HLA-Associated Clinical Progression Correlates with Epitope Reversion Rates in Early Human Immunodeficiency Virus Infection

Human immunodeficiency virus type 1 (HIV-1) can evade immunity shortly after transmission to a new host but the clinical significance of this early viral adaptation in HIV infection is not clear. We present an analysis of sequence variation from a longitudinal cohort study of HIV adaptation in 189 acute seroconverters followed for up to 3 years. We measured the rates of variation within well-defined epitopes to determine associations with the HLA-linked hazard of disease progression. We found early reversion across both the gag and pol genes, with a 10-fold faster rate of escape in gag (2.2 versus 0.27 forward mutations/1,000 amino acid sites). For most epitopes (23/34), variation in the HLA-matched and HLA-unmatched controls was similar. For a minority of epitopes (8/34, and generally associated with HLA class I alleles that confer clinical benefit), new variants appeared early and consistently over the first 3 years of infection. Reversion occurred early at a rate which was HLA-dependent and correlated with the HLA class 1-associated relative hazard of disease progression and death (P = 0.0008), reinforcing the association between strong cytotoxic T-lymphocyte responses, viral fitness, and disease status. These data provide a comprehensive overview of viral adaptation in the first 3 years of infection. Our findings of HLA-dependent reversion suggest that costs are borne by some escape variants which may benefit the host, a finding contrary to a simple immune evasion paradigm. These epitopes, which are both strongly and frequently recognized, and for which escape involves a high cost to the virus, have the potential to optimize vaccine design.The dynamics of viral replication in acute and early human immunodeficiency virus (HIV) infection are not well understood as longitudinal data from large cohorts of seroconverters are hard to assemble. Recent studies have shown that new HIV infections may be the result of a single transmitted variant, that new env gene mutations can be detected within a few weeks (25), and that early immune escape can be detected at sites across the HIV genome (9). These data add to a body of work showing that cytotoxic T cells act early, contributing to the early reduction in viremia (8, 30).Whether early cytotoxic T-lymphocyte (CTL) immune responses influence longer-term clinical outcome is not clear. Antigen-specific CTLs capable of producing gamma interferon and other cytokines are detectable at all stages of HIV infection (1, 3, 24, 41). Much weight is placed on the macaque/simian immunodeficiency virus model in which nearly total peripheral blood CD8⁺ T-cell elimination using monoclonal antibodies results in rising viremia (42). The role of other forms of host immunity (e.g., neutralizing antibodies, natural killer cells, and macrophages) has, to some extent, been pursued with less intensity in light of persuasive evidence that CTLs can control retrovirus infection (46). The extent to which the simian model mirrors HIV infection has been questioned (5) and, despite exhaustive cellular assays of T-cell function—from gamma interferon enzyme-linked immunospot assays(1, 27, 38) to polyfunctional cytokine matrices (2, 6)—no CTL function correlates robustly with HIV plasma viral load or viral dynamics. Moreover, analyses of evolutionary data suggest that CTLs are inefficient at killing HIV-infected cells (4).However, statistical analysis of data from large cross-sectional studies link HLA class I alleles with specific genome-wide HIV polymorphisms, suggestive of a pervasive selection pressure enacted by CTLs (7, 10, 18, 36, 40). It is clear that associations between some HLA class I alleles and particular amino acid polymorphisms are robust although it is disputed whether immune escape influences disease progression. The viral fitness costs resulting from immune escape may even contribute to better clinical outcomes associated with the possession of HLA class I alleles such as B*27, B*57, and B*58 (18).Evolutionary studies of HIV require longitudinal data from large cohorts of patients sampled since seroconversion to detect adaptation in new hosts as it accrues. HIV is one of the few pathogens where it is possible to do this within individuals because of the high viral turnover and rapid intrahost evolution. Here, we investigate a cohort of 189 acute seroconverters—the largest cohort reported to date—followed for up to 3 years to study the rates of viral mutation in individual epitopes within internal HIV proteins and to determine the association between HLA class I alleles and rates of immune escape and reversion.     

