Phase 2, randomized, double-blind, placebo-controlled multi-center trial of the clinical and biological effects of anti-CD14 treatment in hospitalized patients with COVID-19 pneumonia

BACKGROUND

Severe COVID-19 is associated with innate immunopathology, and CD14, a proximal activator of innate immunity, has been suggested as a potential therapeutic target.

METHODS

We conducted the COVID-19 anti-CD14 Treatment Trial (CaTT), a Phase II randomized, double-blind, placebo-controlled trial at 5 US-sites between April 12, 2021 and November 30, 2021 (NCT04391309). Hospitalized adults with COVID-19 requiring supplemental oxygen (<30 LPM) were randomized 1:1 to receive 4 daily doses of intravenous IC14, an anti-CD14 monoclonal antibody, or placebo. All participants received remdesivir. The primary outcome was time-to-resolution of illness, defined as improvement on the 8-point NIH-Ordinal COVID-19 Scale to category ≤3. Secondary endpoints were safety and exploratory endpoints were pro-inflammatory and antiviral mediators in serum on days 0-5 & 7. The trial was stopped after 40 patients were randomized and treated due to slow enrollment.

FINDINGS

40 participants were randomized and treated with IC14 (n = 20) or placebo (n = 20). The median time-to-recovery was 6 days (95% CI, 5-11) in the IC14 group vs. 5 days (95% CI, 4-10) in the Placebo group (recovery rate ratio: 0.77 (95% CI, 0.40, 1.48) (log-rank p = 0.435). The number of adverse events was similar in each group, and no IC14-attributable secondary infections occurred. In repeated-measures mixed-effects analyses, IC14 treatment increased serum sCD14 concentrations, an expected pharmacodynamic effect. Pre-planned, exploratory analyses suggested that IC14 treatment decreased the trajectories of circulating MIP-1β and TNF-α.

INTERPRETATION

IC14 treatment did not improve time-to-resolution of illness in hypoxemic patients with COVID-19 in this small trial. Results of exploratory analyses suggested IC14 had biologic effects that warrant future clinical investigation.

FUNDING

National Institute of Allergy and Infectious Diseases.

Mediators of monocyte chemotaxis and matrix remodeling are associated with the development of fibrosis in patients with COVID-19

Acute respiratory distress syndrome (ARDS) has a fibroproliferative phase that may be followed by pulmonary fibrosis. This has been described in patients with COVID-19 pneumonia, but the underlying mechanisms have not been completely defined. We hypothesized that protein mediators of tissue remodeling and monocyte chemotaxis are elevated in the plasma and endotracheal aspirates of critically ill patients with COVID-19 who subsequently develop radiographic fibrosis. We enrolled COVID-19 patients admitted to the ICU who had hypoxemic respiratory failure, were hospitalized and alive for at least 10 days, and had chest imaging done during hospitalization ( n = 119). Plasma was collected within 24h of ICU admission and at 7d. In mechanically ventilated patients, endotracheal aspirates (ETA) were collected at 24h and 48-96h. Protein concentrations were measured by immunoassay. We tested for associations between protein concentrations and radiographic evidence of fibrosis using logistic regression adjusting for age, sex, and APACHE score. We identified 39 patients (33%) with features of fibrosis. Within 24h of ICU admission, plasma proteins related to tissue remodeling (MMP-9, Amphiregulin) and monocyte chemotaxis (CCL-2/MCP-1, CCL-13/MCP-4) were associated with the subsequent development of fibrosis whereas markers of inflammation (IL-6, TNF-α) were not. After 1 week, plasma MMP-9 increased in patients without fibrosis. In ETAs, only CCL-2/MCP-1 was associated with fibrosis at the later timepoint. This cohort study identifies proteins of tissue remodeling and monocyte recruitment that may identify early fibrotic remodeling following COVID-19. Measuring changes in these proteins over time may allow for early detection of fibrosis in patients with COVID-19.

Cross-reactive and mono-reactive SARS-CoV-2 CD4+ T cells in prepandemic and COVID-19 convalescent individuals

Class II tetramer reagents for eleven common DR alleles and a DP allele prevalent in the world population were used to identify SARS-CoV-2 CD4+ T cell epitopes. A total of 112, 28 and 42 epitopes specific for Spike, Membrane and Nucleocapsid, respectively, with defined HLA-restriction were identified. Direct ex vivo staining of PBMC with tetramer reagents was used to define immunodominant and subdominant T cell epitopes and estimate the frequencies of these T cells in SARS-CoV-2 exposed and naïve individuals. Majority of SARS-CoV-2 epitopes identified have <67% amino acid sequence identity with endemic coronaviruses and are unlikely to elicit high avidity cross-reactive T cell responses. Four SARS-CoV-2 Spike reactive epitopes, including a DPB1*04:01 restricted epitope, with ≥67% amino acid sequence identity to endemic coronavirus were identified. SARS-CoV-2 T cell lines for three of these epitopes elicited cross-reactive T cell responses to endemic cold viruses. An endemic coronavirus Spike T cell line showed cross-reactivity to the fourth SARS-CoV-2 epitope. Three of the Spike cross-reactive epitopes were subdominant epitopes, while the DPB1*04:01 restricted epitope was a dominant epitope. Frequency analyses showed Spike cross-reactive T cells as detected by tetramers were present at relatively low frequency in unexposed people and only contributed a small proportion of the overall Spike-specific CD4+ T cells in COVID-19 convalescent individuals. In total, these results suggested a very limited number of SARS-CoV-2 T cells as detected by tetramers are capable of recognizing ccCoV with relative high avidity and vice versa. The potentially supportive role of these high avidity cross-reactive T cells in protective immunity against SARS-CoV-2 needs further studies.

