An immunogenetic basis for lung cancer risk

Cancer risk is influenced by inherited mutations, DNA replication errors, and environmental factors. However, the influence of genetic variation in immunosurveillance on cancer risk is not well understood. Leveraging population-level data from the UK Biobank and FinnGen, we show that heterozygosity at the human leukocyte antigen (HLA)-II loci is associated with reduced lung cancer risk in smokers. Fine-mapping implicated amino acid heterozygosity in the HLA-II peptide binding groove in reduced lung cancer risk, and single-cell analyses showed that smoking drives enrichment of proinflammatory lung macrophages and HLA-II+ epithelial cells. In lung cancer, widespread loss of HLA-II heterozygosity (LOH) favored loss of alleles with larger neopeptide repertoires. Thus, our findings nominate genetic variation in immunosurveillance as a critical risk factor for lung cancer.

Structural insights into the modulation of coronavirus spike tilting and infectivity by hinge glycans

Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectrometry. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a role of hinge glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays implicated involvement of N1242-glyan in virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.

High-resolution structures with bound Mn2+ and Cd2+ map the metal import pathway in an Nramp transporter

Transporters of the Nramp (Natural resistance-associated macrophage protein) family import divalent transition metal ions into cells of most organisms. By supporting metal homeostasis, Nramps prevent diseases and disorders related to metal insufficiency or overload. Previous studies revealed that Nramps take on a LeuT fold and identified the metal-binding site. We present high-resolution structures of Deinococcus radiodurans (Dra)Nramp in three stable conformations of the transport cycle revealing that global conformational changes are supported by distinct coordination geometries of its physiological substrate, Mn²⁺, across conformations, and by conserved networks of polar residues lining the inner and outer gates. In addition, a high-resolution Cd²⁺-bound structure highlights differences in how Cd²⁺ and Mn²⁺ are coordinated by DraNramp. Complementary metal binding studies using isothermal titration calorimetry with a series of mutated DraNramp proteins indicate that the thermodynamic landscape for binding and transporting physiological metals like Mn²⁺ is different and more robust to perturbation than for transporting the toxic Cd²⁺ metal. Overall, the affinity measurements and high-resolution structural information on metal substrate binding provide a foundation for understanding the substrate selectivity of essential metal ion transporters like Nramps.

Abstract 5376: Protein structure-based modeling to improve MHC class I epitope predictions

The ability to accurately identify peptide ligands for a given major histocompatibility complex class I (MHC-I) molecule has immense value for targeted anticancer therapeutics. However, the highly polymorphic nature of the MHC-I protein makes universal prediction of peptide ligands challenging due to lack of experimental data describing most MHC-I variants. To address this challenge, we have developed a deep convolutional neural network, HLA-Inception, capable of predicting MHC-I peptide binding motifs using electrostatic properties of the MHC-I binding pocket. By approaching this immunological issue using molecular biophysics, we measure the impact of sidechain arrangement and topology on peptide binding, feature not captured by sequence-based MHC-I prediction methods. Through a combination of molecular modeling and simulation, 5821 MHC-I alleles were modeled, providing extensive coverage across human populations. Predicted peptide binding motifs fell into distinct clusters, each defined with different degrees of submotif heterogeneity. Peptide binding scores generated by HLA-Inception are strongly correlated with quantitative MHC-I binding data, indicating predicted peptides can be ranked, both within and between alleles. HLA-inception also showed high precision when predicting naturally presented peptides and can be used for rapid proteome-scale MHC-I peptide binding predictions. Finally, we show that the binding pocket diversity measured by HLA inception predicts response to checkpoint blockade.

Citation Format: Eric A. Wilson, John Kevin Cava, Diego Chowell, Abhishek Singharoy, Karen S. Anderson. Protein structure-based modeling to improve MHC class I epitope predictions. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5376.

Integrated analyses reveal a hinge glycan regulates coronavirus spike tilting and virus infectivity

Coronavirus spike glycoproteins presented on the virion surface mediate receptor binding, and membrane fusion during virus entry and constitute the primary target for vaccine and drug development. How the structure dynamics of the full-length spikes incorporated in viral lipid envelope correlates with the virus infectivity remains poorly understood. Here we present structures and distributions of native spike conformations on vitrified human coronavirus NL63 (HCoV-NL63) virions without chemical fixation by cryogenic electron tomography (cryoET) and subtomogram averaging, along with site-specific glycan composition and occupancy determined by mass spectroscopy. The higher oligomannose glycan shield on HCoV-NL63 spikes than on SARS-CoV-2 spikes correlates with stronger immune evasion of HCoV-NL63. Incorporation of cryoET-derived native spike conformations into all-atom molecular dynamic simulations elucidate the conformational landscape of the glycosylated, full-length spike that reveals a novel role of stalk glycans in modulating spike bending. We show that glycosylation at N1242 at the upper portion of the stalk is responsible for the extensive orientational freedom of the spike crown. Subsequent infectivity assays support the hypothesis that this glycan-dependent motion impacts virus entry. Our results suggest a potential therapeutic target site for HCoV-NL63.

Histology education in an integrated, time-restricted medical curriculum: Academic outcomes and students' study adaptations

In an ever-changing medical curricular environment, time dedicated for anatomical education has been progressively reduced. This happened at the University of Michigan Medical School starting in 2016-2017 when preclinical medical education was condensed to one year. Histology instruction remained integrated in organ system courses but reduced to a lecture-only format without scheduling time for laboratory exercises, requiring students to study virtual histology slides on their own time. In accordance with the shortened instructional time, the number of histology examination questions was reduced more than twofold. This study analyzed students' histology examination results and assessed their motivation to learn histology and use of educational opportunities before and after these curricular changes were implemented. Students' motivation to learn histology and their evaluation of histology lectures increased in the new curriculum. However, students devoted less study time to studying histology. Students' cumulative histology examination scores were significantly lower in the new curriculum and the number of students with overall scores <75%, defined as a substandard performance, increased more than 15-fold. Academically weaker students' histology scores were disproportionately more affected. As medical educational strategies, priorities, and curricular frameworks continue to evolve, traditional didactic topics like histology will need to adapt to continue providing educational value to future health care providers.