Assessing Statistical Significance in Microarray Experiments Using the Distance Between Microarrays

We propose permutation tests based on the pairwise distances between microarrays to compare location, variability, or equivalence of gene expression between two populations. For these tests the entire microarray or some pre-specified subset of genes is the unit of analysis. The pairwise distances only have to be computed once so the procedure is not computationally intensive despite the high dimensionality of the data. An R software package, permtest, implementing the method is freely available from the Comprehensive R Archive Network at http://cran.r-project.org.     

Early Response to Sibutramine in Patients Not Meeting Current Label Criteria: Preliminary Analysis of SCOUT Lead‐in Period

The Sibutramine Cardiovascular Outcomes (SCOUT) trial protocol defines a patient population predominantly outside current European Union label criteria. This article explores responses to sibutramine during the 6‐week, single‐blind, lead‐in period between patients who conformed to the label requirements (“conformers”) and those who did not (“nonconformers”). SCOUT is an ongoing, randomized, double‐blind, placebo‐controlled outcome trial in overweight/obese patients at high risk of a cardiovascular event. In total, 10,742 patients received sibutramine and weight management during the lead‐in period. Initial responses were assessed post hoc in label conformers and nonconformers. Of that 8.1% patients met label criteria; 91.9%, the majority with cardiovascular disease and/or blood pressure >145/90 mm Hg, were nonconformers. Conformers and nonconformers had similar reductions in body weight (median change ?2.2 kg) and waist circumference (women: ?2.0 cm for both groups; men: ?1.5 cm vs. ?2.0 cm for conformers and nonconformers, respectively) over the 6‐week period. Greater blood pressure falls were evident in nonconformers (median change ?3.5/?1.0 vs. ?1.0/0.0 mm Hg). Both groups had small pulse rate increases; median 1.5 bpm (nonconformers) vs. 3.0 bpm (conformers). There was a low incidence of serious adverse events (conformers: 1.0%; nonconformers: 2.8%) and ～93% of patients in both groups completed the 6‐week period. The SCOUT lead‐in period evaluating weight management with sibutramine confirms its good tolerability and efficacy in patients who meet current label criteria. Preliminary data from high‐risk patients for whom sibutramine is currently contraindicated suggest a low discontinuation rate and few serious adverse events but confirmation from the SCOUT outcome data is needed.     

The effects of age on inflammatory and coagulation-fibrinolysis response in patients hospitalized for pneumonia

Objective

To determine whether inflammatory and hemostasis response in patients hospitalized for pneumonia varies by age and whether these differences explain higher mortality in the elderly.

Methods

In an observational cohort of subjects with community-acquired pneumonia (CAP) recruited from emergency departments (ED) in 28 hospitals, we divided subjects into 5 age groups (<50, 51–64, 65–74, 75–84, and ≥85). We measured circulating levels of inflammatory (TNF, IL-6, and IL-10), hemostasis (D-dimer, Factor IX, thrombin-antithrombin complex, antithrombin and plasminogen-activator inhibitor-1), and cell-surface markers (TLR-2, TLR-4, and HLA-DR) during the first week of hospitalization and at discharge and compared 90-day mortality. We used logistic regression to compare odds ratios (OR) for 90-day mortality between age groups, adjusting for differences in pre-infection factors alone and then additionally adjusting for immune markers.