Endomembrane targeting of human OAS1 p46 augments antiviral activity

Many host RNA sensors are positioned in the cytosol to detect viral RNA during infection. However, most positive-strand RNA viruses replicate within a modified organelle co-opted from intracellular membranes of the endomembrane system, which shields viral products from cellular innate immune sensors. Targeting innate RNA sensors to the endomembrane system may enhance their ability to sense RNA generated by viruses that use these compartments for replication. Here, we reveal that an isoform of oligoadenylate synthetase 1, OAS1 p46, is prenylated and targeted to the endomembrane system. Membrane localization of OAS1 p46 confers enhanced access to viral replication sites and results in increased antiviral activity against a subset of RNA viruses including flaviviruses, picornaviruses, and SARS-CoV-2. Finally, our human genetic analysis shows that the OAS1 splice-site SNP responsible for production of the OAS1 p46 isoform correlates with protection from severe COVID-19. This study highlights the importance of endomembrane targeting for the antiviral specificity of OAS1 and suggests that early control of SARS-CoV-2 replication through OAS1 p46 is an important determinant of COVID-19 severity.

Frozen CyTOF panel enables robust and consistent longitudinal assessment of the SARS-CoV-2 immune landscape

During the Coronavirus Disease 2019 (COVID-19) outbreak, a robust and consistent strategy was required for assessing the immune landscape. Our rapid research response to COVID-19 was enabled by use of standardized assays. The assays included a 33-marker mass cytometry (CyTOF) panel that characterized major immune cells subsets in fresh whole blood including both innate and adaptive cells. Intraassay variation, determined by staining of the same fresh whole blood sample independently by two technicians on the same day, was CV&lt;20% for populations with a frequency &gt;5%. However, technical consistency was crucial to accurately capture and compare immune changes. Thus, we tested the stability of an antibody cocktail stored at −80C to limit inherent variability in daily panel preparation. Using lyophilized whole blood and cryopreserved R848-stimulated PBMC as controls encompassing the breadth of cell subsets and markers, we assessed the panel performance 7 times (at days 0, 16, 33, 42, 56, 72 and 96 after freezing). We found stability of staining over time: variability of the frozen cocktail was comparable to repeated cocktail preparations as seen in rare plasmablasts (CV&lt;25% frozen vs 13.1% repeat fresh), but also CD4 T cells (CV&lt;13% vs 10.6%), and neutrophils (CV&lt;4% vs 9.8%). Applying the highly-consistent frozen cocktail to study of 59 COVID-19 subjects revealed changes in common subsets (CD4 central memory T cells increased &gt;30% with severe disease), but also in rare plasmablasts (increased 6% of CD19), and more subtle neutrophil changes (increased 15% of CD45). Thus, freezing a high-content CyTOF panel cocktail provides a reliable method to control variability of staining in assays where sample collection is variable.

Early Prognostic Indicators of Subsequent Hospitalization in Patients with Mild COVID-19

Comprehensive data on early prognostic indicators in patients with mild COVID-19 remains sparse. In this single center case series, we characterized the initial clinical presentation in 180 patients with mild COVID-19 and defined the earliest predictors of subsequent deterioration and need for hospitalization. Three broad patient phenotypes and four symptom clusters were characterized, differentiated by varying risk for adverse outcomes. Among 14 symptoms assessed, subjective shortness of breath (SOB) most strongly associated with adverse outcomes (odds ratio (OR) 21.3, 95% confidence interval (CI): 2.7–166.4; p < 0.0001). In combination, SOB and number of comorbidities were highly predictive of subsequent hospitalization (area under the curve (AUC) 92%). Additionally, initial lymphopenia (OR 21.0, 95% CI: 2.1–210.1; p = 0.002) and male sex (OR 3.5, 95% CI: 0.9–13.0; p = 0.05) were associated with increased risk of poor outcomes. Patients with known comorbidities, especially multiple, and those presenting with subjective SOB or lymphopenia should receive close monitoring and consideration for preemptive treatment, even when presenting with mild symptoms.

The COVID-19 immune landscape is dynamically and reversibly correlated with disease severity

BACKGROUNDDespite a rapidly growing body of literature on coronavirus disease 2019 (COVID-19), our understanding of the immune correlates of disease severity, course, and outcome remains poor.METHODSUsing mass cytometry, we assessed the immune landscape in longitudinal whole-blood specimens from 59 patients presenting with acute COVID-19 and classified based on maximal disease severity. Hospitalized patients negative for SARS-CoV-2 were used as controls.RESULTSWe found that the immune landscape in COVID-19 formed 3 dominant clusters, which correlated with disease severity. Longitudinal analysis identified a pattern of productive innate and adaptive immune responses in individuals who had a moderate disease course, whereas those with severe disease had features suggestive of a protracted and dysregulated immune response. Further, we identified coordinate immune alterations accompanying clinical improvement and decline that were also seen in patients who received IL-6 pathway blockade.CONCLUSIONThe hospitalized COVID-19 negative cohort allowed us to identify immune alterations that were shared between severe COVID-19 and other critically ill patients. Collectively, our findings indicate that selection of immune interventions should be based in part on disease presentation and early disease trajectory due to the profound differences in the immune response in those with mild to moderate disease and those with the most severe disease.FUNDINGBenaroya Family Foundation, the Leonard and Norma Klorfine Foundation, Glenn and Mary Lynn Mounger, and the National Institutes of Health.

Acute limb ischemia as sole initial manifestation of SARS-CoV-2 infection

We present the case of a patient with acute upper limb ischemia as the sole initial manifestation of severe acute respiratory syndrome associated with coronavirus disease 2 infection, without concomitant respiratory symptoms or pneumonia. Viral infection presumably precipitated the patient's thromboembolic event, causing multifocal vascular occlusions. This case illustrates that coronavirus disease-19 must be considered in the differential diagnosis of patients presenting with signs or symptoms of coagulopathy, even in the absence of respiratory symptoms. We believe that an awareness of the variety of clinical presentations in patients with coronavirus disease-19, particularly extrapulmonary manifestations, is critical for optimal patient management as well as implementation of appropriate infection prevention measures.