Identifying highly conserved and immunogenic SARS-CoV-2 CD8+ T Cell Epitopes for Vaccine Design

Vaccines to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) induce antibody responses against the spike (S) protein. However, the continued emergence of variants such as Omicron (B.1.1.529), with 30 amino acid changes in the S protein, underscores the need to find conserved targets that induce adaptive immunity. Natural infection induces CD8+ T cell activation against the viral proteins S, membrane (M), and nucleocapsid (N) as well as NSPs (non-structural proteins). Our study seeks to find conserved and immunogenic MHC class I epitopes throughout the SARS-CoV-2 peptidome. We used Ensemble MHC, a novel consensus predictive algorithm to select highly immunogenic CD8+ T cell epitopes presented by 52 of the most common HLA-I alleles, covering &gt; 98% of the world’s population. We selected 658 high confidence predicted peptides from the SARS-CoV-2 immunopeptidome and prioritized testing 108 structural epitopes derived from the S, M, N, and E proteins. We collected PBMCs from unexposed, healthy, and convalescent individuals (n=31) covering ~ 85% of HLA alleles in the population, and measured T cell immunity by IFNγ secretion ELISpot and Activation Induced Marker (AIM) flow cytometry. In convalescent individuals, all predicted epitopes tested so far (n=36) were immunogenic (IFNγ response &gt;2 fold than background) but 3/19 tested donors were unreactive. Samples from pre-pandemic (2017–19) unexposed healthy donors are reactive to 42% of tested epitopes, which indicate cross-reactivity to common cold coronaviruses (CCC) and possibly pre-existing protection against SARS-CoV-2. In summary, we have identified 45 highly conserved and immunogenic SARS-CoV-2 CD8+ T cell epitopes as potential targets for vaccine design.

Supported by a grant from the Arizona Department of Health Services (AZDHS)

HLA-Inception: A structure-based deep learning framework for MHC-I binding motif prediction

The ability to accurately identify peptide ligands for a given major histocompatibility complex class I (MHC-I) molecule has immense value for targeted anticancer and antiviral therapeutics. However, the highly polymorphic nature of the MHC-I protein makes universal prediction of peptide ligands challenging due to lack of experimental data describing most MHC-I variants, and the vast number of protein variants precludes comprehensive experimental determination. Therefore, there is a need for a framework to cluster MHC-I alleles to prioritize for experimental validation as well as identify alleles with potential disease associations.

To address this challenge, we have developed a deep convolutional neural network, HLA-Inception, capable of predicting MHC-I peptide binding motif using data derived from the structure of the MHC-I binding pocket. By approaching this problem from a 3-dimensional perspective, we can fully consider the impact of sidechain arrangement and topology of the MHC-I binding pocket on peptide binding motif, which is not inherently captured by the popular protein sequence-based approaches. Through a combination of homology modeling and biophysical simulations, we created protein structure models for all full-length HLA-ABC alleles. The topology and interaction forces within the MHC-I binding pocket were accounted for by solving the 3-dimensional electrostatic potential near the surface of the protein. HLA-Inception was then trained on all MHC-I alleles with known MHC-I binding motifs and applied to the full set of MHC-I models. We found that predicted peptide binding motifs fell into distinct and well-defined clusters which maintained known peptide binding and disease associations.

Utility of a Telephone Triage Hotline in Response to the COVID-19 Pandemic: Longitudinal Observational Study

Background

During the initial months of the COVID-19 pandemic, rapidly rising disease prevalence in the United States created a demand for patient-facing information exchanges that addressed questions and concerns about the disease. One approach to managing increased patient volumes during a pandemic involves the implementation of telephone-based triage systems. During a pandemic, telephone triage hotlines can be employed in innovative ways to conserve medical resources and offer useful population-level data about disease symptomatology and risk factor profiles.

Objective

The aim of this study is to describe and evaluate the COVID-19 telephone triage hotline used by a large academic medical center in the midwestern United States.

Methods

Michigan Medicine established a telephone hotline to triage inbound patient calls related to COVID-19. For calls received between March 24, 2020, and May 5, 2020, we described total call volume, data reported by callers including COVID-19 risk factors and symptomatology, and distribution of callers to triage algorithm endpoints. We also described symptomatology reported by callers who were directed to the institutional patient portal (online medical visit questionnaire).

Results

A total of 3929 calls (average 91 calls per day) were received by the call center during the study period. The maximum total number of daily calls peaked at 211 on March 24, 2020. Call volumes were the highest from 6 AM to 11 AM and during evening hours. Callers were most often directed to the online patient portal (1654/3929, 42%), nursing hotlines (1338/3929, 34%), or employee health services (709/3929, 18%). Cough (126/370 of callers, 34%), shortness of breath (101/370, 27%), upper respiratory infection (28/111, 25%), and fever (89/370, 24%) were the most commonly reported symptoms. Immunocompromised state (23/370, 6%) and age >65 years (18/370, 5%) were the most commonly reported risk factors.

Conclusions

The triage algorithm successfully diverted low-risk patients to suitable algorithm endpoints, while directing high-risk patients onward for immediate assessment. Data collected from hotline calls also enhanced knowledge of symptoms and risk factors that typified community members, demonstrating that pandemic hotlines can aid in the clinical characterization of novel diseases.

Total predicted MHC-I epitope load is inversely associated with population mortality from SARS-CoV-2

Polymorphisms in MHC-I protein sequences across human populations significantly affect viral peptide binding capacity, and thus alter T cell immunity to infection. In the present study, we assess the relationship between observed SARS-CoV-2 population mortality and the predicted viral binding capacities of 52 common MHC-I alleles. Potential SARS-CoV-2 MHC-I peptides are identified using a consensus MHC-I binding and presentation prediction algorithm called EnsembleMHC. Starting with nearly 3.5 million candidates, we resolve a few hundred highly probable MHC-I peptides. By weighing individual MHC allele-specific SARS-CoV-2 binding capacity with population frequency in 23 countries, we discover a strong inverse correlation between predicted population SARS-CoV-2 peptide binding capacity and mortality rate. Our computations reveal that peptides derived from the structural proteins of the virus produce a stronger association with observed mortality rate, highlighting the importance of S, N, M, and E proteins in driving productive immune responses.