Results

Of 2,183 subjects, 495, 444, 403, 583, and 258 subjects were <50, 51–64, 65–74, 75–84, and ≥85 years of age, respectively. Large age-related differences were observed in 90-day mortality (0.82% vs. 3.2% vs. 6.4% vs. 12.8% vs. 13.6%, p<0.01). No age-related differences in inflammatory and cell surface markers occurred during the first week. Older subjects had higher pro-coagulant markers on ED presentation and over first week (p≤0.03), but these differences were modest (1.0–1.7-fold differences). Odds of death for older adults changed minimally in models incorporating differences in hemostasis and inflammatory markers (for subjects ≥85 compared to those <50, OR = 4.36, when adjusted for pre-infection factors and OR = 3.49 when additionally adjusted for hemostasis markers). At discharge, despite clinical recovery as evidenced by normal vital signs in >85% subjects, older subjects had modestly increased hemostasis markers and IL-6 levels (p<0.01).

Conclusions

Modest age-related increases in coagulation response occur during hospitalization for CAP; however these differences do not explain the large differences in mortality. Despite clinical recovery, immune resolution may be delayed in older adults at discharge.     

The Lin28/let-7 axis regulates glucose metabolism

The let-7 tumor suppressor microRNAs are known for their regulation of oncogenes, while the RNA-binding proteins Lin28a/b promote malignancy by inhibiting let-7 biogenesis. We have uncovered unexpected roles for the Lin28/let-7 pathway in regulating metabolism. When overexpressed in mice, both Lin28a and LIN28B promote an insulin-sensitized state that resists high-fat-diet induced diabetes. Conversely, muscle-specific loss of Lin28a or overexpression of let-7 results in insulin resistance and impaired glucose tolerance. These phenomena occur, in part, through the let-7-mediated repression of multiple components of the insulin-PI3K-mTOR pathway, including IGF1R, INSR, and IRS2. In addition, the mTOR inhibitor, rapamycin, abrogates Lin28a-mediated insulin sensitivity and enhanced glucose uptake. Moreover, let-7 targets are enriched for genes containing SNPs associated with type 2 diabetes and control of fasting glucose in human genome-wide association studies. These data establish the Lin28/let-7 pathway as a central regulator of mammalian glucose metabolism.     

Accelerated care versus standard care among patients with hip fracture: the HIP ATTACK pilot trial

Background:

A hip fracture causes bleeding, pain and immobility, and initiates inflammatory, hypercoagulable, catabolic and stress states. Accelerated surgery may improve outcomes by reducing the duration of these states and immobility. We undertook a pilot trial to determine the feasibility of a trial comparing accelerated care (i.e., rapid medical clearance and surgery) and standard care among patients with a hip fracture.

Methods:

Patients aged 45 years or older who, during weekday, daytime working hours, received a diagnosis of a hip fracture requiring surgery were randomly assigned to receive accelerated or standard care. Our feasibility outcomes included the proportion of eligible patients randomly assigned, completeness of follow-up and timelines of accelerated surgery. The main clinical outcome, assessed by data collectors and adjudicators who were unaware of study group allocations, was a major perioperative complication (i.e., a composite of death, preoperative myocardial infarction, myocardial injury after noncardiac surgery, pulmonary embolism, pneumonia, stroke, and life-threatening or major bleeding) within 30 days of randomization.

Results:

Of patients eligible for inclusion, 80% consented and were randomly assigned to groups (30 to accelerated care and 30 to standard care) at 2 centres in Canada and 1 centre in India. All patients completed 30-day follow-up. The median time from diagnosis to surgery was 6.0 hours in the accelerated care group and 24.2 hours in the standard care group (p < 0.001). A major perioperative complication occurred in 9 (30%) of the patients in the accelerated care group and 14 (47%) of the patients in the standard care group (hazard ratio 0.60, 95% confidence interval 0.26–1.39).

