 20 months. Mean serum creatinine at the time of discharge after transplantation and at the time of acute AMR diagnosis was 1.14 ± 0.19 mg/dl and 2.26 ± 0.57 mg/dl, respectively. After standard therapy, it was 2.68 ± 0.62 mg/dl. One patient died of Pseudomonas sepsis and three patients progressed to end-stage renal disease (ESRD). Four biopsies showed significant plasma cell infiltrations. Mean serum creatinine among non-ESRD patients at the end of 1 year progressed from 2.3 ± 0.4 to 3.8 ± 1.2 mg/dl (P value 0.04). eGFR prior to therapy and at the end of 1 year were 34.4 ± 6.18 and 20.8 ± 7.69 ml/min (P value 0.04), respectively. Only one patient showed improvement in graft function in whom donor-specific antibody (DSA) titers showed significant improvement. Rituximab may not be effective in late acute AMR unlike in early acute AMR. Monitoring of DSA has a prognostic role in these patients and plasma cell rich rejection is associated with poor prognosis.

Effect of a simple two-step warfarin dosing algorithm on anticoagulant control as measured by time in therapeutic range: a pilot study

BACKGROUND

The efficacy and safety of vitamin K antagonists for the prevention of thromboembolism are dependent on the time for which the International Normalized Ratio (INR) is in the therapeutic range. The objective of our study was to determine the effect of introducing a simple two-step dosing algorithm, as compared with dosing by anticoagulation clinic staffs on the basis of their experience, on time in therapeutic range (TTR) of warfarin therapy.

METHODS

We compared TTRs of all clinic patients before and after the introduction of a simple two-step dosing algorithm at a single anticoagulation clinic in Canada, between 1 August 2006 and 24 December 2008. TTR was calculated using the linear interpolation method of Rosendaal.

RESULTS

We included 873 patients in the 'before' phase and 1088 patients in the 'after' phase. Introduction of the dosing algorithm significantly increased TTR of patients with a therapeutic INR range of 2-3 from 67.2% to 73.2% (P < 0.001), and that of patients with a therapeutic INR range of 2.5-3.5 from 49.8% to 63.8% (P < 0.001).

CONCLUSIONS

The introduction of a simple two-step warfarin-dosing algorithm in place of dosing by experienced anticoagulation clinic staff significantly improved mean TTR for patients in a tertiary-care anticoagulation clinic. This inexpensive and widely applicable algorithm has the potential to improve warfarin control.

Experimental lead toxicosis of raccoons (Procyon lotor)

Four pairs of raccoons were treated orally with the following doses of lead acetate (mg/kg; 5 days/week, for 8 weeks): 0 (control), 1, 2 and 4. In the six experimental animals, this treatment produced dose-dependent increases in blood lead, without clinical signs or changes in haematological parameters. After 8 weeks, the liver and kidney of all lead-treated animals and the calvarium and radius of those receiving doses of 2 and 4 mg/kg contained elevated concentrations of lead. Acid-fast inclusions were observed by light and electron microscopy in the kidneys of all raccoons receiving the two highest doses and in one animal receiving the lowest dose. Hepatic acid-fast inclusions were seen in only one animal (dose 4 mg/kg). No inclusions were seen in osteoclasts of the radius. It is suggested that the findings, which support earlier observations that raccoons are fairly resistant to lead, may be of value in studying interactions between lead exposure and oral vaccination of wildlife against rabies.

Herpesvirus-like infection in a raccoon (Procyon lotor)

During March 1990, a subadult raccoon found dead in northeastern Pennsylvania (USA) had gross lesions of multifocal hepatitis. Microscopically, multifocal randomly distributed areas of acute necrosis with intranuclear viral inclusions were seen in liver, spleen, adrenal glands, and tongue. Ultrastructural and immunoperoxidase results of formalin fixed liver were compatible with herpesvirus infection. This virus could be unique to the raccoon or may have been acquired from another species.

The synthesis and in vitro evaluation of a 99mtechnetium-nitroimidazole complex based on a bis(amine-phenol) ligand: comparison to BMS-181321

We have developed a 99mTechnetium complex for imaging of hypoxic tissue (BMS-181321). Recently, another nitroimidazole derivative, based upon a bis(amine-phenol) ligand, was described in the patent literature. To compare this compound to BMS-181321, we have synthesized the ligand, prepared its 99mTc complex, and evaluated its performance in two in vitro assays of bioefficacy: membrane permeability and uptake in normoxic and anoxic cardiocytes. In attempting to reproduce the synthesis of the ligand described in the patent application, we found that one intermediate could not be made by the method described, and alternative routes were investigated. Complexation of the bis(amine-phenol) nitroimidazole with 99mTc gave an apparent single complex; this appeared as a broad peak on HPLC analysis. Purification by a solid-phase method gave a complex with 95% radiochemical purity. This complex was not permeable to cultured bovine brain endothelial cells nor did it show preferential uptake in anoxic myocytes.

Imaging ischemic tissue at risk of infarction during stroke

Autoradiograms obtained after middle cerebral artery occlusion (MCAO) in spontaneously hypertensive rats show that the 99mTc complex of a 2-nitroimidazole-derivatized propylene amine oxime (BMS-181321) is selectively retained in acutely ischemic brain before disruption of the blood-brain barrier (BBB), but not in the ischemic infarct. BMS-181321 is therefore a marker of ischemic tissue at risk of infarction and its uptake, unlike that of x-ray and magnetic resonance contrast agents, does not require disruption of the BBB. In keeping with this conclusion, we have found that the single-pass cerebral extraction fraction of BMS-181321 is 0.67 at normal rat whole-brain blood flow. Sequential single-photon emission computed tomographic images obtained from cats after MCAO show that the initial distribution of BMS-181321 approximates regional CBF and that selective retention subsequently produces a positive image within the ischemic territory. BMS-181321 is the first Tc complex able to indicate not only ischemia, but also ischemic tissue at risk of infarction. Use of this novel Tc complex to monitor biochemical events during ischemia may contribute to the clinical management of acute stroke.