Ontogeny of different subsets of yellow fever virus-specific circulatory CXCR5+ CD4+ T cells after yellow fever vaccination

Monitoring the frequency of circulatory CXCR5⁺ (cCXCR5⁺) CD4⁺ T cells in periphery blood provides a potential biomarker to draw inferences about T follicular helper (T_FH) activity within germinal center. However, cCXCR5⁺ T cells are highly heterogeneous in their expression of ICOS, PD1 and CD38 and the relationship between different cCXCR5 subsets as delineated by these markers remains unclear. We applied class II tetramer reagents and mass cytometry to investigate the ontogeny of different subsets of cCXCR5⁺ T cell following yellow fever immunization. Through unsupervised analyses of mass cytometry data, we show yellow fever virus-specific cCXCR5 T cells elicited by vaccination were initially CD38⁺ICOS⁺PD1⁺, but then transitioned to become CD38⁺ICOS^-PD1⁺ and CD38^-ICOS^-PD1⁺ before coming to rest as a CD38^-ICOS^-PD1^- subset. These results imply that most antigen-specific cCXCR5⁺ T cells, including the CD38^-ICOS^-PD1^- CXCR5⁺ T cells are derived from the CXCR5⁺CD38⁺ICOS⁺PD1⁺ subset, the subset that most resembles preT_FH/T_FH in the germinal center.

Antimicrobial stewardship through a one health lens

Purpose

– Antibiotic resistance (AR) is a global health crisis that is attracting focussed attention from healthcare, public health, governmental agencies, the public, and food producers. The purpose of this paper is to describe the work in Washington State to combat resistance and promote antimicrobial stewardship from a one health perspective.

Design/methodology/approach

– In 2014, the Washington State Department of Health convened a One Health Steering Committee and two workgroups to focus on AR, the One Health Antimicrobial Stewardship work group and the One Health Antimicrobial Resistance Surveillance work group. The group organized educational sessions to establish a basic understanding of epidemiological factors that contribute to resistance, including antibiotic use, transmission of resistant bacteria, and environmental contamination with resistant bacteria and antibiotic residues.

Findings

– The authors describe the varied uses of antibiotics; efforts to promote stewardship in human, and animal health, including examples from the USA and Europe; economic factors that promote use of antibiotics in animal agriculture; and efforts, products and next steps of the workgroups.

Originality/value

– In Washington, human, animal and environmental health experts are working collaboratively to address resistance from a one health perspective. The authors are establishing a multi-species resistance database that will allow tracking resistance trends in the region. Gaps include measurement of antibiotic use in humans and animals; integrated resistance surveillance information; and funding for AR and animal health research.

Neuroinvasive West Nile Infection Elicits Elevated and Atypically Polarized T Cell Responses That Promote a Pathogenic Outcome

Most West Nile virus (WNV) infections are asymptomatic, but some lead to neuroinvasive disease with symptoms ranging from disorientation to paralysis and death. Evidence from animal models suggests that neuroinvasive infections may arise as a consequence of impaired immune protection. However, other data suggest that neurologic symptoms may arise as a consequence of immune mediated damage. We demonstrate that elevated immune responses are present in neuroinvasive disease by directly characterizing WNV-specific T cells in subjects with laboratory documented infections using human histocompatibility leukocyte antigen (HLA) class II tetramers. Subjects with neuroinvasive infections had higher overall numbers of WNV-specific T cells than those with asymptomatic infections. Independent of this, we also observed age related increases in WNV-specific T cell responses. Further analysis revealed that WNV-specific T cell responses included a population of atypically polarized CXCR3+CCR4+CCR6- T cells, whose presence was highly correlated with neuroinvasive disease. Moreover, a higher proportion of WNV-specific T cells in these subjects co-produced interferon-γ and interleukin 4 than those from asymptomatic subjects. More globally, subjects with neuroinvasive infections had reduced numbers of CD4+FoxP3+ Tregs that were CTLA4 positive and exhibited a distinct upregulated transcript profile that was absent in subjects with asymptomatic infections. Thus, subjects with neuroinvasive WNV infections exhibited elevated, dysregulated, and atypically polarized responses, suggesting that immune mediated damage may indeed contribute to pathogenic outcomes.

Cyclophosphamide Treatment for Acquired Factor VIII Inhibitor in a Patient with AIDS-Associated Progressive Multifocal Leukoencephalopathy

Acquired hemophilia A (AHA) is a severe bleeding disorder with high mortality rates resulting from the development of autoantibodies to factor VIII (FVIII). Patients typically present with hemorrhages in the skin, subcutaneous tissues, and muscles, which are frequently severe. They can also develop life-threatening retroperitoneal hematomas and compartment syndromes. We describe the case of a man with a long history of AIDS complicated by progressive multifocal leukoencephalopathy (PML), who developed AHA while on stable antiretroviral therapy and then presented with new onset bleeding and hypotension. We treated our patient with incrementally increasing doses of cyclophosphamide resulting in resolution of coagulopathy. We review the medical literature for additional cases of HIV-associated AHA and discuss the challenges in the care of our patient, since the immunosuppression needed to eradicate the FVIII inhibitor had the potential to cause recrudescence of his PML.

Longitudinal study of CD4 T cell responses following Japanese encephalitis virus vaccination (VIR2P.1165)

Japanese encephalitis virus (JEV) is the leading cause of viral encephalitis worldwide. There are currently a number of vaccines shown to effectively prevent disease. In the United States, an alum adsorbed vaccine, which consists of a formaldehyde-inactivated, attenuated JEV strain is available. Vaccine protection has been shown to be mediated by neutralizing antibody responses. However, the CD4 T cell response associated with vaccine protection has not been fully characterized. In particular, the JEV model also presents an opportunity to study the kinetics of T cell responses elicited by a multi-dose vaccination in human subjects. In this study, we characterized the longitudinal response of JEV-specific CD4 T cells following vaccination using tetramer guided epitope mapping (TGEM), direct ex vivo MHC class II tetramer staining, and intracellular cytokine staining. A total of 67 epitopes restricted by 7 common HLA-DRB1 alleles and one DRB5 allele were identified. Vaccination elicited a robust CD4 T cell response, which was substantially boosted after the second dose of vaccine was administered. JEV-specific CD4 T cells exhibited a memory phenotype and expressed CCR4 and CXCR3. Consistent with this surface phenotype, JEV specific responses were polyfunctional, secreting IFN-g, IL-4 and sometimes IL-17a. These results indicate that JEV vaccination induces a robust, polyfunctional CD4 T cell response that is similar in magnitude to other highly effective vaccines.

