Vδ1 Effector and Vδ2 γδ T-Cell Subsets Shift in Frequency and Are Linked to Plasma Inflammatory Markers During Antiretroviral Therapy-Suppressed HIV Infection

BACKGROUND

Chronic inflammation is prevalent with antiretroviral therapy (ART)-suppressed human immunodeficiency virus (HIV) infection and one immune cell subset putatively driving this phenomenon is TIGIT+ γδ T cells.

METHODS

To elucidate γδ T-cell phenotypic diversity, spectral flow cytometry was performed on blood lymphocytes from individuals of a HIV and aging cohort and data were analyzed using bioinformatic platforms. Plasma inflammatory markers were measured and correlated with γδ T-cell subset frequencies.

RESULTS

Thirty-nine distinct γδ T-cell subsets were identified (22 Vδ1+, 14 Vδ2+, and 3 Vδ1-Vδ2-Vγ9+) and TIGIT was nearly exclusively found on the Vδ1+CD45RA+CD27- effector populations. People with ART-suppressed HIV infection (PWH) exhibited high frequencies of distinct clusters of Vδ1+ effectors distinguished via CD8, CD16, and CD38 expression. Among Vδ2+ cells, most Vγ9+ (innate-like) clusters were lower in PWH; however, CD27+ subsets were similar in frequency between participants with and without HIV. Comparisons by age revealed lower 'naive' Vδ1+CD45RA+CD27+ cells in older individuals, regardless of HIV status. Plasma inflammatory markers were selectively linked to subsets of Vδ1+ and Vδ2+ cells.

CONCLUSIONS

These results further elucidate γδ T-cell subset complexity and reveal distinct alterations and connections with inflammatory pathways of Vδ1+ effector and Vδ2+ innate-like subsets during ART-suppressed HIV infection.

Medical correlates of first-term attrition in US Navy personnel

INTRODUCTION

First-term attrition (FTA), or failure of a military service member to complete their initial service contract, is a major financial burden and source of lost manpower in the US Navy. The objective of the present study was to examine medical correlates of FTA using healthcare and disability rating data.

METHODS

In this retrospective cohort study, all US Navy-enlisted personnel between the years 2003 and 2018 with FTA (n=58 777) and regular discharge (n=203 084) were identified for analysis from accession dates in the Career History Archival Medical and Personnel System. Medical diagnoses from outpatient and inpatient records were abstracted from the Military Health System Data Repository. For a subgroup of the study population discharged with a disability rating (n=12 880), diagnoses were identified from the Integrated Disability Evaluation System. The FTA and regular discharge groups were compared using relative risks (RRs) and 95% CIs, and per cent differences for the disability subgroup analysis.

RESULTS

Compared with regular discharges, those with FTA were more likely to have outpatient and inpatient diagnoses for mental health disorders. Personality disorder yielded the strongest association with FTA in both outpatient (RR=10.45, 95% CI 9.79 to 11.16) and inpatient settings (RR=18.97, 95% CI 14.16 to 25.42). Other disorders associated with FTA included schizophrenia, substance-related disorders, poisoning by psychotropic agents and adjustment disorders. In the disability analysis, the FTA group relative to regular discharges had the largest per cent differences for 'arthritis, degenerative (hypertrophic or osteoarthritis)' (10.8% vs 2.5%) and 'tibia and fibula, impairment' (3.0% vs 0.4%).

CONCLUSIONS

This study provides evidence that FTA is associated with both mental and physical health conditions. Mental and physical factors related to FTA require further examination, particularly whether pre-enlistment screening or early career intervention could lead to mitigation strategies. Future research should extend this analysis to other services and population subgroups.

Opioid use does not limit potent low-dose HIV-1 latency reversal agent boosting

The combined effects of the HIV-1 and opioid epidemics on virus reservoir dynamics are less well characterized. To assess the impact of opioid use on HIV-1 latency reversal, we studied forty-seven suppressed participants with HIV-1 and observed that lower concentrations of combination latency reversal agents (LRA) led to synergistic virus reactivation ex vivo, regardless of opioid use. The use of a Smac mimetic or low-dose protein kinase C agonist, compounds that did not reverse latency alone, in combination with low-dose histone deacetylase inhibitors generated significantly more HIV-1 transcription than phorbol 12-myristate 13-acetate (PMA) with ionomycin, the maximal known HIV-1 reactivator. This LRA boosting did not differ by sex or race and associated with greater histone acetylation in CD4+ T cells and modulation of T cell phenotype. Virion production and the frequency of multiply spliced HIV-1 transcripts did not increase, suggesting a post-transcriptional block still limits potent HIV-1 LRA boosting.

Integrase Inhibitor Use Associated with Weight Gain in Women and Incident Diabetes Mellitus

Excessive weight gain associated with integrase strand transfer inhibitor (InSTI) antiretrovirals is an emerging issue; however, the metabolic consequences of this effect have not been established. Our objective was to evaluate for InSTI-emergent weight gain and potential associated type 2 diabetes mellitus (T2DM) among a diverse HIV patient cohort. For this retrospective cohort study, we obtained clinical warehouse data for HIV+ patients between fiscal years 2007-17. We compared patients initiated on an InSTI with those started on an alternate regimen. Our primary outcome was percentage weight change from baseline to 24 months postinitiation using the linear mixed-effects model fit by restricted maximum likelihood. Our secondary outcome was incident T2DM as defined by a new prescription for antihyperglycemic medication within 18 months after antiretroviral therapy (ART) start. Diabetes-free survival was estimated using the Kaplan-Meier method, log-rank test, and Cox proportional-hazards model. The cohort included 1,235 individuals initiating ART, 136 (11.0%) with an InSTI. InSTI use in women was significantly associated with greater weight gain compared with non-InSTIs (11.0%, 95% confidence interval, CI: 5.22 to 16.8, p < .01), after adjusting for potential confounding variables. In a univariate analysis, InSTI use was associated with more incident T2DM diagnoses compared with non-InSTI regimens (unadjusted hazard ratio = 3.27, p = .01), although incident T2DM was not associated with weight gain. InSTIs were significantly associated with weight gain among females. We also observed an increased risk of incident diabetes mellitus among both sexes, however, unrelated to weight changes. Further prospective studies will be necessary to confirm this finding and investigate its mechanism.