Interpretation:

These results show the feasibility of a trial comparing accelerated and standard care among patients with hip fracture and support a definitive trial. Trial registration: ClinicalTrials.gov, no. {"type":"clinical-trial","attrs":{"text":"NCT01344343","term_id":"NCT01344343"}}NCT01344343.Annually in North America, 0.8% of women and 0.4% of men aged 65 years or older experience a hip fracture.¹ Patients who sustain a hip fracture face a high risk of serious complications (i.e., cardiovascular, venous thrombotic, infectious and hemorrhagic)^2,3 that can result in a prolonged hospital stay and death: 30-day mortality is 9% among men and 5% among women.¹ Among surviving patients who were community-dwelling before their fracture, 11% become bed-ridden and 16% are admitted to a long-term care facility.⁴A hip fracture results in pain, bleeding and immobility. These factors initiate inflammatory, hypercoagulable, catabolic and stress states that can precipitate medical complications.^5–11 Early surgery shortens the exposure to these harmful states and, therefore, may reduce morbidity and mortality. Furthermore, earlier surgery may shorten the period of immobility, which may improve functional outcomes and reduce costs.A meta-analysis of observational studies evaluating the timing of surgery for a hip fracture included 5 studies (involving 4208 patients and 721 deaths) that reported the adjusted risk of mortality.¹² Earlier surgery, irrespective of the cut-off for delay (24, 48 or 72 h), was associated with significantly lower mortality (adjusted relative risk 0.81, 95% confidence interval [CI] 0.68–0.96, p = 0.01). Although these data are encouraging, the apparent benefit may be a result of residual confounding (e.g., sicker patients may have had surgery delayed for medical optimization, which may not have been adequately adjusted for in the analyses). Conversely, the real potential of early surgery may be underestimated because the greatest impact may occur when a hip fracture is treated much more quickly than the timelines assessed in the observational studies (24, 48 or 72 h), similar to how treatment of an acute myocardial infarction or stroke within hours has the most dramatic impact.^13,14In many countries, including Canada, most patients with a hip fracture wait longer than 24 hours to undergo surgery. The 2 main reasons for delay are preoperative medical clearance and operating room access,^15–21 both of which are potentially modifiable. We undertook a pilot trial to determine the feasibility (as assessed by the proportion of eligible patients randomly assigned, completeness of follow-up and timeliness of accelerated surgery) of a large randomized controlled trial (RCT) comparing accelerated care and standard care among adults with a hip fracture.     

Resistance to Erythropoiesis Stimulating Agents in Patients Treated with Online Hemodiafiltration and Ultrapure Low-Flux Hemodialysis: Results from a Randomized Controlled Trial (CONTRAST)

Resistance to erythropoiesis stimulating agents (ESA) is common in patients undergoing chronic hemodialysis (HD) treatment. ESA responsiveness might be improved by enhanced clearance of uremic toxins of middle molecular weight, as can be obtained by hemodiafiltration (HDF). In this analysis of the randomized controlled CONvective TRAnsport STudy (CONTRAST; {"type":"clinical-trial","attrs":{"text":"NCT00205556","term_id":"NCT00205556"}}NCT00205556), the effect of online HDF on ESA resistance and iron parameters was studied. This was a pre-specified secondary endpoint of the main trial. A 12 months'' analysis of 714 patients randomized to either treatment with online post-dilution HDF or continuation of low-flux HD was performed. Both groups were treated with ultrapure dialysis fluids. ESA resistance, measured every three months, was expressed as the ESA index (weight adjusted weekly ESA dose in daily defined doses [DDD]/hematocrit). The mean ESA index during 12 months was not different between patients treated with HDF or HD (mean difference HDF versus HD over time 0.029 DDD/kg/Hct/week [−0.024 to 0.081]; P = 0.29). Mean transferrin saturation ratio and ferritin levels during the study tended to be lower in patients treated with HDF (−2.52% [−4.72 to −0.31]; P = 0.02 and −49 ng/mL [−103 to 4]; P = 0.06 respectively), although there was a trend for those patients to receive slightly more iron supplementation (7.1 mg/week [−0.4 to 14.5]; P = 0.06).In conclusion, compared to low-flux HD with ultrapure dialysis fluid, treatment with online HDF did not result in a decrease in ESA resistance.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00205556","term_id":"NCT00205556"}}NCT00205556     