A novel [99m]technetium-labeled nitroheterocycle capable of identification of hypoxia in heart

A novel [99m]technetium-labeled nitroimidazole was preferentially taken up and retained by hypoxic cardiac muscle. In rat hearts perfused with O2 or N2 equilibrated cell-free medium, uptake of the infused nitroheterocycle and its subsequent washout displayed biphasic kinetics. For both uptake and washout, the early phase was very rapid whereas the late phase was much slower. The amount of radioactivity retained after 40 min of clearance was about two-fold greater in hypoxic hearts than in normoxic hearts. Cardiac myocytes and mitochondria isolated from rat heart also accumulated the nitroheterocycle. Association of the compound with heart cells was inversely related to the level of available oxygen and was independent of intracellular energy level or mitochondrial redox state in the presence of oxygen. The results indicate that this [99mTc]labeled nitroimidazole may serve as a sensitive marker of hypoxic myocardium.

Experimental oral administration of canine adenovirus (type 2) to raccoons (Procyon lotor)

Canine adenovirus type 2 (CAV2) has been proposed for recombinant vaccines to control rabies in wild animals. To evaluate the suitability of CAV2 as a safe vector for the genetically engineered vaccines, seven wild-caught raccoons (three males and four females) were administered CAV2 per os. Two of the animals were euthanatized on each of post-infection days 3, 6, and 14, and one was euthanatized on day 21. Two other control raccoons (a male and a female) were also euthanatized on day 21. Microscopic pulmonary lesions of multifocal necrotizing bronchiolitis with basophilic intranuclear inclusions were seen in 3/4 raccoons euthanatized on post-infection days 3 and 6. Ultrastructural examination of lungs with pulmonary lesions revealed hexagonal viral particles characteristic of adenoviruses. CAV2 is potentially pathogenic for raccoons, and this susceptibility should be of concern to developers of recombinant vaccines who intend to use CAV2 as a vaccine vector.

Retrospective study of testicular degeneration in raccoons with canine distemper infection

A 6-year (1985-1990) retrospective survey of raccoons with canine distemper infection and an outbreak of the disease in 1988 on South Island, South Carolina, are described. During this epizootic, 3 male raccoons with the clinical disease had gross testicular lesions that, on histopathologic examination, revealed severe diffuse degeneration and mineralization of seminiferous tubules. The testicular pathology of canine distemper in raccoons has not been previously reported.

Pennyroyal oil toxicosis in a dog

A dog was treated for fleas with the application of pennyroyal oil obtained by the owner at a health food store. Vomiting ensued within 2 hours, and despite emergency treatment, the dog died within 48 hours. At necropsy, pennyroyal oil was determined to be the cause of death.

Empyema of gallbladder in a child with homozygous sickle-cell disease

A 13-year-old boy with homozygous sickle-cell (SS) disease followed from birth in a cohort study of sickle-cell disease developed empyema of the gallbladder after a known 3-year history of gallstones. At this age, gallstones occur in 30% of cohort study children with SS disease but this is the first patient with specific symptoms.

Synthesis and biological properties of purine and pyrimidine 5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl analogues of AMP, GMP, IMP, and CMP

Methyl 2,3-O-isopropylidene-D-ribofuranoside (1) was converted to 1-O-acetyl-5-bromo-5-deoxy-2,3-di-O-benzoyl-D-ribofuranose (6) in five steps with good yield. The Arbuzov condensation of compound 6 with triethyl phosphite resulted in the synthesis of 1-O-acetyl-2,3-di-O-benzoyl-5-deoxy-5-(diethoxyphosphinyl)-D-ribofuranos e (7). Compound 7 was used for direct glycosylation of both purine and pyrimidine bases. The glycosylation was accomplished with the dry silylated heterocyclic base in the presence of trimethylsilyl triflate. Deblocking of the glycosylation products gave exclusively the beta anomer of the 5'-phosphonate analogues of 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]adenine (13), 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]guanosin e (16), 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]hypoxant hine (17), and 9-[5'-deoxy-5'-(dihydroxyphosphinyl)-beta-D-ribofuranosyl]cytosine (15), described here for the first time. The target compounds as well as their intermediates showed no in vitro antiviral or antitumor activity, although phosphorylation of 15 and 16 to di- and triphosphate analogues was demonstrated with use of isolated cellular enzymes.

Synthesis and antileukemic activity of bis[[(carbamoyl)oxy]methyl]- substituted pyrrolo[2,1-a]isoquinolines, pyrrolo[1,2-a]quinolines, pyrrolo[2,1-a]isobenzazepines, and pyrrolo[1,2-a]benzazepines

A series of bis[[(carbamoyl)oxy]methyl]-substituted pyrrole-fused tricyclic heterocycles were synthesized by using 1,3-dipolar cycloaddition reactions with a trifluoromethanesulfonate salt of an appropriate Resissert compound or with a mesoionic oxazolone intermediate. All of the bis(carbamates) were active in vivo against P388 lymphocytic leukemia with 5,6-dihydro-8-methoxy-1,2- bis(hydroxymethyl)pyrrolo[2,1-a]isoquinoline bis[N-(2-propyl)carbamate] (3c) showing the highest level of activity.