Intragenic proviral elements support transcription of defective HIV-1 proviruses

HIV-1 establishes a persistent proviral reservoir by integrating into the genome of infected host cells. Current antiretroviral treatments do not target this persistent population of proviruses which include latently infected cells that upon treatment interruption can be reactivated to contribute to HIV-1 rebound. Deep sequencing of persistent HIV proviruses has revealed that greater than 90% of integrated HIV genomes are defective and unable to produce infectious virions. We hypothesized that intragenic elements in the HIV genome support transcription of aberrant HIV-1 RNAs from defective proviruses that lack long terminal repeats (LTRs). Using an intact provirus detection assay, we observed that resting CD4+ T cells and monocyte-derived macrophages (MDMs) are biased towards generating defective HIV-1 proviruses. Multiplex reverse transcription droplet digital PCR identified env and nef transcripts which lacked 5' untranslated regions (UTR) in acutely infected CD4+ T cells and MDMs indicating transcripts are generated that do not utilize the promoter within the LTR. 5'UTR-deficient env transcripts were also identified in a cohort of people living with HIV (PLWH) on ART, suggesting that these aberrant RNAs are produced in vivo. Using 5' rapid amplification of cDNA ends (RACE), we mapped the start site of these transcripts within the Env gene. This region bound several cellular transcription factors and functioned as a transcriptional regulatory element that could support transcription and translation of downstream HIV-1 RNAs. These studies provide mechanistic insights into how defective HIV-1 proviruses are persistently expressed to potentially drive inflammation in PLWH.

Novel ELISA Protocol Links Pre-Existing SARS-CoV-2 Reactive Antibodies With Endemic Coronavirus Immunity and Age and Reveals Improved Serologic Identification of Acute COVID-19 via Multi-Parameter Detection

The COVID-19 pandemic has drastically impacted work, economy, and way of life. Sensitive measurement of SARS-CoV-2 specific antibodies would provide new insight into pre-existing immunity, virus transmission dynamics, and the nuances of SARS-CoV-2 pathogenesis. To date, existing SARS-CoV-2 serology tests have limited utility due to insufficient reliable detection of antibody levels lower than what is typically present after several days of symptoms. To measure lower quantities of SARS-CoV-2 IgM, IgG, and IgA with higher resolution than existing assays, we developed a new ELISA protocol with a distinct plate washing procedure and timed plate development via use of a standard curve. Very low optical densities from samples added to buffer coated wells at as low as a 1:5 dilution are reported using this 'BU ELISA' method. Use of this method revealed circulating SARS-CoV-2 receptor binding domain (RBD) and nucleocapsid protein (N) reactive antibodies (IgG, IgM, and/or IgA) in 44 and 100 percent of pre-pandemic subjects, respectively, and the magnitude of these antibodies tracked with antibody levels of analogous viral proteins from endemic coronavirus (eCoV) strains. The disease status (HIV, SLE) of unexposed subjects was not linked with SARS-CoV-2 reactive antibody levels; however, quantities were significantly lower in subjects over 70 years of age compared with younger counterparts. Also, we measured SARS-CoV-2 RBD- and N- specific IgM, IgG, and IgA antibodies from 29 SARS-CoV-2 infected individuals at varying disease states, including 10 acute COVID-19 hospitalized subjects with negative serology results by the EUA approved Abbott IgG chemiluminescent microparticle immunoassay. Measurements of SARS-CoV-2 RBD- and N- specific IgM, IgG, IgA levels measured by the BU ELISA revealed higher signal from 9 of the 10 Abbott test negative COVID-19 subjects than all pre-pandemic samples for at least one antibody specificity/isotype, implicating improved serologic identification of SARS-CoV-2 infection via multi-parameter, high sensitive antibody detection. We propose that this improved ELISA protocol, which is straightforward to perform, low cost, and uses readily available commercial reagents, is a useful tool to elucidate new information about SARS-CoV-2 infection and immunity and has promising implications for improved detection of all analytes measurable by this platform.

946. Risk factors and Metabolic Implications of Integrase Inhibitor Associated Weight Gain

Background

Excessive weight gain associated with integrase strand transfer inhibitor (InSTI) antiretrovirals is an emerging issue in the current antiretroviral treatment (ART) era. Despite the known association between excess weight and impaired glucose tolerance in the general population, the metabolic implications of InSTI-associated weight gain have not been established. The objective of this study was to evaluate the presence of InSTI-associated weight gain amongst a diverse, urban population and to investigate potential risk factors and metabolic implications.

Methods

We obtained demographic, pharmacy and laboratory data from the hospital clinical data warehouse for ART-naïve adult HIV+ patients at Boston Medical Center between fiscal year (FY) 2007-2017. We compared patients who initiated on an InSTI to those with an alternate regimen (i.e. PI, NNRTI) who remained on their initial regimen for at least 18 months. Individuals with diabetes mellitus (DM) prescription or ICD 9/10 code prior to ART initiation were excluded. Our primary outcome was percent weight change in the first 24 months of ART estimated by linear mixed effects model fit by restricted maximum likelihood. Our secondary outcome was incident DM diagnosis in the 18 months after ART using progression-free survival (PFS). PFS rates were estimated by the Kaplan-Meier method and log-rank test, and Cox proportional-hazards model were determined, all using R v3.6.2.