Gqα/G11α deficiency in dorsomedial hypothalamus leads to obesity resulting from decreased energy expenditure and impaired sympathetic nerve activity

The G-protein subunits G_qα and G₁₁α (G_q/11α) couple receptors to phospholipase C, leading to increased intracellular calcium. In this study we investigated the consequences of G_q/₁₁α deficiency in the dorsomedial hypothalamus (DMH), a critical site for the control of energy homeostasis. Mice with DMH-specific deletion of G_q/11α (DMHGq/11KO) were generated by stereotaxic injection of adeno-associated virus (AAV)-Cre-green fluorescent protein (GFP) into the DMH of G_qα^flox/flox:G₁₁α^-/- mice. Compared with control mice that received DMH injection of AAV-GFP, DMHGq/11KO mice developed obesity associated with reduced energy expenditure without significant changes in food intake or physical activity. DMHGq/11KO mice showed no defects in the ability of the melanocortin agonist melanotan II to acutely stimulate energy expenditure or to inhibit food intake. At room temperature (22°C), DMHGq/11KO mice showed reduced sympathetic nervous system activity in brown adipose tissue (BAT) and heart, accompanied with decreased basal BAT uncoupling protein 1 (Ucp1) gene expression and lower heart rates. These mice were cold intolerant when acutely exposed to cold (6°C for 5 h) and had decreased cold-stimulated BAT Ucp1 gene expression. DMHGq/11KO mice also failed to adapt to gradually declining ambient temperatures and to develop adipocyte browning in inguinal white adipose tissue although their BAT Ucp1 was proportionally stimulated. Consistent with impaired cold-induced thermogenesis, the onset of obesity in DMHGq/11KO mice was significantly delayed when housed under thermoneutral conditions (30°C). Thus our results show that G_qα and G₁₁α in the DMH are required for the control of energy homeostasis by stimulating energy expenditure and thermoregulation.NEW & NOTEWORTHY This paper demonstrates that signaling within the dorsomedial hypothalamus via the G proteins G_qα and G₁₁α, which couple cell surface receptors to the stimulation of phospholipase C, is critical for regulation of energy expenditure, thermoregulation by brown adipose tissue and the induction of white adipose tissue browning.

A11 Evaluation of phylogenetic inference methods to determine direction of HIV transmission

It has been postulated that the direction of HIV transmission between two individuals can be determined by phylogenetic analysis of HIV sequences. This approach may be problematic, since HIV sequences from newly infected individuals are often more similar to index sequences from samples collected years before transmission, compared to those from samples collected at the time of transmission. We evaluated the accuracy of phylogenetic methods for determining the direction of HIV transmission by analyzing next-generation sequencing (NGS) data from index–partner pairs enrolled in the HIV Prevention Trials Network (HPTN) 052 trial. HIV-infected index and HIV-uninfected partner participants were enrolled as serodiscordant couples; samples were analyzed from couples with index-to-partner HIV transmission that was confirmed by genetic linkage studies. NGS for HIV gp41 (HXB2 coordinates: 7691–8374) was performed using plasma samples from thirty-nine index–partner pairs (seventy-eight samples collected within 3 months of partner seroconversion). Maximum likelihood trees were generated using the entire dataset using FastTree v.2. Topological patterns of HIV from each index–partner pair were analyzed. The analysis included 9,368 consensus sequences and 521,145 total sequence reads for the seventy-eight samples analyzed. In 10 per cent (four out of thirty-nine) of couples, the phylogeny was inconsistent with the known direction of transmission. In 26 per cent (ten out of thirty-nine) of couples, the phylogeny results could not discern directionality. In 64 per cent (twenty-five out of thirty-nine) of couples, the results correctly indicated index-to-partner transmission; in two of these twenty-five cases, only one index sequence was closest to the most recent common ancestor. Phylogenetic analysis of NGS data obtained from samples collected within 3 months of transmission correctly determined the direction of transmission in 64 per cent of the cases analyzed. In 36 per cent of the cases, the phylogenetic topology did not support the known direction of infection, and in one-third of these cases the observed topology was opposite to the known direction of transmission. This demonstrates that phylogenetic topology alone may not be sufficient to accurately determine the direction of HIV transmission.

Gsα deficiency in the dorsomedial hypothalamus leads to obesity, hyperphagia, and reduced thermogenesis associated with impaired leptin signaling

OBJECTIVE

G_sα couples multiple receptors, including the melanocortin 4 receptor (MC4R), to intracellular cAMP generation. Germline inactivating G_sα mutations lead to obesity in humans and mice. Mice with brain-specific G_sα deficiency also develop obesity with reduced energy expenditure and locomotor activity, and impaired adaptive thermogenesis, but the underlying mechanisms remain unclear.

METHODS

We created mice (DMHGsKO) with G_sα deficiency limited to the dorsomedial hypothalamus (DMH) and examined the effects on energy balance and thermogenesis.

RESULTS

DMHGsKO mice developed severe, early-onset obesity associated with hyperphagia and reduced energy expenditure and locomotor activity, along with impaired brown adipose tissue thermogenesis. Studies in mice with loss of MC4R in the DMH suggest that defective DMH MC4R/G_sα signaling contributes to abnormal energy balance but not to abnormal locomotor activity or cold-induced thermogenesis. Instead, DMHGsKO mice had impaired leptin signaling along with increased expression of the leptin signaling inhibitor protein tyrosine phosphatase 1B in the DMH, which likely contributes to the observed hyperphagia and reductions in energy expenditure, locomotor activity, and cold-induced thermogenesis.

CONCLUSIONS

DMH G_sα signaling is critical for energy balance, thermogenesis, and leptin signaling. This study provides insight into how distinct signaling pathways can interact to regulate energy homeostasis and temperature regulation.