Quantitative and qualitative differences in CD4+ T cell responses for subjects with symptomatic and asymptomatic West Nile virus infection (P6125)

The West Nile virus (WNV), a mosquito-borne flavivirus, induces a wide range of clinical manifestations in humans. While the majority of infections are essentially asymptomatic, a small percentage of inflections lead to neuroinvasive disease with symptoms ranging from mild disorientation to paralysis and death. Increased risk of symptomatic infection in immunosuppressed subjects could suggest that lack of effective immune responses against WNV may lead to worse outcomes. In this study, we utilized HLA class II tetramers to characterize the epitope specificity, frequency, and phenotype of WNV-specific T cells in subjects who had previously documented WNV infection. CD4+ T cell epitopes were present within all WNV fever proteins allowing broad characterization of WNV-specific responses. Ex vivo tetramer analysis revealed that WNV-specific CD4+ T cells were present at significantly higher frequencies in subjects with symptomatic infection than in those with no symptoms. CD4+ T cells had a memory phenotype in all WNV infected subjects, exhibited varying levels of activation, and produced multiple cytokines, including interferon-γ and IL-17. T cells from symptomatic subjects had a distinct phenotype, producing higher levels of Th2 cytokines after re-activation in vitro. Therefore, quantitative and qualitative differences in CD4+ T cell responses toward WNV are associated with neuroinvasive disease.

CD4+ T cells recognize unique and conserved 2009 H1N1 influenza hemagglutinin epitopes after natural infection and vaccination

Influenza A/California/4/2009 (H1N1/09) is a recently emerged influenza virus capable of causing serious illness or death in otherwise healthy individuals. Serious outcomes were most common in young adults and children, suggesting that pre-existing heterologous immunity may influence the severity of infection. Using tetramers, we identified CD4(+) T-cell epitopes within H1N1/09 hemagglutinin (HA) that share extensive homology with seasonal influenza and epitopes that are unique to H1N1/09 HA. Ex vivo tetramer staining revealed that T cells specific for conserved epitopes were detectable within the memory compartment, whereas T cells specific for unique epitopes were naive and infrequent prior to infection or vaccination. Following infection, the frequencies of T cells specific for unique epitopes were 11-fold higher, reaching levels comparable to those of T cells specific for immunodominant epitopes. In contrast, the frequencies of T cells specific for conserved epitopes were only 2- to 3-fold higher following infection. In general, H1HA-reactive T cells exhibited a memory phenotype, expressed CXCR3 and secreted IFN-γ, indicating a predominantly Th1-polarized response. A similar Th1 response was seen in vaccinated subjects, but the expansion of T cells specific for HA epitopes was comparatively modest after vaccination. Our findings indicate that CD4(+) T cells recognize both strain-specific and conserved epitopes within the influenza HA protein and suggest that naive T cells specific for HA epitopes undergo significant expansion, whereas memory T cells specific for the conserved epitopes undergo more restrained expansion.

Incidence and types of post extubation complications following endotracheal intubation and tracheostomy

This study was undertaken to study early and late post extubation complications following endotracheal intubation and tracheostomy. A total 60 patients who were admitted in Dayanand Medical College and Hospital were studied prospectively. They were divided into 3 groups and were screened with various modalities like fiberoptic laryngoscopy. Bronchoscope, X-Ray Soft Tissue Neck and CT Scan, Complications like glottic edema, vocal tears, vocal granuhmas and tracheal stenosis were seen and were accordingly managed.

Functional properties and epitope characteristics of T-cells recognizing natural HIV-1 variants

To understand how broad recognition of HIV-1 variants may be achieved we examined T-cell reactivity in newly infected persons as well as vaccine recipients to a broad spectrum of potential T-cell epitope (PTE) variants containing conservative, semi-conservative and non-conservative amino acid substitutions. Among early infected persons T-cells recognized epitope variants with one substitution at a significantly higher frequency versus those with two (P=0.0098) and three (P=0.0125) substitutions. Furthermore T-cells recognized variants containing conservative substitutions at a higher frequency versus those containing semi-conservative (P=0.0029) and non-conservative (P<0.0001) substitutions. Similar effects were observed on recognition of variants by vaccine-induced T-cells. Moreover even when variants were recognized, the IFN-gamma and granzyme B responses as well as T-cell proliferation were of lower magnitude. Finally, we show that epitope distribution is strongly influenced by both processing preferences and amino acid entropy. We conclude that induction of broad immunity is likely to require immunogen sequences that encompass multiple variants. However, cost-effective design of peptide and sequence based vaccine immunogens that provide maximal coverage of circulating sequences may be achieved through emphasis on virus domains likely to be T-cell targets.

T Cell Receptor β Gene Polymorphism and Rheumatoid Arthritis

Susceptibility to rheumatoid arthritis is, in part, conferred by genetic factors. Previous studies have suggested that inheritance of a particular allele of a restriction fragment length polymorphism (RFLP) detected in the T cell receptor beta (TCR beta) gene complex is associated with rheumatoid arthritis (RA). We have specifically tested this hypothesis in ethnically and geographically matched populations of RA patients and controls. We were unable to confirm previous observations of a TCR beta association with RA even after stratifying our study and control populations by HLA type.

Enhanced detection of human immunodeficiency virus type 1 (HIV-1) Nef-specific T cells recognizing multiple variants in early HIV-1 infection

A human immunodeficiency virus (HIV)-preventive vaccine will likely need to induce broad immunity that can recognize antigens expressed within circulating strains. To understand the potentially relevant responses that T-cell based vaccines should elicit, we examined the ability of T cells from early infected persons to recognize a broad spectrum of potential T-cell epitopes (PTE) expressed by the products encoded by the HIV type 1 (HIV-1) nef gene, which is commonly included in candidate vaccines. T cells were evaluated for gamma interferon (IFN-gamma) secretion using two peptide panels: subtype B consensus (CON) peptides and a novel peptide panel providing 70% coverage of PTE in subtype B HIV-1 Nef. Eighteen of 23 subjects' T cells recognized HIV-1 Nef. In one subject, Nef-specific T cells were detected with the PTE but not with the CON peptides. The greatest frequency of responses spanned Nef amino acids 65 to 103 and 113 to 147, with multiple epitope variants being recognized. Detection of both the epitope domain number and the response magnitude was enhanced using the PTE peptides. On average, we detected 2.7 epitope domains with the PTE peptides versus 1.7 domains with the CON peptides (P = 0.0034). The average response magnitude was 2,169 spot-forming cells (SFC)/10(6) peripheral blood mononuclear cells (PBMC) with the PTE peptides versus 1,010 SFC/10(6) PBMC with CON peptides (P = 0.0046). During early HIV-1 infection, Nef-specific T cells capable of recognizing multiple variants are commonly induced, and these responses are readily detected with the PTE peptide panel. Our findings suggest that Nef responses induced by a given vaccine strain before HIV-1 exposure may be sufficiently broad to recognize most variants within subtype B HIV-1.