Results

Between FY 2007-2017, 139 patients were initiated on InSTIs and 1117 were initiated on alternative anchor regimens. Approximately, one third of the cohort was female and more than 75% were non-white. InSTI use in women was associated with increased weight gain in the first 24 months of ART compared to non-InSTIs (+9.57%, p = 0.002, Figure 1). InSTI use was associated with more incident DM diagnoses in the first 18 months of ART compared to non-InSTI regimens (HR = 3.27, p = 0.014).

Figure 1: Percentage weight change from baseline at ART initiation between InSTI and non-InSTI regimens

Conclusion

Females have higher InSTI-associated weight gain which suggests they may be more susceptible to adverse metabolic issues. InSTI use appears to be associated with an increased incidence of DM diagnoses following ART initiation. Further prospective and controlled studies will be necessary to describe the mechanism of this effect and refine HIV management strategies.

Disclosures

Archana Asundi, MD, Gilead (Scientific Research Study Investigator)Merck (Scientific Research Study Investigator)ViiV (Scientific Research Study Investigator) Nina H. Lin, MD, Gilead Sciences (Scientific Research Study Investigator)ViiV (Scientific Research Study Investigator)

Vaccine elicitation of HIV broadly neutralizing antibodies from engineered B cells

HIV broadly neutralizing antibodies (bnAbs) can suppress viremia and protect against HIV infection. However, their elicitation is made difficult by low frequencies of appropriate precursor B cell receptors and the complex maturation pathways required to generate bnAbs from these precursors. Antibody genes can be engineered into B cells for expression as both a functional antigen receptor on cell surfaces and as secreted antibody. Here, we show that HIV bnAb-engineered primary mouse B cells can be adoptively transferred and vaccinated in immunocompetent mice resulting in the expansion of durable bnAb memory and long-lived plasma cells. Somatic hypermutation after immunization indicates that engineered cells have the capacity to respond to an evolving pathogen. These results encourage further exploration of engineered B cell vaccines as a strategy for durable elicitation of HIV bnAbs to protect against infection and as a contributor to a functional HIV cure.

HIV-1 Transcription but Not Intact Provirus Levels are Associated With Systemic Inflammation

Individuals infected with human immunodeficiency virus (HIV) 1 have increased inflammation, which has been associated with age-associated diseases. Plasma markers, cell-associated virus levels, and ability to stimulate RNA transcription in latently infected cell lines was examined in younger and older HIV-1-infected individuals with suppressed virus. Cell-associated RNA, but not intact provirus level, had positive correlation with plasma D-dimer levels. Compared with the younger group, the older group had higher D-dimer levels and a trend toward more cell-associated RNA but similar levels of intact proviruses. Even though all measured inflammatory markers were relatively higher in the older group, this greater inflammation did not induce more HIV-1 transcription in latently infected cell lines. Inflammation and HIV-1 RNA expression increase with age despite similar levels of intact infectious HIV DNA. While plasma inflammation is correlated with HIV-1 RNA expression in peripheral blood mononuclear cells, it does not induce HIV-1 transcription in latently infected cell lines.

Targeted Chromatinization and Repression of HIV-1 Provirus Transcription with Repurposed CRISPR/Cas9

The major barrier to HIV-1 cure is the persistence of latent provirus, which is not eradicated by antiretroviral therapy. The "shock and kill" approach entails stimulating viral production with latency-reversing agents followed by the killing of cells actively producing the virus by immune clearance. However, this approach does not induce all intact proviruses, leaving a residual reservoir. CRISPR/Cas9 has been utilized to excise integrated Human Immunodeficiency Virus (HIV) DNA from infected cells in an RNA-guided, sequence-specific manner. Here, we seek to epigenetically silence the proviral DNA by introducing nuclease-deficient disabled Cas9 (dCas9) coupled with a transcriptional repressor domain derived from Kruppel-associated box (KRAB). We show that specific guide RNAs (gRNAs) and dCas9-KRAB repress HIV-1 transcription and reactivation of latent HIV-1 provirus. This repression is correlated with chromatin changes, including decreased H3 histone acetylation and increased histone H3 lysine 9 trimethylation, histone marks that are associated with transcriptional repression. dCas9-KRAB-mediated inhibition of HIV-1 transcription suggests that CRISPR can be engineered as a tool for block-and-lock strategies.

SNAPflex: a paper-and-plastic device for instrument-free RNA and DNA extraction from whole blood

Nucleic acid amplification tests (NAATs), which amplify and detect pathogen nucleic acids, are vital methods to diagnose diseases, particularly in cases where patients exhibit low levels of infection. For many blood-borne pathogens such as HIV or Plasmodium falciparum, it is necessary to first extract pathogen RNA or DNA from patient blood prior to NAAT analysis. Traditional nucleic acid extraction methods are expensive, resource-intensive and are often difficult to deploy to resource-limited areas where many blood-borne infections are widespread. Here, we describe a portable, paper-and-plastic device, called SNAPflex, for instrument-free nucleic acid extraction from whole blood, which builds upon our previous work for RNA extraction using a pressure-driven extraction system. SNAPflex shows improved HIV RNA extraction from simulated patient samples compared to traditional extraction methods as well as long-term stability of extracted RNA without the need for cold storage. We further demonstrated successful extraction and recovery of P. falciparum DNA from cultured parasites in whole blood. SNAPflex was designed to be easily manufacturable and deployable to resource-limited settings.