Cognitive Function in Ambulatory Patients with Systolic Heart Failure: Insights from the Warfarin versus Aspirin in Reduced Cardiac Ejection Fraction (WARCEF) Trial

We sought to determine whether cognitive function in stable outpatients with heart failure (HF) is affected by HF severity. A retrospective, cross-sectional analysis was performed using data from 2, 043 outpatients with systolic HF and without prior stroke enrolled in the Warfarin versus Aspirin in Reduced Cardiac Ejection Fraction (WARCEF) Trial. Multivariable regression analysis was used to assess the relationship between cognitive function measured using the Mini-Mental Status Exam (MMSE) and markers of HF severity (left ventricular ejection fraction [LVEF], New York Heart Association [NYHA] functional class, and 6-minute walk distance). The mean (SD) for the MMSE was 28.6 (2.0), with 64 (3.1%) of the 2,043 patients meeting the cut-off of MMSE <24 that indicates need for further evaluation of cognitive impairment. After adjustment for demographic and clinical covariates, 6-minute walk distance (β-coefficient 0.002, p<0.0001), but not LVEF or NYHA functional class, was independently associated with the MMSE as a continuous measure. Age, education, smoking status, body mass index, and hemoglobin level were also independently associated with the MMSE. In conclusion, six-minute walk distance, but not LVEF or NYHA functional class, was an important predictor of cognitive function in ambulatory patients with systolic heart failure.     

Prediction of Cardiovascular Events in Statin-Treated Stable Coronary Patients of the Treating to New Targets Randomized Controlled Trial by Lipid and Non-Lipid Biomarkers

Several plasma non-lipid biomarkers have been shown to predict major cardiovascular events (MCVEs) in population studies. Our objective was to investigate the relationship between lipid and non-lipid biomarkers levels achieved during statin therapy and the incidence of MCVEs in patients with stable coronary heart disease (CHD). We conducted a substudy of the TNT (Treating to New Targets) study, which was a randomized trial that compared the efficacy of high (80 mg) versus low (10 mg) dose atorvastatin for the secondary prevention of CHD. Fasting plasma levels of standard lipids and of 18 non-lipid biomarkers were obtained after an 8-week run-in period on atorvastatin 10 mg in 157 patients who experienced MCVEs during the 4.9 years of study follow-up and in 1349 controls. MCVE was defined as CHD death, nonfatal, non-procedure-related myocardial infarction, resuscitated cardiac arrest, and fatal or nonfatal stroke. After adjusting for age, sex and treatment arm, plasma levels of high-density lipoprotein (HDL) cholesterol, triglycerides, high-sensitivity C-reactive protein (hsCRP), insulin, neopterin, N-terminal pro-brain natriuretic peptide (BNP), lipoprotein(a) [Lp(a)], and the soluble receptor for advanced glycation end products (sRAGE) were predictive of recurrent MCVEs (P≤0.02 for each doubling of plasma concentration). However, no significant association was observed between the risk of recurrent MCVEs and plasma levels of low-density lipoprotein cholesterol, adiponectin, cystatin C, lipoprotein-associated phospholipase A2, monocyte chemotactic protein-1, matrix metalloproteinase-9, myeloperoxidase, osteopontin, soluble CD40 ligand, soluble intercellular adhesion molecule-1, or soluble vascular cell adhesion molecule-1. After further adjustment for diabetes, hypertension, smoking, and BMI, the relationship between hsCRP, insulin and MCVE were no longer significant, while the relationship between Lp(a), neopterin, NT-proBNP and sRAGE and MCVE remained statistically significant. In conclusion, in patients with CHD treated with atorvastatin, plasma levels of Lp(a), neopterin, NT-proBNP, and sRAGE are associated with the risk of recurrent MCVEs.

Trial Registration

ClinicalTrials.gov {"type":"clinical-trial","attrs":{"text":"NCT00327691","term_id":"NCT00327691"}}NCT00327691.