Clarifying dairy calf mortality phenotypes through postmortem analysis

Health problems can be thought of as phenotypic expressions of the complex relationships between genes, environments, and phenomes as a whole. Detailed evaluations of phenotypic expressions of illness are required to characterize important biological outcomes. We hypothesized that classifying dairy calf mortality phenotypes via a systematic postmortem analysis would identify different cause-of-death diagnoses than those derived from treatments alone. This cross-sectional study was carried out on a dairy calf ranch in the northwestern United States from June to September 2017 and focused on calves ≤90 d of age. Comparisons were made between causes of death based on 3 levels of information: on-farm treatment records alone, necropsy-based postmortem analyses in addition to treatment records, and Washington Animal Disease Diagnostic Laboratory (WADDL) results in addition to all other information. A total of 210 dairy calves were necropsied during this study, of which 122 cases were submitted to WADDL. Necropsy- and WADDL-derived mortality phenotypes were in almost perfect agreement (Cohen's κ = 0.86) when broadly categorized as diarrhea, respiratory, diarrhea and respiratory combined, or other causes. The level of agreement between on-farm treatment records and postmortem-derived results was low and varied by the level of diagnostic detail provided. There was just fair agreement (κ = 0.22) between treatment-based and necropsy-based phenotypes without WADDL input and only slight agreement (κ = 0.13) between treatment-based and corresponding necropsy-based phenotypes with WADDL input. Even for those cases in which causes of death aligned along a comparable pathologic spectrum, the lack of detail inherent to standard treatment-based causes of death failed to identify meaningful target areas for intervention. This was especially apparent for numerous cases of necrotizing enteritis and typhlitis (cecal inflammation) that were variously categorized as diarrhea and pneumonia by treatment-based diagnoses. The specificity of these lesions stood in stark contrast to the otherwise generic cause of death diagnoses derived from treatments. The findings from this study supported the hypothesis and highlighted the value of on-farm necropsies and laboratory-based diagnostics to (1) detect antemortem disease misclassifications, (2) provide detail regarding disease processes and mortality phenotypes, and (3) direct disease mitigation strategies.

Lost in the crowd: identifying targetable MHC class I neoepitopes for cancer immunotherapy

INTRODUCTION

The recent development of checkpoint blockade immunotherapy for cancer has led to impressive clinical results across multiple tumor types. There is mounting evidence that immune recognition of tumor derived MHC class I (MHC-I) restricted epitopes bearing cancer specific mutations and alterations is a crucial mechanism in successfully triggering immune-mediated tumor rejection. Therapeutic targeting of these cancer specific epitopes (neoepitopes) is emerging as a promising opportunity for the generation of personalized cancer vaccines and adoptive T cell therapies. However, one major obstacle limiting the broader application of neoepitope based therapies is the difficulty of selecting highly immunogenic neoepitopes among the wide array of presented non-immunogenic HLA ligands derived from self-proteins. Areas covered: In this review, we present an overview of the MHC-I processing and presentation pathway, as well as highlight key areas that contribute to the complexity of the associated MHC-I peptidome. We cover recent technological advances that simplify and optimize the identification of targetable neoepitopes for cancer immunotherapeutic applications. Expert commentary: Recent advances in computational modeling, bioinformatics, and mass spectrometry are unlocking the underlying mechanisms governing antigen processing and presentation of tumor-derived neoepitopes.

The stimulatory G protein Gsα is required in melanocortin 4 receptor-expressing cells for normal energy balance, thermogenesis, and glucose metabolism

Central melanocortin 4 receptors (MC4Rs) stimulate energy expenditure and inhibit food intake. MC4Rs activate the G protein G_sα, but whether G_sα mediates all MC4R actions has not been established. Individuals with Albright hereditary osteodystrophy (AHO), who have heterozygous G_sα-inactivating mutations, only develop obesity when the G_sα mutation is present on the maternal allele because of tissue-specific genomic imprinting. Furthermore, evidence in mice implicates G_sα imprinting within the central nervous system (CNS) in this disorder. In this study, we examined the effects of G_sα in MC4R-expressing cells on metabolic regulation. Mice with homozygous G_sα deficiency in MC4R-expressing cells (MC4RGsKO) developed significant obesity with increased food intake and decreased energy expenditure, along with impaired insulin sensitivity and cold-induced thermogenesis. Moreover, the ability of the MC4R agonist melanotan-II (MTII) to stimulate energy expenditure and to inhibit food intake was impaired in MC4RGsKO mice. MTII failed to stimulate the secretion of the anorexigenic hormone peptide YY (PYY) from enteroendocrine L cells, a physiological response mediated by MC4R-G_sα signaling, even though baseline PYY levels were elevated in these mice. In G_sα heterozygotes, mild obesity and reduced energy expenditure were present only in mice with a G_sα deletion on the maternal allele in MC4R-expressing cells, whereas food intake was unaffected. These results demonstrate that G_sα signaling in MC4R-expressing cells is required for controlling energy balance, thermogenesis, and peripheral glucose metabolism. They further indicate that G_sα imprinting in MC4R-expressing cells contributes to obesity in G_sα knockout mice and probably in individuals with Albright hereditary osteodystrophy as well.

A Random Forest based approach to MHC class I epitope prediction and analysis

Background

Increased hydrophobicity of the contact regions between MHC class I-restricted peptides and TCR is associated with increased immunogenicity. To improve prediction of antigenic peptides and to identify additional biochemical properties associated with immunogenicity, we have created a random forest (RF)-based computational model that evaluates target epitopes using 66 parameters that cover a range of amino acid biochemical properties.

Method

A dataset of publicly available 9 mer epitopes with experimentally defined immunogenicity (n=29,874) and/or HLA binding (n=108,069) were collected from IEDB and the MassIVE database. Epitopes restricted to target HLA alleles were scored based on the biochemical parameters of each amino acid, and used to train a RF model specific to that HLA. For biochemical property analysis, redundant features were removed with a wrapper algorithm before being used to train the RF model.