A new cell line for assessing HIV-1 antibody dependent cellular cytotoxicity against a broad range of variants

Human immunodeficiency virus type 1 (HIV-1) studies suggest that antibody-dependent cellular cytotoxicity (ADCC) influences both virus acquisition and subsequent disease outcome. Technical issues with currently available assays, however, have limited the ability to comprehensively assess the impact of ADCC on transmission and disease progression. Commonly used ADCC assays use a target cell line, CEM.NKr-CCR5-Luc, that often does not support replication of relevant HIV-1 variants. Thus, the extent of ADCC responses against a large panel of HIV-1 strains often cannot be assessed using the currently available methods. We developed two new reporter cell-lines (MT4-CCR5-Luc and PM1-CCR5-Luc) to overcome these issues. MT4-CCR5-Luc cells are resistant, whereas PM1-CCR5-Luc cells are susceptible, to killing by a natural killer cell line, CD16⁺KHYG-1, in the absence of antibody. Polyclonal HIVIG gave similar ADCC estimates against HIV-1 isolate, NL4-3, regardless of which of the three cell lines were used as the targets. In contrast to CEM.NKr-CCR5-Luc and PM1-CCR5-Luc, however, MT4-CCR5-Luc target cells produce significantly higher luciferase after exposure to various HIV-1 strains, including transmitted founder variants and viruses incorporating specific envelopes of interest. This higher luciferase expression does not yield spurious results because ADCC estimates are similar when killing is assessed by both reporter protein expression and flow cytometry. Furthermore, ADCC estimates derived from MT4-CCR5-Luc cells are not skewed by non-antibody contents present in human plasma. In aggregate, the MT4-CCR5-Luc cell line can be used to estimate monoclonal antibody or plasma-induced ADCC responses against a diverse range of HIV-1 envelopes relevant for transmission and disease progression studies.

Targeting HIV-1 proviral transcription

Despite the success of antiretroviral therapies, there is no cure for HIV-1 infection due to the establishment of a long-lived latent reservoir that fuels viral rebound upon treatment interruption. 'Shock-and-kill' strategies to diminish the latent reservoir have had modest impact on the reservoir leading to considerations of alternative approaches to target HIV-1 proviruses. This review explores approaches to target HIV-1 transcription as a way to block the provirus expression.

A retrospective cohort study comparing dairy calf treatment decisions by farm personnel with veterinary observations of clinical signs

Antimicrobials are frequently administered to calves with diarrhea, despite evidence suggesting questionable efficacy. Even if efficacious, providing the appropriate therapy to an animal requires accurate disease detection. The objective of this study was to use previously collected data and compare clinical scoring by a veterinarian to treatment decisions by on-farm personnel. Data describing daily clinical scores and farm treatments were previously collected from 4 farms for calves from birth to age 28 d. In this data set, a total of 460 calves were enrolled. Daily observations and clinical assessments were made on each farm by the same veterinarian, for a total of 12,101 calf observation days. Farm personnel made all treatment decisions based on their own observations, and these treatments were recorded by study personnel. Overall, the cumulative incidence of a calf exhibiting at least one abnormal clinical sign over the 28-d observation period was 0.93, with cumulative incidences of 0.85 and 0.33 for diarrhea and dehydration, respectively. The cumulative incidence of any treatment (including antibiotics and electrolytes) was 0.85, although the majority of treatments used an antimicrobial. The farm-specific probabilities that a calf with clinical signs of dehydration or diarrhea, respectively, received fluid or electrolyte therapy ranged from 0.08 to 0.27 and 0.03 to 0.12. These probabilities were greater for the day a clinical sign was first observed. The farm-specific probabilities that a calf with clinical signs of diarrhea received an antimicrobial was 0.23 to 0.65, and the probability that a calf exhibiting clinical signs of respiratory disease received an antimicrobial was 0.33 to 0.76. The first observation of diarrhea had similar probabilities to those for all observations of diarrhea. There was greater probability of treatment for calves with their first observed abnormal respiratory signs. Probabilities that treatment with antimicrobials, or fluids or electrolytes, was associated with an abnormal clinical sign were low-that is, calves received treatments in the absence of any abnormal clinical signs. This study illustrates incongruity between treatment decisions by calf treaters (the designated personnel on each farm responsible for calf health assessment and treatment decisions) and those of an observer using a clinical scoring system to identify calves with abnormal clinical signs. These findings indicate opportunities and the need for dairy farmers and advisors to evaluate calf treatment protocols, reasons for treatment, and training programs for calf health and disease detection, as well as to develop monitoring programs for treatment protocol compliance and health outcomes following therapy.

Multivariate Computational Analysis of Gamma Delta T Cell Inhibitory Receptor Signatures Reveals the Divergence of Healthy and ART-Suppressed HIV+ Aging

Even with effective viral control, HIV-infected individuals are at a higher risk for morbidities associated with older age than the general population, and these serious non-AIDS events (SNAEs) track with plasma inflammatory and coagulation markers. The cell subsets driving inflammation in aviremic HIV infection are not yet elucidated. Also, whether ART-suppressed HIV infection causes premature induction of the inflammatory events found in uninfected elderly or if a novel inflammatory network ensues when HIV and older age co-exist is unclear. In this study we measured combinational expression of five inhibitory receptors (IRs) on seven immune cell subsets and 16 plasma markers from peripheral blood mononuclear cells (PBMC) and plasma samples, respectively, from a HIV and Aging cohort comprised of ART-suppressed HIV-infected and uninfected controls stratified by age (≤35 or ≥50 years old). For data analysis, multiple multivariate computational algorithms [cluster identification, characterization, and regression (CITRUS), partial least squares regression (PLSR), and partial least squares-discriminant analysis (PLS-DA)] were used to determine if immune parameter disparities can distinguish the subject groups and to investigate if there is a cross-impact of aviremic HIV and age on immune signatures. IR expression on gamma delta (γδ) T cells exclusively separated HIV+ subjects from controls in CITRUS analyses and secretion of inflammatory cytokines and cytotoxic mediators from γδ T cells tracked with TIGIT expression among HIV+ subjects. Also, plasma markers predicted the percentages of TIGIT+ γδ T cells in subjects with and without HIV in PSLR models, and a PLS-DA model of γδ T cell IR signatures and plasma markers significantly stratified all four of the subject groups (uninfected younger, uninfected older, HIV+ younger, and HIV+ older). These data implicate γδ T cells as an inflammatory driver in ART-suppressed HIV infection and provide evidence of distinct “inflamm-aging” processes with and without ART-suppressed HIV infection.