Comprehensive epitope analysis of cross-clade Gag-specific T-cell responses in individuals with early HIV-1 infection in the US epidemic

To elucidate the mechanisms underlying cross-clade T-cell reactivity, we evaluated responses to Gag peptides based on clades A, B, C, and M-group sequences at the epitope level by IFN-gamma ELISpot assay in 25 subjects following primary clade B infection. T-cell reactivity to CON (consensus), COT (center of tree), and ANC (most recent common ancestor) B peptides was similar and a high level of cross-reactivity was noted to clade A, C, and M-group peptides. T-cell responses to 15 of the 16 epitopes reacted with at least 1 of the 2 heterologous peptides (A or C or both) and 7 epitopes were invariant across all 3 clades. The remaining 9 epitopes were associated with a total of 11 variant sequences, and with the exception of 1, all substitutions were outside the HLA anchor positions. We conclude that Gag-specific cross-clade T-cell responses producing IFN-gamma can be detected in primary HIV-1 infection. Cross-reactivity is attributable to the recognized epitopes being either invariant across clades or differing by single amino acid substitutions outside the HLA anchor sites. Semi-conservative and non-conservative substitutions that presumably involve the T-cell receptor contact sites have significant effects on T-cell recognition. Finally, further studies are needed to determine if the detection of cross-clade IFN-gamma T-cell responses indeed translates to cross-reactive antiviral activity.

Peptide selection for human immunodeficiency virus type 1 CTL-based vaccine evaluation

Dozens of human immunodeficiency virus-type 1 (HIV-1) vaccine candidates specifically designed to elicit cytotoxic T-lymphocyte (CTL) responses have entered the pipeline of clinical trials. Evaluating the immunogenicity and potential efficacy of these HIV-1 vaccine candidates is challenging in the face of the extensive viral genetic diversity of circulating strains. Standardized peptide reagents to define the magnitude and potential breadth of the T-cell response, especially to circulating strains of HIV-1, are needed. For this purpose we developed a biometric approach based on T-cell recognition pattern for defining standardized reagents. Circulating strains in the Los Alamos database were evaluated and standardized algorithms to define all potential T-cell epitopes (PTEs) were generated. While many unique PTEs could be identified, a finite number based upon prevalence of circulating strains in the database, which we define as vaccine-important PTEs (VIPs), were used to select a common standardized panel of HIV-1 peptides for CTL-based vaccine evaluation. The usability of PTE peptide set was manifested by detection of Nef-specific CTL responses in HIV-1 subtype B infections.

Transcription factor NFkB a potential molecular marker for predicting and improving treatment efficacy in esophageal cancer

10065

Background: Esophageal/gastroesophageal junction adenocarcinoma (E/GEJAC) remains one of the most aggressive malignancies. Chemoradiotherapy (CTXRT) followed by surgery has been used for localized E/GEJAC. Patients (pts) achieving pathologic complete response (pathCR) have an improved survival, but ≈70% of pts exhibit at surgery resistant residual, highly aggressive tumors despite CTXRT. There is a need to identify this high-risk population and target molecular pathways associated with cancer resistance. We have shown that nuclear NFκB was associated with poor clinical outcome of E/GEJAC pts undergoing 5FU, Docetaxel and Cisplatinum therapy. To validate our findings, we examined the impact of nuclear NFκB on clinical outcome of pts undergoing diverse CTXRT regimens. Methods: Pre- treatment tumor biopsies and post-treatment resected residual tumors were analyzed from pts receiving neo-adjuvant CT or CTXRT. NFκB protein expression was assessed by immunochemistry and correlated to pathCR and clinical outcome. Tumors were considered NFκB positive (pos) when ≥5% of cells expressed nuclear NFκB. Results: 80 pts, clinically staged II, III and IVA, were studied. All pts received antifolates, and 80%, 65% & 31% received taxanes, topo-1 inhibitors and/or platinum analogues, respectively. Radiation therapy was 50.4 Gy at 1.8 Gy once a day to all pts. 75/80 pts had available pre-treatment biopsies, all 58 pts with <pathCR had available residual tumors. Pre-treatment NFκB was predictive for lack of response to CTXRT [NFκB pos: 2/22 pathCR vs 27/53 <pathCR; P=.006]. In multivariate analysis, including clinical stage, tumor histology, pathCR and lymph nodes metastasis, pre-treatment NFκB was an independent prognostic factor of progression-free (P=.0029, HR=2.90, 95%CI:1.44–5.86) and overall (P=.0073,HR=2.70, 95%CI:1.30–5.60) survivals. NFκB was associated with recurrent disease [pre-treatment NFκB pos 14/29 (48%) vs NFκB negative11/46 (24%), P=.04; pre- or post- NFκB pos 22/47 (47%) vs NFκB neg 4/33 (12%), P=.003]. Conclusions: our data suggest that NFκB defines cancer biology and patterns to therapy response irrespective of the type of chemoradiation used. NFκB may serve as potential molecular target to improve treatment efficacy.

No significant financial relationships to disclose.

Abacavir hypersensitivity reaction in primary HIV infection

OBJECTIVE

To evaluate risk factors associated with the abacavir hypersensitivity reaction during primary HIV infection (PHI).