Results

The RF model specific for HLA-A*02:01 (n=5500) was evaluated for HLA binding and immunogenicity prediction accuracy using a mutually-exclusive testing set of HLA-restricted peptides that were non-immunogenic, immunogenic, or non-binders. The model showed an immunogenicity prediction accuracy of 83% with an AUC of 0.88, and a HLA binding prediction accuracy of 97.4%, with a sensitivity of 95.2% and specificity of 99.9%. The RF model confirmed that hydrophobic interactions at peptide positions 4 and 8 as well as H-bonding at position 1 were important for immunogenicity.

Conclusion

RF-based algorithms can be used to identify biochemical parameters associated with immunogenic class I-restricted T cell epitopes. This model is being expanded to other HLA alleles.

Gsα deficiency in the dorsomedial hypothalamus underlies obesity associated with Gsα mutations

Gsα, encoded by Gnas, mediates hormone and neurotransmitter receptor-stimulated cAMP generation. Heterozygous Gsα-inactivating mutations lead to obesity in Albright hereditary osteodystrophy (AHO) patients, but only when the mutations occur on the maternal allele. This parent-of-origin effect is due to Gsα imprinting in the CNS, although the relevant CNS regions are unknown. We have now shown that mice with a Gnas gene deletion disrupting Gsα expression on the maternal allele, but not the paternal allele, in the dorsomedial nucleus of the hypothalamus (DMH) developed obesity and reduced energy expenditure without hyperphagia. Although maternal Gnas deletion impaired activation of brown adipose tissue (BAT) in mice, their responses to cold environment remained intact. Similar findings were observed in mice with DMH-specific deficiency of melanocortin MC4R receptors, which are known to activate Gsα. Our results show that Gsα imprinting in the DMH underlies the parent-of-origin metabolic phenotype that results from Gsα mutations and that DMH MC4R/Gsα signaling is important for regulation of energy expenditure and BAT activation, but not the metabolic response to cold.

Adjunctive pregabalin for uncontrolled partial-onset seizures: findings from a prospective audit

AIMS

Pregabalin (PGB) was licensed in Europe as an add-on antiepileptic drug (AED) for the treatment of partial-onset seizures in 2004. This audit assessed the response to adjunctive PGB in patients with uncontrolled seizures.

METHODS

PGB was titrated in 135 patients [73 men; 62 women, aged 18-76 (median 44 years) until one of the following occurred: ≥ 6 months' seizure freedom, ≥ 50% or < 50% seizure reduction over 6 months; PGB withdrawal because of adverse effects, lack of efficacy or both.

RESULTS

Of the 135 patients, 14 (10.4%) became seizure-free for ≥ 6 months (median PGB dose 300 mg/day; range 75-600 mg). A ≥ 50% seizure reduction occurred in 33 (24.4%) patients; 20 (14.8%) had < 50% reduction. PGB was withdrawn in 68 (50.4%) (40 adverse effects, seven lack of efficacy and 21 both). Commonest problems resulting in withdrawal were sedation (n = 18), weight gain (n = 14) and ataxia (n = 9). There was a positive correlation between increasing dose and weight gain (r = 0.42, P = 0.045).

CONCLUSIONS

Add-on PGB benefited 50% of patients, but only 10% achieved 6 months' seizure freedom. Adverse effects, most commonly sedation, dose-related weight gain and ataxia, led to drug discontinuation by 45%. Prospective audits of novel AEDs are a useful adjunct to randomized, controlled trials in managing epilepsy.

Feline systemic reactive angioendotheliomatosis: eight cases and literature review

A rare, multisystemic intravascular proliferative disorder was identified postmortem in eight cats. The majority of these cats died or were euthanized following episodes of dyspnea, lethargy, and anorexia. Microscopic examination revealed occlusive, intraluminal proliferations of spindle cells within small vessels. The heart was consistently involved, and myocardial dysfunction was the probable cause of illness in all cats. Immunohistochemically, the majority of intravascular cells expressed von Willebrand factor, and a smaller number expressed smooth muscle actin, compatible with a dual population of endothelial cells and pericytes, suggesting a reactive rather than a neoplastic process. Four cases of a similar feline vascular disorder from the veterinary literature are reviewed. The histopathology resembles reactive angioendotheliomatosis in humans, a benign cutaneous intravascular endothelial and pericytic proliferative condition. However, in contrast, this feline disease is multisystemic and fatal. We propose the name "feline systemic reactive angioendotheliomatosis" for this unique, idiopathic disorder of domestic cats.

Stewardship or clinical freedom? variations in dialysis decision making

BACKGROUND

It is generally agreed that acceptance criteria for dialysis have varied and changed over time and that implicit rationing, to some extent forced on clinicians by limited capacity, has been widely practised. Our objective was to study the basis and extent of variation in dialysis decision making among nephrologists in one NHS region.

DESIGN AND METHODS

In a clinical judgement analysis, linear regression models were employed to reflect the impact of clinical and non-clinical cues on nephrologists' decisions to offer dialysis to 60 'paper patients' under current capacity constraints and under an assumption of no capacity limit. A short questionnaire was also completed by eight nephrologists to elicit their expressed decision drivers, which were subsequently compared with those tacitly derived from the appraisal of the 60 clinical vignettes.

RESULTS

Doctors showed substantial variation in their propensity to offer dialysis and in their perceptions of the benefits of dialysis. Even for the five patients where the discordance in propensity to offer dialysis was least, the range in perceived gain in life expectancy was from 24 to 264 months (mean 91 months). The decision models had relatively good explanatory power with an average r(2) of 0.67 (0.39-0.90) and 0.70 (0.47-0.95) for decisions made under current capacity constraints and under an assumption of no limit capacity respectively. Surprisingly, for most doctors, the patient's age had very little impact on dialysis decisions but the magnitude of the beta-coefficients for the patient's mental state (mean -30.7) was of a similar order of magnitude to the coefficient for the principal 'renal' drivers (e.g. the mean coefficient for uraemic symptomatology under current capacity constraints was 47.7). The influence of other non-renal factors on the doctor's likelihood to offer dialysis was largely independent of the capacity assumption. A comparison of the doctor's stated decision drivers with those tacitly derived from their decision models showed only modest correlation.