HIV-1 replicates and persists in vaginal epithelial dendritic cells

HIV-1 acquisition occurs most commonly after sexual contact. To establish infection, HIV-1 must infect cells that support high-level replication, namely CD4⁺ T cells, which are absent from the outermost genital epithelium. Dendritic cells (DCs), present in mucosal epithelia, potentially facilitate HIV-1 acquisition. We show that vaginal epithelial DCs, termed CD1a⁺ VEDCs, are unlike other blood- and tissue-derived DCs because they express langerin but not DC-SIGN, and unlike skin-based langerin⁺ DC subset Langerhans cells (LCs), they do not harbor Birbeck granules. Individuals primarily acquire HIV-1 that utilizes the CCR5 receptor (termed either R5 or R5X4) during heterosexual transmission, and the mechanism for the block against variants that only use the CXCR4 receptor (classified as X4) remains unclear. We show that X4 as compared with R5 HIV-1 shows limited to no replication in CD1a⁺ VEDCs. This differential replication occurs after fusion, suggesting that receptor usage influences postentry steps in the virus life cycle. Furthermore, CD1a⁺ VEDCs isolated from HIV-1–infected virologically suppressed women harbor HIV-1 DNA. Thus, CD1a⁺ VEDCs are potentially infected early during heterosexual transmission and also retain virus during treatment. Understanding the interplay between HIV-1 and CD1a⁺ VEDCs is important for future prevention and cure strategies.

Inhibitory receptor signatures on gamma delta T cells predict ART-suppressed HIV infection, are synergistically altered by HIV and aging, and co-vary with inflammatory plasma analytes

Virologically suppressed HIV+ individuals have an increased risk and earlier onset of age-associated diseases such as cardiovascular atherosclerosis, cancer, and osteoporosis, referred to as HIV-Associated Non-AIDS conditions (HANAs). Whether HIV drives HANAs via same mechanisms as normal aging or other processes is unclear. We analyzed PBMC from 45 ART-suppressed HIV+ subjects (20 ≤35yo ‘younger’, 25 ≥50yo ‘older’) and 39 uninfected controls (20 younger, 19 older) with a 16-color flow cytometry panel that measures the inhibitory receptors (IRs) PD-1, TIGIT, CD160, TIM-3, and LAG-3 on CD4+ T cells, CD8+ T cells, NK cells, iNKT cells, and gd T cells. Bioinformatic (CITRUS) analysis revealed that gd T cell IR expression exclusively differentiated HIV+ subjects from controls. Also, a synergistic effect of HIV and aging on TIGIT+ and ≥ 2 IR gd T cell percentages was found. gd T cell functional profiling revealed a positive association between TIGIT expression and spontaneous release of granzymes A and B from HIV+ subjects but not controls. Using supervised multivariate modeling (Partial Least Squares discriminant analysis, PLS) of gd T IR signatures, gd T cell cytokine secretion, and inflammatory plasma analytes, all four subject groups (HIV+ and uninfected, ≤35 and ≥50yo) were effectively distinguished. Also, a statistically significant covariance between gd T cell IR signatures and levels of inflammatory plasma analytes, including IL-6, IL-1b and fibrinogen was found. Our data implicate gd T cells as a key inflammatory driver in ART-suppressed HIV infection and our PLS results suggest a divergence of ART-suppressed HIV inflammation and healthy aging processes, revealing differential “inflammaging” with and without HIV infection.

Novel inhibitory receptor signatures revealed by 18 parameter flow cytometry and mapped via a combination of automated analysis algorithms

Inhibitory Receptors (IRs) such as PD-1, TIM-3, CD160, and TIGIT are upregulated during activated, exhausted, and pathological immune cell states. How the combinational expression of multiple IRs on individual cells tracks with functional status and/or fate is largely unknown. Due to paucity of human samples, large panels for immune cell characterization are of a high value, and combining them with automated platforms of multi-dimensional single cell analysis would allow objective and comprehensive population characterization. We report an 18-parameter (16-color) fluorescent panel that allows IR signature analysis as well as cell sorting for functional studies, and adopt algorithmic methods previously used for mass cytometry into a novel platform to analyze fluorescent datasets in an unbiased analytical workflow. PBMC from diseased and healthy control subjects as well as tumor specimens were stained and analyzed on a FACSARIA cell sorter. For the automated analysis, the datasets were processed with t-SNE algorithm into a 2D map of phenotypic space that was subsequently clustered using SPADE. From the samples, a 32-plex combinational IR signature was determined for the CD4+ T, CD8+ T, NK, iNKT, and γδ T cell lineages. The results indicate novel combinational IR ‘hits’ for particular immune subsets and some immune subset IR signatures correlated with disease status. In conclusion, 18-parameter flow cytometry with automated analysis provides robust results from human blood and solid tissue samples. In combination with functional and other readouts, measurement of single immune cell IR signatures could provide new insight into activation, exhaustion, and pathogenic processes and potentially reveal novel therapeutic targets.