DESIGN

Acute HIV Infection and Early Disease Research Program protocol (AIEDRP) AI-02-001 provided antiretroviral therapy including abacavir. This retrospective analysis evaluated variables potentially associated with hypersensitivity in the cohort enrolled in AI-02-001 at the University of Washington Primary Infection Clinic.

METHODS

Cases of suspected hypersensitivity were identified prospectively and reviewed retrospectively using a standardized case definition. Controls were the remaining cohort without hypersensitivity. Univariate analyses were performed by linear logistic regression.

RESULTS

Nine (18%) of 50 individuals treated with abacavir developed suspected hypersensitivity. Two of nine cases and no controls were HLA-B5701 positive. When antiretroviral medications were started, cases had lower mean CD8 T-cell percentage and plasma HIV RNA value. After 2 weeks on abacavir, cases had a lower mean HIV RNA value and a trend towards greater decrease in RNA. Cases began abacavir a median of 103 days after HIV acquisition compared to 48 days for controls. There was no significant in vitro abacavir-specific lymphoproliferation or IFN-gamma production in peripheral blood mononuclear cells from individuals following the suspected hypersensitivity reaction.

CONCLUSIONS

Abacavir use during PHI may be associated with increased risk of hypersensitivity. As in chronic infection, HLA-B5701 is associated with the abacavir hypersensitivity reaction in PHI. Although levels of CD8 T cells and HIV RNA may be risk factors for hypersensitivity, the observed association may be due to correlation with HLA-B5701. The interesting temporal association of hypersensitivity with initiation of abacavir later in PHI merits future investigation.

CD4+ T cell receptor repertoire perturbations in HIV-1 infection: association with plasma viremia and disease progression

CD4+ T cell depletion and dysfunction are the hallmark of HIV-1 disease. Our primary objectives were to define the diversity of the CD4+ T cell receptor Vbeta (TCRBV) repertoire in subjects with HIV-1 infection by CDR3 (complementarity-determining region) length spectratyping and to determine the correlates of CD4+ repertoire perturbation and its restoration with virus suppression. During primary HIV-1 infection, the proportion of perturbed CD4+ TCRBV subfamilies was significantly greater compared to HIV-1 seronegative subjects (median 48% vs. 10%, P = 0.0159). During chronic infection, the extent of repertoire perturbation was significantly associated with higher levels of plasma viremia (Spearman Correlation coefficient, R = 0.65, P = 0.049) and disease progression. Restoration of the repertoire with antiretroviral therapy was variable despite adequate virologic suppression. We speculate that the use of immunomodulators as an adjunct to antiretroviral drugs may enhance immune reconstitution in persons with suboptimal increases in CD4+ T cell counts despite adequate virus suppression.

Effect of adjunct hydroxyurea on helper T cell immunity in HIV type 1-infected patients with virological suppression

Hydroxyurea (HU) has preferential activity in virus reservoirs not effectively targeted by current antiretroviral drug regimens, but concern for potential toxicity has precluded its routine use. The effect of adjunct HU on T cell proliferative responses and phenotypic markers was examined in a randomized study of 39 chronically HIV-1-infected patients with virological suppression on potent antiretroviral therapy. While patients in the HU arm showed modest declines in the median CD4(+) T cell counts (total, -151 cells/mm(3); naive, -91 cells/mm(3)), no significant differences were noted in the Candida, HIV-1 p24, and HIV-1 gp160 responses between the treatment arms following 24 weeks of therapy. In conclusion, although adjunct HU was associated with modest declines in the CD4(+) T cell counts, there was no significant adverse effect on helper T cell function. Further trials to address the role of HU in HIV-1 treatment may be appropriate after careful selection of HU dose and the adjunct drugs to avoid nonhematological toxicity.

HIV-1-infected patients with envelope-specific lymphoproliferation or long-term nonprogression lack antibodies suppressing glycoprotein 120 antigen presentation

BACKGROUND

Antibodies to the CD4-binding domain (CD4bd) of human immunodeficiency virus type 1 (HIV-1) glycoprotein 120 (gp120) inhibit gp120 antigen presentation to CD4 T cells. These findings imply that the presence of anti-CD4bd antibodies might contribute to the dearth of envelope-specific T helper responses observed in most HIV-1-positive patients. In the absence of these antibodies, however, anti-envelope T helper responses might be maintained.

METHODS

We used ELISA to evaluate the levels of anti-CD4bd antibodies in rare HIV-1-positive patients who exhibit envelope-specific lymphoproliferation. Subsequently, we examined the contribution of anti-CD4bd antibodies to disease progression by comparing anti-CD4bd antibody levels in 3 cohorts of HIV-1-positive patients with distinct rates of disease progression.

RESULTS

Although most HIV-1-positive individuals produce anti-CD4bd antibodies, 77% of patients with envelope-specific lymphoproliferation have undetectable anti-CD4bd antibody levels. Moreover, comparison of the 3 HIV-1-positive cohorts revealed that individuals with long-term nonprogression have significantly lower anti-CD4bd antibody titers than do those with rapid or slow progression. Unlike immunoglobulin G (IgG) from rapid progressors, IgG from nonprogressors had no suppressive effects on glycoprotein (gp) 120-specific T cell proliferation.

CONCLUSIONS

Low anti-CD4bd antibody levels are associated with the absence of disease progression. A number of HIV-1-positive individuals without these antibodies also appear to sustain gp120-specific T helper responses needed to help control the infection.

Association of T cell proliferative responses and phenotype with virus control in chronic progressive HIV-1 disease

The role of T cell immunity in virus control during chronic infection was examined in 79 human immunodeficiency virus type 1 (HIV-1)-infected subjects randomized to receive antiretroviral therapy. HIV-1 p24-specific responses were detected in 20% of the subjects at baseline, increasing to 28% of the subjects at weeks 16-24. Induction of virologic suppression was associated with lower plasma HIV-1 RNA levels and a higher percentage of Fas+ CD8+ T cells at baseline, whereas maintenance of suppression was associated with higher CD4+ T cell counts and, marginally, with a higher percentage of Fas+ CD4+ T cells at weeks 16-24. These findings indicate that Fas coexpression on T cells, in addition to plasma HIV-1 RNA levels and CD4+ T cell counts, may predict virologic outcome.