CONCLUSIONS

The extent to which doctors vary in their propensity to offer dialysis is substantial. Very few non-clinical cues appear to influence the decision to offer dialysis. The most important non-renal factor in determining dialysis decisions was the patient's mental state.

Revising appointment, promotion, and tenure procedures to incorporate an expanded definition of scholarship: the University of Kentucky College of Medicine experience

Scholarly activity and scholarly productivity are key features of the academic health center (AHC) and the work of college of medicine faculty. Recent changes in the academic environment of the University of Kentucky (UK) College of Medicine led to an examination of its appointment, promotion, and tenure procedures. This, in turn, led to a re-examination of the college's definition of scholarship. This article describes three of UK's scholarship-related challenges, particularly those related to clinical departments. The authors describe some of the new procedures being implemented to address these challenges; these include new faculty designations, clearer articulation of promotion procedures, explicit recognition of multiple forms of scholarship, expectations for investment in junior faculty, and mandatory discussion of faculty success in chairs' annual reviews. Faculty reactions, positive and negative, to these changes in procedures are also presented.

High dose gabapentin in refractory partial epilepsy: clinical observations in 50 patients

Fifty patients with refractory partial seizures took part in a prospective, observational study of adjuvant gabapentin (GBP) in increasing doses. Thirty-three were started on 400 mg GBP daily with further weekly increments of 400 mg until seizures came under control for at least 6 months or to the limit of tolerability. A further 17 patients, not fully controlled on low dose GBP, followed the same regimen. All patients took the drug three times daily. Comparisons were made with seizure numbers during a 3-month baseline during which antiepileptic medication remained unchanged. Overall, 24 of the 50 patients documented a seizure reduction of 50% or more. Fifteen did so at or below 2400 mg GBP daily. Three of these patients became seizure-free. The remaining nine appeared to respond to higher daily doses of GBP (1:2800 mg; 3:3600 mg; 1:4000 mg; 1:4800 mg; 3:6000 mg), with two becoming seizure-free. Side-effects most commonly reported included tiredness, dizziness, headache and diplopia. On GBP doses exceeding 3600 mg daily, three patients developed flatulence and diarrhoea and two more had myoclonic jerks. Mean circulating GBP concentrations (mg/l) at each 1200 mg dose level were as follows: 1200 mg-4.1; 2400 mg-8.6; 3600 mg 13.2; 4800 mg 15.5; 6000 mg-17.2. In six patients, including three taking 6000 mg daily, GBP concentrations continued to rise linearly at each dosage increment. Although limited, our results do not support the suggestion that GBP absorption is saturable. High dose GBP may be effective in controlling seizures in patients with refractory partial epilepsy.

Multiple options and unique pathways: a new direction for EMS?

The same forces transforming the health care delivery system also are reshaping EMS. The changing economic and organizational structures of the health services delivery system may predict how EMS systems will redesign themselves. We discuss one template for future EMS systems.

The Kentucky medical curriculum. A response to the call for educational reform: a GPEP report card

The resources of an important educational grant provided by the Robert Wood Johnson Foundation, as well as designated local college and medical center funds, provided support for the renewal of the undergraduate medical education program at the University of Kentucky College of Medicine. The fully revised medical curriculum, adapted to changing professional and societal needs and completely in place by the 1994-95 academic year, was influenced by the recommendations of the General Professional Education of the Physician (GPEP) Report, issued by the Association of American Medical Colleges in 1984. This paper details each of the student-centered curricular changes in the context of the GPEP recommendation that it particularly addresses.

New antiepileptic drugs

No fewer than eight new antiepileptic drugs (AEDs) with diverse mechanisms of action have been introduced into clinical practice in the 1990s. Short monographs on lamotrigine, vigabatrin, gabapentin, oxcarbazepine, felbamate, topiramate and vigabatrin have been prepared for this review. Details are provided of mechanisms of action, clinical pharmacokinetics and adverse drug interactions. Each section concentrates on the efficacy, tolerability and practical use of these drugs. The areas where they have potential for superiority over the established AEDs have been highlighted. Specific indications and dosage schedules have been provided. As many of these AEDs have, as yet, limited licences, an attempt has been made to identify ongoing studies and important omissions. Where possible, the eventual place of the new agent in the pharmacological management of epilepsy has been assessed. A more limited summary has been included of zonisamide which, although licensed in Japan, is still regarded as an investigational drug elsewhere. Short discussions of three of the most promising investigational compounds, namely remacemide, losigamone and levetiracetam, complete the picture.

Nursing futures: a process to promote change in the delivery of care

In this era of healthcare reform, performing care using resources in an efficient manner is essential. "Nursing Futures," a process used by a 24-bed general rehabilitation unit in a 530-bed facility, helped the unit to identify key components of care, determine opportunities for improvement, and create a new system for the delivery of care that maximized resources and improved customer satisfaction. A Nursing Futures Committee, composed of nursing staff from all levels and from all shifts, used a continuous quality improvement process to focus on the problems in care delivery and developed ways to solve these problems using the time and talents of registered nurses in the most effective way. The committee also identified expectations of staff by various customer groups; analyzed the delivery system and defined its shortcomings; developed the ideal patient care unit within financial and institutional constraints; and executed the plan, considering cost and evaluation of patient and staff satisfaction before and after the system was implemented. The new system provided consistency in patient care assignments by reorganizing the unit into two nursing teams and by creating a new nursing position, the patient care manager.

Does technique or material used affect bladder tissue reactions when injecting teflon or silicone paste?

OBJECTIVES

Submucosal injections of polytetrafluoroethylene (PTFE) and polydimethylsiloxane (PDMS) paste continue to be used for the correction of vesicoureteral reflux and urinary incontinence. Potential distant particle migration and foreign body tissue reactions are thought to be significantly affected by the technique of injection and the paste material used. A study to determine if injection technique, paste material, or pretreatment of the injection site significantly affects local tissue reaction was performed on 44 New Zealand white rabbits.