Distribution and evolution of het gene homologs in the basidiomycota

In filamentous fungi a system known as somatic incompatibility (SI) governs self/non-self recognition. SI is controlled by a regulatory signaling network involving proteins encoded at the het (heterokaryon incompatible) loci. Despite the wide occurrence of SI, the molecular identity and structure of only a small number of het genes and their products have been characterized in the model fungi Neurospora crassa and Podospora anserina. Our aim was to identify and study the distribution and evolution of putative het gene homologs in the Basidiomycota. For this purpose we used the information available for the model fungi to identify homologs of het genes in other fungi, especially the Basidiomycota. Putative het-c, het-c2 and un-24 homologs, as well as sequences containing the NACHT, HET or WD40 domains present in the het-e, het-r, het-6 and het-d genes were identified in certain members of the Ascomycota and Basidiomycota. The widespread phylogenetic distribution of certain het genes may reflect the fact that the encoded proteins are involved in fundamental cellular processes other than SI. Although homologs of het-S were previously known only from the Sordariomycetes (Ascomycota), we also identified a putative homolog of this gene in Gymnopus luxurians (Basidiomycota, class Agaricomycetes). Furthermore, with the exception of un-24, all of the putative het genes identified occurred mostly in a multi-copy fashion, some with lineage and species-specific expansions. Overall our results indicated that gene duplication followed by gene loss and/or gene family expansion, as well as multiple events of domain fusion and shuffling played an important role in the evolution of het gene homologs of Basidiomycota and other filamentous fungi.

Immunoproteomics strategy for automation of chemoresistance and chemosensitivity array

20076

Background: Chemotherapy sensitivity and resistance assays (CSRAs) often guide therapeutic regimen selection based on patient cancer cells response to chemotherapeutics in culture. Current CSRAs rely on highly time- and skill- dependent biochemical and microscopic endpoint assays of apoptosis. Instead, the assay under development uses immunoproteomic array readout of biomarkers. Such automation may broaden the use of CSRAs for guiding clinical use of increasingly costly chemotherapeutic options. Methods: Specimens from 30 ovarian cancer patients were cultured with and without cisplatinum according to established CSRA procedures (http://weisenthal.org/w_ovarian_cp.pdf). Cells pelleted and fixed at experimental points (0 and 96 hrs cisplatin, and 96 hrs non-treated) were paraffin embedded for construction of immunoproteomic microarrays. A panel of 57 NIH cancer cell lines was similarly arrayed. Protein profiling is performed with monospecific antibodies for 35 select markers of cell cycle, apoptosis, cell signalling, and transcription. Immunostaining results, including rate of cell death and marker expression level are quantitated manually (immunoscore assigned for cell core) and automatically (algorithm by Aperio, Inc). Results: Evaluation of readouts differentiates responders from non-responders aiming to predict clinical chemotherapy outcome. For a subset of imunoproteomic markers, observed expression corresponds to either induced apoptosis or to cisplatin resistance. Selected markers were subjected to cytologic analysis and time line westerns; results corroborate protein profiling data. Correspondence to the results of the classic CSRAs and individual patient therapeutic response will be unblinded. Conclusions: Use of immunoproteomic arrays to replicate classic CSRAs by establishing concordant results may allow automated guidance for chemotherapeutic choices.

[Table: see text]

RNAi Codex: a portal/database for short-hairpin RNA (shRNA) gene-silencing constructs

Use of RNA interference (RNAi) in forward genetic screens is proliferating. Currently, short-interfering RNAs (siRNAs) and short-hairpin RNAs (shRNAs) are being used to silence genes to tease out functional information. It is becoming easier to harness RNAi to silence specific genes, owing to the development of libraries of readymade shRNA and siRNA gene-silencing constructs by using a variety of sources. RNAi Codex, which consists of a database of shRNA related information and an associated website, has been developed as a portal for publicly available shRNA resources and is accessible at . RNAi Codex currently holds data from the Hannon–Elledge shRNA library and allows the use of biologist-friendly gene names to access information on shRNA constructs that can silence the gene of interest. It is designed to hold user-contributed annotations and publications for each construct, as and when such data become available. We will describe features of RNAi Codex and explain the use of the tool.

Consequences of immunogenicity to the therapeutic monoclonal antibodies ReoPro and Remicade

The clinical consequences of immune antibodies generated to abciximab (ReoPro) and infliximab (Remicade) are described. Abciximab, a chimaeric Fab fragment that binds to the beta3 integrin of the GPIIb/IIIa and alphavbeta3 receptors on human platelets, is approved in the US and Europe for use in percutaneous coronary intervention (PCI) to prevent cardiac ischaemic complications. The effects of induced antibodies upon the safety and efficacy of repeat administration of abciximab have been evaluated in the ReoPro Re-administration Registry Study, in which 5.7% of patients were HACA positive before re-treatment. An interim evaluation of 1000 patients has indicated that re-administration of abciximab can be accomplished in the setting of PCI with an acceptable safety and efficacy profile. Infliximab is a chimaeric IgG1 antibody specific for human TNFalpha, and is approved in the US and Europe for the acute treatment of the signs and symptoms of Crohn's disease and for the chronic treatment of rheumatoid arthritis (RA). The incidence of antibodies to infliximab is reported to be approximately 10%; however, an inverse dose-immunogenicity relationship was observed, indicating that higher doses of infliximab (> or = 3 to 10 mg/kg) could reduce the incidence of immune antibodies. The induction of immune antibodies could also be reduced by concomitant administration of low-dose methotrexate and other immunosuppressant agents. Although antibodies to infliximab appeared to be associated with lower serum infliximab concentrations and a slightly higher incidence of infusion reactions, these immune antibodies were generally not associated with a reduction in clinical efficacy. In addition, the antibodies induced to infliximab are specific for infliximab, and do not cross-react with other currently available therapeutic antibodies.