Evolution of CD8+ T cell immunity and viral escape following acute HIV-1 infection

Induction of HIV-1-specific CD8(+) T cells during acute infection is associated with a decline in viremia. The role CD8(+) effectors play in subsequently establishing viral set point remains unclear. To address this, we focused on two acutely infected patients with the same initial Tat-specific CD8(+) response, analyzing their CD8(+) T cell responses longitudinally in conjunction with viral load and sequence evolution. In one patient initiating treatment during acute infection, the frequencies of Tat-specific CD8(+) T cells gradually diminished but persisted, and the Tat epitope sequence was unaltered. By contrast, in the second patient who declined treatment, the Tat-specific CD8(+) T cells disappeared below detection, in conjunction with Gag-specific CD4(+) T cell loss, as plasma viremia reached a set point. This coincided with the emergence of an escape variant within the Tat epitope and an additional Vpr epitope. New CD8(+) T cell responses emerged but with no further associated decline in viremia. These findings indicate that, in the absence of treatment, the initial CD8(+) T cell responses have the greatest impact on reducing viremia, and that later, continuously evolving responses are less efficient in further reducing viral load. The results also suggest that T cell help may contribute to the antiviral efficiency of the acute CD8(+) T cell response.

Early induction and maintenance of Env-specific T-helper cells following human immunodeficiency virus type 1 infection

Mounting evidence points to a role for CD4+ T-helper (Th) cell activities in controlling human immunodeficiency virus type 1 (HIV-1) infection. To determine the induction and evolution of Th responses following acute infection, we prospectively analyzed Env- and Gag-specific Th responses longitudinally for 92 patients with acute (n = 28) or early (n = 64) HIV-1 infection (median, 55 days postinfection [DPI]). The probability of detecting HIV-1-specific lymphoproliferative responses was remarkably low, and when present, the responses were more likely to be Gag specific than Env specific (16 versus 5%). Env-specific responses were significantly more common in patients presenting at <30 DPI than in those presenting at 30 to 365 DPI (21 versus 0.5%, P = 0.001). By contrast, Gag-specific responses occurred with similar frequencies among subjects presenting at <30 DPI and 30 to 365 DPI (13 versus 17%, P = 0.6). After treatment, and regardless of the duration of infection before therapy, Gag-specific Th responses predominated. Furthermore, some acutely infected subjects lost detectable Env-specific Th proliferative responses, which failed to reemerge upon treatment. Detailed analysis for one such subject revealed Env-specific lymphoproliferation at 11 DPI but no detectable Env-specific lymphoproliferation or ex vivo gamma interferon (IFN-gamma) secretion at multiple subsequent time points. Env-specific CD4+ T-cell clones from 11 DPI recognized six epitopes in both conserved and variable regions within gp120 and gp41, exhibited major histocompatibility complex-restricted cytotoxicity, and secreted high levels of antiviral cytokines. T-cell receptor clonal transcript analyses and autologous virus sequencing revealed that Th cells induced during acute infection were maintained and there were no Th escape mutations. Subsequent analysis for this subject and six of seven others revealed detectable IFN-gamma-secreting cells, but only following in vitro gp160 stimulation. In summary, we conclude that Env-specific Th responses are elicited very early in acute infection and may precede Gag-specific responses. The inability to detect Env-specific Th responses over time and despite antiretroviral therapy may reflect low frequencies and impaired proliferative capacity, and viral escape is not necessary for this to occur.

Pneumonia and sepsis due to fluoroquinolone-resistant Capnocytophaga gingivalis after autologous stem cell transplantation

Human oral Capnocytophaga species have been only rarely described as a cause of sepsis in patients following stem cell or marrow transplantation, and pneumonia has not been reported in this setting. In addition, fluoroquinolone resistance is rarely seen in these species, and has never been reported in C. gingivalis. We report a case of pneumonia (confirmed by culture of bronchoalveolar lavage fluid) and sepsis due to fluoroquinolone- resistant Capnocytophaga gingivalis in a patient following autologous stem cell transplantation, who responded to treatment with linezolid and metronidazole. Capnocytophaga infections should be considered in patients with fever following stem cell or marrow transplantation, especially those with neutropenia and mucositis. Susceptibility testing is needed given the existence of multidrug-resistant isolates.

Role for HLA class II molecules in HIV-1 suppression and cellular immunity following antiretroviral treatment

HIV-1-infected patients treated early with combination antiretrovirals respond favorably, but not all maintain viral suppression and improved HIV-specific Th function. To understand if genetic factors contribute to this variation, we prospectively evaluated over 18 months 21 early-treated patients stratified by alleles of class II haplotypes. All seven subjects with the DRB1*13-DQB1*06 haplotype, but only 21% of other subjects, maintained virus suppression at every posttreatment measurement. Following HIV-1 p24 antigen stimulation, PBMCs from patients with this haplotype demonstrated higher mean lymphoproliferation and IFN-gamma secretion than did cells from patients with other haplotypes. Two DRB1*13-restricted Gag epitope regions were identified, a promiscuous one that bound its putative restriction element with nanomolar affinity, and another that mapped to a highly conserved region. These findings suggest that class II molecules, particularly the DRB1*13 haplotype, have an important impact on virologic and immunologic responses. The advantage of the haplotype may relate to selection of key HIV-1 Th1 epitopes in highly conserved regions with avid binding to class II molecules. Eliciting responses to the promiscuous epitope region may be beneficial in vaccine strategies.

Effect of combination antiretroviral therapy on T-cell immunity in acute human immunodeficiency virus type 1 infection

T-cell responses were evaluated prospectively in 41 patients with acute human immunodeficiency virus type 1 (HIV-1) infection (30 untreated and 11 receiving zidovudine, lamivudine, and indinavir) and in 38 uninfected adults. By 6-12 months, treated patients had significantly greater median Candida and tetanus lymphoproliferative responses (stimulation index [SI], 76 and 55, respectively) than did untreated patients (SI, 7 and 6, P=.02 and.001, respectively), and the responses of treated patients surpassed those of uninfected adults (SI, 19 and 32, P= .002 and .101, respectively). Unlike the patients in the untreated group, the patients in the treated group mounted a 6-fold increased HIV-1 p24 response (SI increase, 1.0 to 5.7, P= .01) within 3 months. HIV-1-specific cytotoxicity remained detectable in most treated patients. Thus, combination therapy administered within 3-4 months of infection was associated with improved T-cell memory responses that were distinct from those of untreated patients. The amplified HIV-1-specific T-cell responses may help maintain cytotoxic activities.