METHODS

Animals were randomly assigned to undergo four distinct injection treatments into the submucosa or bladder muscularis. Prior to injecting 0.1 cc of the PTFE or PDMS paste, some sites were pretreated with 0.1 cc saline to separate tissue planes, epinephrine to cause vasoconstriction, or doxycycline to provide sclerosis. Pretreatment controls were also performed without injecting PTFE or PDMS paste. Animals were killed, and quadrant bladder biopsies were performed at 1 hour (9), 1 day (9), 7 days (10), 1 month (8), and 6 months (8). A single pathologist, blinded to the injection treatments, performed a histologic evaluation to determine bleb location and the degree of inflammation, fibrosis, and epithelial necrosis.

RESULTS

Seven of the 12 submucosal PTFE injection treatments were found on biopsy to be primarily within the muscularis, compared to 1 of 9 with PDMS paste. Three of the 24 PTFE injections could not be found at autopsy. Of these, two were injected into the muscularis, and all were discovered at least 1 month following injection. Particles were present in all 22 PDMS injection sites that were retrieved. Pretreatments, especially with doxycycline, resulted in significant epithelial necrosis at 1 and 7 days. At 1 and 6 months there were no differences in inflammation or fibrosis between PTFE and PDMS or any pretreatment combinations with saline or epinephrine.

CONCLUSIONS

Correctly injected, silicone (PDMS) paste appears most likely to remain in the submucosal space. Pretreatment injections may cause early epithelial necrosis. PTFE and PDMS elicit similar foreign body reactions over time.

Physicians for the 21st century: implications for medical practice, undergraduate preparation, and medical education

Changes in medical education and the practice of medicine have resulted from the push for both education and health care reforms. Undergraduates planning application to medical school should broaden their preparation to include communications, computers, economics, and multicultural educational experiences. To prepare graduates for medical practice in the new millennium, the University of Kentucky College of Medicine has implemented a new curriculum focusing on integration of basic and clinical sciences, primary care in ambulatory sites, health promotion and disease prevention, and attention to the ethical, social, psychologic, and financial impact of disease upon the patient, family, and society.

Synaptic organization of serotonin-like immunoreactive amacrine cells in the larval tiger salamander retina

Immunoelectron microscopy was used to investigate the ultrastructural features and synaptic relationships of serotonin-like immunoreactive amacrine cells in the larval tiger salamander retina. Serotonin-positive somas exhibited an evenly distributed peroxidase reaction product throughout their cytoplasm. Their nuclei were unstained and possessed indented nuclear membranes. Serotonin-immunoreactive processes were generally stained throughout with the exception of their mitochondria, whose morphology was often disrupted by the staining reaction. They were further characterized by an occasional dense-cored vesicle/s in addition to a generally homogeneous population of small, round, clear synaptic vesicles. Serotonin-immunoreactive amacrine cell processes formed conventional synapses that were characterized by symmetrical synaptic membrane densities. A total of 222 synaptic arrangements were observed that involved the immunostained processes of serotonin-amacrine cells. As presynaptic elements, they primarily contacted amacrine cells processes (37.8%). They also provided substantial synaptic input to processes that lacked synaptic vesicles (16.2%) and whose origin was unidentified. Serotonin-processes provided a far fewer number of synaptic contacts onto the processes of bipolar cells (1.4%) and the somas of cells in the amacrine cell layer (0.5%). As postsynaptic elements, they received synaptic inputs from amacrine cells (27.9%) and bipolar cells (16.2%). With the exception of their synapses onto bipolar cells and the somas of cells in the amacrine cell layer, each of the synaptic relationships of serotonin-amacrine cells was observed in each of sublayers 1-5 of the inner plexiform layer.

Expression of plasminogen activator (PA) and a PA inhibitor in human granulosa cells from preovulatory follicles

Studies with rat ovarian cells indicate that proteolytic enzymes, such as plasminogen activator (PA), play a role in the tissue remodeling that occurs before ovulation. In the rat, gonadotropins appear to increase granulosa cell tissue-type plasminogen activator (t-PA) content by increasing the cellular concentration of t-PA mRNA as well as by modulating the activity of a specific PA inhibitor (PAI). We obtained granulosa cells from preovulatory follicles of women undergoing either in vitro fertilization or gamete intra-fallopian tube transfer in order to evaluate the roles of PA and PAI in human ovulation. Samples of granulosa cell total RNA were hybridized with probes for t-PA, urokinase-type PA, PAI type 1 (PAI-1), or inhibin A-chain (as a control). Northern analyses revealed that the RNA of granulosa cells from preovulatory follicles contained little or no detectable PA mRNA. In contrast, two species of PAI mRNA were detected in relative abundance. The signal intensity produced by the PAI-1 probe varied by about 8-fold among patient samples, suggesting that PAI-1 may be useful as a marker of follicular maturation and differentiation. These results demonstrate that human granulosa cells collected immediately before ovulation contain PA inhibitor mRNA, yet have little or no PA mRNA.

Identification and characterization of metalloproteinase inhibitor activity in human ovarian follicular fluid

Metalloproteinase inhibitors regulate collagenase activity in the extracellular matrix. To assess the role of metalloproteinase inhibitors in the ovulatory process, inhibitor activity was examined in human follicular fluid collected 2-4 h before ovulation. The relationship between inhibitor activity and steroid content was determined, and the inhibitors were partially purified and characterized. Inhibitory activity in follicular fluid (n = 25) correlated with both follicular estradiol (P less than 0.001) and progesterone (P less than 0.02) concentrations per follicle. Chromatographic separation of the follicular fluid on Sepharose 6B isolated two peaks of inhibitory activity. The inhibitor from the small mol wt (Mr) peak shared many of the properties of tissue inhibitors of metalloproteinase. It was stable in response to heat (60 C) and methylamine (200 mM), and was destroyed by reduction and alkylation, a procedure reported to destroy previously characterized inhibitors. Partial purification by affinity and ion exchange chromatography demonstrated the inhibitor to be a glycoprotein with an approximate Mr of 28-29K. The large Mr inhibitor had an approximate size of 700K and exhibited many of the characteristics of alpha 2-macroglobulin, a serum-derived metalloproteinase inhibitor. It was sensitive to heat, methylamine, and reduction and alkylation. Thus, follicular fluid contains metalloproteinase inhibitor activity that is steroid related and may be hormonally regulated. Ovarian metalloproteinase inhibitors may act to regulate connective tissue remodeling during follicular rupture.