Separating effects of orthographic similarity and contour summation in the identification of masked letter strings

We separated effects of contour summation and orthographic similarity under masking conditions, by comparing identification with simultaneous and sequentially presented letter strings, which either did or did not overlap spatially. With overlapping simultaneous stimuli, performance was better for strings with similar contours than for strings with the same letters (the orthographic similarity condition). This suggests that contour summation effects were strongest in the condition where stimuli had similar contours. With sequential presentations, performance in the similar contour and the orthographically similar conditions was equated when the stimuli were overlapping. However, effects of contour summation decreased when prime and target letters were spatially displaced, whereas performance in the orthographically similar condition was maintained. We conclude that effects of orthographic similarity can be distinguished from effects of contour summation, under masking conditions.

The effects of case mixing on word recognition: evidence from a PET study

The early stages of visual word recognition were investigated by scanning participants using PET as they took part in implicit and explicit reading tasks with visually disrupted stimuli. CaSe MiXiNg has been shown in behavioral studies to increase reaction times (RTs) in naming and other word recognition tasks. In this study, we found that during both an implicit (feature detection) task and an explicit word-naming task, mixed-case words compared to same-case words produced increased activation in an area of the right parietal cortex previously associated with visual attention. No effect of case was found in this area for pseudowords or consonant strings. Further, lowering the contrast of the stimuli slowed RTs as much as case mixing, but did not lead to the same increase in right parietal activation. No significant effect of case mixing was observed in left-hemisphere language areas. The results suggest that reading mixed-case words requires increased attentional processing. However, later word recognition processes may be relatively unaffected by the disruption in presentation.

Children and guns in a well child cohort

BACKGROUND

The purpose of this study was to estimate the extent of and to identify predictors of preadolescent gun use in a well child cohort with matched parent and child data.

METHODS

We analyzed self-report questionnaires from children and their parents using conditional logistic regression models. Questionnaires were given to 3,145 ten- to twelve-year-old children and 3,145 parents enrolled by their pediatricians in a prevention cohort study.

RESULTS

Thirty-two percent of the children lived in households with guns. Children and parents generally agreed about the presence of guns in their homes; 17% had access to unlocked guns in their homes; 22% had fired guns. In this preadolescent cohort, firing guns was associated with being male, having guns in the home, having friends who use guns, and initiation of alcohol use.

CONCLUSIONS

In this well child cohort, significant numbers of preadolescent, healthy boys in white, middle-class U.S. homes have access to guns, are using guns, and have friends who use guns. These children are also early alcohol adopters. Safety interventions with parents of preadolescents about the risks for accidental injury, death, and suicide due to child gun use may prove beneficial.

Monocyte chemoattractant protein 1 (MCP-1) in temporal arteritis and polymyalgia rheumatica

OBJECTIVE

To examine the localisation of monocyte chemoattractant protein 1 (MCP-1) in the inflamed vessel wall in temporal arteritis (TA) and to measure MCP-1 in plasma both in patients with TA and patients with polymyalgia rheumatica (PMR).

METHODS

By immunohistochemical techniques MCP-1 was localised to the vessel wall in patients with TA. In TA, PMR, and healthy controls MCP-1 was quantified by enzyme linked immunosorbent assay (ELISA) in plasma.

RESULTS

MCP-1 was localised to the majority of mononuclear cells, some smooth muscle cells, and giant cells in the arterial biopsy specimens from 12 patients with histologically verified TA. In all sections, including the vasa vasorum, the endothelium stained positive. In the intima 73% (range 57-91%), in the media 49% (range 32-67%), and in the adventitia 74% (range of 62-91%) of all cells stained positive. In plasma MCP-1 was significantly raised in untreated TA (n=33) and untreated PMR (n=27) compared with healthy controls (n=12). Untreated TA plasma levels of MCP-1 (mean 391 pg/ml (range 82-778 pg/ml)) were similar to untreated PMR plasma levels (mean 402 pg/ml (range 29-1153 pg/ml)), and no significant difference was found between the two groups of patients. In both patients with TA and patients with PMR no correlation was found between the plasma level of MCP-1 and the erythrocyte sedimentation rate, haemoglobin concentration, and CD4/CD8 ratio.

CONCLUSIONS

These results show that MCP-1 plays a part in the disease processes of TA and PMR.

Differential effects of word length and visual contrast in the fusiform and lingual gyri during reading

Previous studies have shown differential responses in the fusiform and lingual gyri during reading and suggested that the former is engaged in processing local features of visual stimuli and the latter is engaged in global shape processing. We used positron emission tomography in order to investigate how these regions are modulated by two common variables in reading: word length (three, six and nine letters) and perceptive similarity to the background (high and low contrast). Increasing both word length and visual contrast had a positive monotonic effect on activation in the bilateral fusiform. However, in the lingual gyrus, activation increased with increasing word length but decreased with increasing contrast. On the basis of previous studies, we suggest that (i) increasing word length increases the demands on both local feature and global shape processing, but (ii) increasing visual contrast increases the demands on local feature processing while decreasing the demands on global shape processing.

Fractionating the binding process: neuropsychological evidence distinguishing binding of form from binding of surface features

We present neuropsychological evidence demonstrating that the binding of form elements into shapes dissociates from the binding of surface detail to shape. Data are reported from a patient with bilateral parietal lesions, GK, who manifests left-side visual extinction along with many illusory conjunctions when asked to discriminate both surface and form information about stimuli. We show that there are effects of grouping on both extinction and illusory conjunctions when the tasks require report of object shape. In contrast, illusory conjunctions involving surface and form information were unaffected by grouping based on shape. In addition, grouping was stronger when forms were presented within the same hemifield than when they appeared in different hemifields, whilst illusory conjunctions of form and colour occurred equally often within and across hemifields. These results support a two-stage account of visual binding: form elements are first bound together locally into shapes, and this is followed by a second stage of binding in which shapes are integrated with surface details. The second but not the first stage of binding is impaired in this patient.

