A community resource benchmarking predictions of peptide binding to MHC-I molecules

Recognition of peptides bound to major histocompatibility complex (MHC) class I molecules by T lymphocytes is an essential part of immune surveillance. Each MHC allele has a characteristic peptide binding preference, which can be captured in prediction algorithms, allowing for the rapid scan of entire pathogen proteomes for peptide likely to bind MHC. Here we make public a large set of 48,828 quantitative peptide-binding affinity measurements relating to 48 different mouse, human, macaque, and chimpanzee MHC class I alleles. We use this data to establish a set of benchmark predictions with one neural network method and two matrix-based prediction methods extensively utilized in our groups. In general, the neural network outperforms the matrix-based predictions mainly due to its ability to generalize even on a small amount of data. We also retrieved predictions from tools publicly available on the internet. While differences in the data used to generate these predictions hamper direct comparisons, we do conclude that tools based on combinatorial peptide libraries perform remarkably well. The transparent prediction evaluation on this dataset provides tool developers with a benchmark for comparison of newly developed prediction methods. In addition, to generate and evaluate our own prediction methods, we have established an easily extensible web-based prediction framework that allows automated side-by-side comparisons of prediction methods implemented by experts. This is an advance over the current practice of tool developers having to generate reference predictions themselves, which can lead to underestimating the performance of prediction methods they are not as familiar with as their own. The overall goal of this effort is to provide a transparent prediction evaluation allowing bioinformaticians to identify promising features of prediction methods and providing guidance to immunologists regarding the reliability of prediction tools.

In higher organisms, major histocompatibility complex (MHC) class I molecules are present on nearly all cell surfaces, where they present peptides to T lymphocytes of the immune system. The peptides are derived from proteins expressed inside the cell, and thereby allow the immune system to “peek inside” cells to detect infections or cancerous cells. Different MHC molecules exist, each with a distinct peptide binding specificity. Many algorithms have been developed that can predict which peptides bind to a given MHC molecule. These algorithms are used by immunologists to, for example, scan the proteome of a given virus for peptides likely to be presented on infected cells. In this paper, the authors provide a large-scale experimental dataset of quantitative MHC–peptide binding data. Using this dataset, they compare how well different approaches are able to identify binding peptides. This comparison identifies an artificial neural network as the most successful approach to peptide binding prediction currently available. This comparison serves as a benchmark for future tool development, allowing bioinformaticians to document advances in tool development as well as guiding immunologists to choose good prediction algorithm.

Ten years of bacterial genome sequencing: comparative-genomics-based discoveries

It has been more than 10 years since the first bacterial genome sequence was published. Hundreds of bacterial genome sequences are now available for comparative genomics, and searching a given protein against more than a thousand genomes will soon be possible. The subject of this review will address a relatively straightforward question: "What have we learned from this vast amount of new genomic data?" Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. One of the most obvious conclusions from examining the sequences from several hundred bacterial genomes is the enormous amount of diversity--even in different genomes from the same bacterial species. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages. An examination of the 20 Escherichia coli genomes sequenced so far dramatically illustrates this, with the genome size ranging from 4.6 to 5.5 Mbp; much of the variation appears to be of phage origin. This review also addresses mobile genetic elements, including pathogenicity islands and the structure of transposable elements. There are at least 20 different methods available to compare bacterial genomes. Metagenomics offers the chance to study genomic sequences found in ecosystems, including genomes of species that are difficult to culture. It has become clear that a genome sequence represents more than just a collection of gene sequences for an organism and that information concerning the environment and growth conditions for the organism are important for interpretation of the genomic data. The newly proposed Minimal Information about a Genome Sequence standard has been developed to obtain this information.

Improved method for predicting linear B-cell epitopes

BACKGROUND

B-cell epitopes are the sites of molecules that are recognized by antibodies of the immune system. Knowledge of B-cell epitopes may be used in the design of vaccines and diagnostics tests. It is therefore of interest to develop improved methods for predicting B-cell epitopes. In this paper, we describe an improved method for predicting linear B-cell epitopes.