Classification of endometriotic implants by morphologic appearance and capacity to synthesize prostaglandin F

The severity of the symptoms of endometriosis has not always correlated well with the anatomic severity of the disease. This lack of correlation may be due to variations in the metabolic activity of the endometriotic implants present at different stages of the disease. Because prostaglandin F (PGF) has been implicated as a hormonal mediator of the clinical symptoms of endometriosis, PGF synthesis and content was measured in implants from 14 patients with mild, moderate, severe, or extensive disease. To assess whether PGF production was related to the status of implants, the authors classified implants, based on gross and histologic criteria, as petechial or reddish; intermediate or brown; or powder-burn or black. PGF production of implants from patients with mild or moderate disease was greater than that of implants from patients with severe or extensive disease (P less than 0.05), and PGF content was similar for all stages of endometriosis. Petechial implants produced twice the amount of PGF than intermediate implants (P less than 0.05), which in turn produced more PGF than powder-burn implants (P less than 0.05). Powder-burn implants did not have the in vitro capacity to produce PGF, and the amount of PGF contained in implants of all classes was similar. Therefore, endometriotic implant PGF production and possibly other biochemical activities are dependent on the physical status of the implant. The classification of implants by morphologic appearance may afford additional assistance in determining the prognosis of the disease and in the examination of the subtle effects of the disease on symptoms.

Natural history of diabetes presenting age 40-69 years: a prospective study of the influence of intensive dietary therapy

Two hundred and twenty-three newly-diagnosed symptomatic diabetic patients with onset age 40-69 years enrolled in a prospective study of intensive dietary management of diabetes were observed for a period of six years and the data obtained is analysed. The variables studied were weight and fasting levels of plasma glucose and insulin, and of serum total cholesterol and triglyceride. These tests were monitored throughout the study and in addition the oral glucose tolerance test was analysed at entry to the study, after six months intensive dietary management and again after 72 months. Blood pressure, electrocardiogram and the presence of posterior tibial artery pulsation were recorded at entry to the study and at 36 months and 72 months. Approximately 80 per cent of the patients were managed solely by dietary restriction for the entire six years, but 25 patients received oral hypoglycaemic drugs and 26 required insulin treatment. Weight, and fasting glucose and triglyceride values fell in the first few months of intensive dietary management. Analysis of possible risk factors in survivors and patients dead at six years showed no significant differences, apart from a higher mean age at diagnosis in those who died. During the six years of intensive dietary management the mortality from all causes in these diabetic patients was no greater than that for the general population of Northern Ireland.

Dietary history and nutritional state in treated coeliac patients

The gluten content and nutritional adequacy of the diet of a group of adult coeliac patients supposedly following a gluten-free diet for at least one year were assessed. Results were considered in relation to the nutritional state of these patients, determined by anthropometric measurement, and the histological appearance of jejunal biopsies taken at the time of nutritional assessment. Imperfect gluten avoidance, mild malnutrition and mild histological abnormalities on jejunal biopsy were frequent findings. A careful dietary and nutritional assessment when considered in light of histological findings at jejunal biopsy helps to identify the causes of persisting symptoms or malnutrition in treated coeliac patients. A normal jejunal biopsy in a malnourished patient whose dietary compliance is good should prompt a search for an alternative diagnosis.

Studies on the surgical induction of endometriosis in the rat

As a model to examine the pathophysiologic attributes of endometriosis, attempts were made to surgically induce the disease in the rat by autotransplanting endometrial or uterine tissue to the peritoneum. Rats (n = 46) were randomly assigned to one of four surgical techniques: (1) four uterine squares sutured to the peritoneal cavity; (2) uterine luminal lavages instilled into the peritoneal cavity; (3) endometrial scrapings flushed into the peritoneal cavity; and (4) sham-operated controls. Rats were examined at various days after surgery for the presence of endometrial implants. The autotransplantation of uterine squares to the peritoneal cavity was the only treatment that yielded healthy endometriotic implants. These implants grew into ellipsoidal cystic structures that were composed of both endometrial glands and stroma and were found to contain prostaglandin F (202 ng/mg) at concentrations similar to those measured in uterine tissue (205 ng/mg). To examine the effect of surgically induced endometriosis upon fecundity, rats (n = 40) were autotransplanted with uterine squares or were sham operated and mated. The presence of ectopic endometrial tissue reduced the number of pups at term by 48% and the number of day 14 embryos by 28% (P less than 0.05). Peritoneal adhesions were greater in rats with induced endometriosis than in sham-operated controls (P less than 0.05); however, in rats with induced endometriosis, no differences were noted in the severity of adhesions between pregnant and nonpregnant rats. Endometriotic implants underwent complete regression in the day 14 pregnant rat but had doubled in size in the nonpregnant rat. At term, the endometriotic implants were larger than in the day 14 pregnant rat (P less than 0.05) and similar to their original size. The successful growth and development of surgically transplanted endometrial tissue in the rat offers a research model that can be used to study those aspects of endometriosis that cannot be adequately investigated in women.

Experimental microvascular polytetrafluoroethylene grafts: 6-month patency

The efficacy of 1-mm internal-diameter polytetrafluoroethylene as a microvascular prosthesis is unclear. In this study, 8-mm-long segments of this material were implanted into the femoral arteries of 30 rats. Animals were examined every 2 weeks up to 6 months by Doppler ultrasound. Cumulative patency by the life-table method was 86.7 percent at 6 months. There were 26 patent grafts, 2 occlusions, and 2 deaths. Intimal hyperplasia adjacent to the anastomoses was seen in the native arteries. The pseudointima lining the grafts was cellular near the anastomoses but usually acellular in midgraft regions. It is concluded that if early failure does not occur, then good long-term patency is possible with 1-mm polytetrafluoroethylene in this setting and that patency is not dependent on development of a cellular pseudointima. Longer graft segments should be evaluated in future studies.