Variability in T cell receptor V beta gene usage in human peripheral blood lymphocytes. Studies of identical twins, siblings, and insulin-dependent diabetes mellitus patients

Recent studies focused on the diversity and molecular organization of the human TCR-beta complex have begun to establish the genetic basis for the potential repertoire of V beta specificities in T cells. The scope and variability of the actual repertoire derived from this potential repertoire, however, remains to be clarified. In this study, V beta usage by human peripheral T cells derived from serial samples of the same individual, identical twins, and the members of three nuclear families that include four members with insulin-dependent diabetes mellitus (IDDM) was assessed by both quantitative polymerase chain reaction and Northern blotting with V beta subfamily-specific probes. Samples taken from the same individual over a period of 21 months and analyzed in separate experiments indicated stability in the peripheral repertoire, whereas the similarity in peripheral V beta usage in a pair of identical twins suggested a strong role for genetics in shaping the peripheral T cell repertoire. In contrast, V beta usage in siblings and in unrelated individuals was observed to differ substantially. In particular, peripheral expression of V beta 3 and V beta 20 differed by more than sixfold among members of two different families. Segregation analysis of TCR and HLA haplotypes in these families suggested that variation in V beta 20 expression was TCR haplotype specific. Subsequent nucleotide sequence analysis of the V beta 20 gene segment in multiple members of these families revealed the presence of a null allele for V beta 20 expression. No consistent significant differences in V beta usage were observed in IDDM patients relative to their siblings or between identical twins discordant for IDDM. These results suggest that the repertoire of peripheral T cell specificities present in different individuals in human populations varies dramatically because of the effects of multiple factors, including TCR germ-line polymorphism.

Variability in T cell receptor V beta gene usage in human peripheral blood lymphocytes. Studies of identical twins, siblings, and insulin-dependent diabetes mellitus patients

Recent studies focused on the diversity and molecular organization of the human TCR-beta complex have begun to establish the genetic basis for the potential repertoire of V beta specificities in T cells. The scope and variability of the actual repertoire derived from this potential repertoire, however, remains to be clarified. In this study, V beta usage by human peripheral T cells derived from serial samples of the same individual, identical twins, and the members of three nuclear families that include four members with insulin-dependent diabetes mellitus (IDDM) was assessed by both quantitative polymerase chain reaction and Northern blotting with V beta subfamily-specific probes. Samples taken from the same individual over a period of 21 months and analyzed in separate experiments indicated stability in the peripheral repertoire, whereas the similarity in peripheral V beta usage in a pair of identical twins suggested a strong role for genetics in shaping the peripheral T cell repertoire. In contrast, V beta usage in siblings and in unrelated individuals was observed to differ substantially. In particular, peripheral expression of V beta 3 and V beta 20 differed by more than sixfold among members of two different families. Segregation analysis of TCR and HLA haplotypes in these families suggested that variation in V beta 20 expression was TCR haplotype specific. Subsequent nucleotide sequence analysis of the V beta 20 gene segment in multiple members of these families revealed the presence of a null allele for V beta 20 expression. No consistent significant differences in V beta usage were observed in IDDM patients relative to their siblings or between identical twins discordant for IDDM. These results suggest that the repertoire of peripheral T cell specificities present in different individuals in human populations varies dramatically because of the effects of multiple factors, including TCR germ-line polymorphism.

HLA and T cell receptor polymorphisms in pauciarticular-onset juvenile rheumatoid arthritis

The immunogenetic basis of pauciarticular-onset juvenile rheumatoid arthritis is unclear. We therefore analyzed the HLA and T cell receptor genes present in a clinically well-defined group of patients. We found that the DR8 haplotype contributes most of the HLA-associated risk, although alleles at other loci contribute independently. A candidate disease-associated T cell receptor polymorphism, in contrast, was not identified in this population. Mechanistic implications of these findings are discussed.

Further mapping of an ataxia-telangiectasia locus to the chromosome 11q23 region

We recently mapped the gene for ataxia-telangiectasia group A (ATA) to chromosome 11q22-23 by linkage analysis, using the genetic markers THY1 and pYNB3.12 (D11S144). The most likely order was cent-AT-S144-THY1. The present paper describes further mapping of the AT locus by means of a panel of 10 markers that span approximately 60 cM in the 11q22-23 region centered around S144 and THY1. Location scores indicate that three contiguous subsegments within the [S144-THY1] segment, as well as three contiguous segments telomeric to THY1, are each unlikely to contain the AT locus, while the more centromeric [STMY-S144] segment is most likely to contain the AT locus. These data, together with recent refinements in the linkage and physical maps of 11q22-23, place the AT locus at 11q23.

The ataxia-telangiectasia gene (ATA) on chromosome II is distinct from the ETS-1 gene

We have studied the segregation of an RFLP detected with a human ETS-1 genomic probe in 25 families containing members affected with ataxia-telangiectasia (AT) and in 27 families from the Centre d'Etude du Polymorphisme Humain (CEPH) panel. We have recently mapped a gene for AT to 11q22-23 by linkage to the markers THY1 and D11S144. Multipoint linkage analysis of the CEPH families indicated that ETS-1 is located on chromosome 11q approximately 19.2 centimorgans telomeric to THY1. Analysis of the segregation of ETS-1 alleles in AT families yields strongly negative LOD scores, excluding an AT gene from a region extending 15 cM to either side of ETS-1. Multipoint mapping of ETS-1, D11S144, THY1, and AT also excludes the possibility that an AT gene is telomeric to ETS-1.

An anonymous marker [HGM provisional #D11S415] maps to human chromosome 11 near the catalase (CAT) gene

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