Systematic analysis of deficits in visual attention

A variety of impairments in visual attention can follow damage to the brain. The authors develop systematic methods for analyzing such impairments in terms of C. Bundesen's (1990) Theory of Visual Attention and apply these in a group of 9 patients with parietal lobe lesions and variable spatial neglect. In whole report, patients report letters from brief, vertical arrays in left or right visual field. The results show substantial, largely bilateral impairments in processing capacity, implying a major nonlateralized aspect to neglect. In partial report, arrays contain 1 or 2 letters in red and/or green. The task is to report only those letters in a specified target color. In addition to the expected bias against left-sided letters, patients show striking, bilateral preservation of top-down control, or attentional priority for targets. The results show how differentiation of attentional impairments can be informed by a theory of normal function.

Systematic analysis of deficits in visual attention

A variety of impairments in visual attention can follow damage to the brain. The authors develop systematic methods for analyzing such impairments in terms of C. Bundesen's (1990) Theory of Visual Attention and apply these in a group of 9 patients with parietal lobe lesions and variable spatial neglect. In whole report, patients report letters from brief, vertical arrays in left or right visual field. The results show substantial, largely bilateral impairments in processing capacity, implying a major nonlateralized aspect to neglect. In partial report, arrays contain 1 or 2 letters in red and/or green. The task is to report only those letters in a specified target color. In addition to the expected bias against left-sided letters, patients show striking, bilateral preservation of top-down control, or attentional priority for targets. The results show how differentiation of attentional impairments can be informed by a theory of normal function.

Guideline for the management of pediatric idiopathic constipation and soiling. Multidisciplinary team from the University of Michigan Medical Center in Ann Arbor

OBJECTIVE

To develop an evidence-based guideline for the primary pediatric care of children (birth to 18 years old) with idiopathic constipation and soiling.

DATA SOURCES

References were identified through a MEDLINE search from January 1975 through January 1998 to address 3 focus questions: (1) the best path to early, accurate diagnosis; (2) best methods for adequate clean-out; and (3) best approaches to promote patient and family compliance with management.

DATA SELECTION

Twenty-five references were identified.

DATA EXTRACTION

References were reviewed by a multidisciplinary team and graded according to the following criteria: randomized controlled trial; controlled trial, no randomization; observational study; and expert opinion. Evidence tables were developed for each focus question.

DATA SYNTHESIS

An algorithm and clinical care guideline were developed by consultation and consensus among team members. Emphasis was placed on methods to promote early identification of pediatric idiopathic constipation and soiling, to recognize points of referral, and to increase patient and family compliance with treatment through use of education, developmentally based interventions, and variables for tracking success of management.

CONCLUSION

An algorithm and guideline for pediatric idiopathic constipation and soiling are presented for use by primary care physicians.

Importance of factor VIIa Gla-domain residue Arg-36 for recognition of the macromolecular substrate factor X Gla-domain

Macromolecular substrate docking with coagulation enzyme-cofactor complexes involves multiple contacts distant from the enzyme's catalytic cleft. Here we characterize the binding of the Gla-domain of macromolecular substrate coagulation factor X to the complex of tissue factor (TF) and VIIa. Site-directed mutagenesis of charged residue side chains in the VIIa Gla-domain identified Arg-36 as being important for macromolecular substrate docking. Ala substitution for Arg-36 resulted in an increased KM and a decreased rate of X activation. X with a truncated Gla-domain was activated by mutant and wild-type VIIa at indistinguishable rates, demonstrating that Arg-36 interactions require a properly folded Gla-domain of the macromolecular substrate. VIIa Arg-36 was also required for effective docking of the X Gla-domain in the absence of phospholipid, demonstrating that the Gla-domain of VIIa participates in protein-protein interactions with X. In the absence of TF, the mutant VIIa had essentially normal function, indicating that the cofactor positions VIIa's Gla-domain for optimal macromolecular substrate docking. Computational docking suggests multiple charge complementary contacts of the X Gla-domain with TF.VIIa. A prominent interaction is made by the functionally important X residue Gla-14 with the center of the extended docking site created by residues in the carboxyl module of TF and the contiguous VIIa Gla-domain. These data demonstrate the functional importance of interactions of the Gla-domains of enzyme and substrate, and begin to elucidate the molecular details of the ternary TF.VIIa.X complex.

Developmental surface dysgraphia: what is the underlying cognitive impairment?

The purpose of this study was to investigate the cognitive causes underlying spelling difficulties in a case of developmental surface dysgraphia, AW. Our results do not support a number of possibilities that could be the cause of AW's poor orthographic lexicon, including difficulties in phonological processing, phonological short-term memory, configurational visual memory, and lexical semantic memory. We have found instead that AW performs poorly in tasks that involve detection of the order of adjacent letters in a word or the order of adjacent units in strings of consonants or symbols. Finally, he performs poorly in tasks that involve reconstructing the order of a series of complex visual characters (Japanese and Hindi characters) especially when these are presented sequentially. We advance the hypothesis that AW's poor spelling and good reading skills stem from an underlying pattern of cognitive abilities where a very good visual configurational memory is coupled with a poor ability to encode serial order. This may have resulted in a holistic word-based reading strategy, which, together with the original problem of encoding order, may have had detrimental effects for the acquisition of spelling.