RESULTS

In order to do this, three data sets of linear B-cell epitope annotated proteins were constructed. A data set was collected from the literature, another data set was extracted from the AntiJen database and a data sets of epitopes in the proteins of HIV was collected from the Los Alamos HIV database. An unbiased validation of the methods was made by testing on data sets on which they were neither trained nor optimized on. We have measured the performance in a non-parametric way by constructing ROC-curves.

CONCLUSION

The best single method for predicting linear B-cell epitopes is the hidden Markov model. Combining the hidden Markov model with one of the best propensity scale methods, we obtained the BepiPred method. When tested on the validation data set this method performs significantly better than any of the other methods tested. The server and data sets are publicly available at http://www.cbs.dtu.dk/services/BepiPred.

The immune epitope database and analysis resource: from vision to blueprint

A planned repository of immune epitope data with associated analysis tools should be a boon to vaccine development

SARS CTL vaccine candidates; HLA supertype-, genome-wide scanning and biochemical validation

Abstract:  An effective Severe Acute Respiratory Syndrome (SARS) vaccine is likely to include components that can induce specific cytotoxic T‐lymphocyte (CTL) responses. The specificities of such responses are governed by human leukocyte antigen (HLA)‐restricted presentation of SARS‐derived peptide epitopes. Exact knowledge of how the immune system handles protein antigens would allow for the identification of such linear sequences directly from genomic/proteomic sequence information (Lauemoller et al., Rev Immunogenet 2001: 2: 477–91). The latter was recently established when a causative coronavirus (SARS‐CoV) was isolated and full‐length sequenced (Marra et al., Science 2003: 300: 1399–404). Here, we have combined advanced bioinformatics and high‐throughput immunology to perform an HLA supertype‐, genome‐wide scan for SARS‐specific CTL epitopes. The scan includes all nine human HLA supertypes in total covering >99% of all individuals of all major human populations (Sette & Sidney, Immunogenetics 1999: 50: 201–12). For each HLA supertype, we have selected the 15 top candidates for test in biochemical binding assays. At this time (approximately 6 months after the genome was established), we have tested the majority of the HLA supertypes and identified almost 100 potential vaccine candidates. These should be further validated in SARS survivors and used for vaccine formulation. We suggest that immunobioinformatics may become a fast and valuable tool in rational vaccine design.

An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions

Reverse immunogenetic approaches attempt to optimize the selection of candidate epitopes, and thus minimize the experimental effort needed to identify new epitopes. When predicting cytotoxic T cell epitopes, the main focus has been on the highly specific MHC class I binding event. Methods have also been developed for predicting the antigen-processing steps preceding MHC class I binding, including proteasomal cleavage and transporter associated with antigen processing (TAP) transport efficiency. Here, we use a dataset obtained from the SYFPEITHI database to show that a method integrating predictions of MHC class I binding affinity, TAP transport efficiency, and C-terminal proteasomal cleavage outperforms any of the individual methods. Using an independent evaluation dataset of HIV epitopes from the Los Alamos database, the validity of the integrated method is confirmed. The performance of the integrated method is found to be significantly higher than that of the two publicly available prediction methods BIMAS and SYFPEITHI. To identify 85% of the epitopes in the HIV dataset, 9% and 10% of all possible nonamers in the HIV proteins must be tested when using the BIMAS and SYFPEITHI methods, respectively, for the selection of candidate epitopes. This number is reduced to 7% when using the integrated method. In practical terms, this means that the experimental effort needed to identify an epitope in a hypothetical protein with 85% probability is reduced by 20-30% when using the integrated method. The method is available at http://www.cbs.dtu.dk/services/NetCTL. Supplementary material is available at http://www.cbs.dtu.dk/suppl/immunology/CTL.php.

Hemodynamic function of the standard St. Jude bileaflet disc valve has no clinical impact 10 years after aortic valve replacement

OBJECTIVES

Size mismatch and impaired left ventricular function have been shown to determine the hemodynamic function of the standard St. Jude bileaflet disc valve early after aortic valve replacement (AVR). We aimed to analyse St. Jude valve hemodynamic function and its clinical impact in the survivors of a prospective series 10 years after AVR for aortic stenosis.

DESIGN

Forty-three survivors aged 32-90 years from a prospective series attended a follow-up study with Doppler echo and radionuclide cardiography 10 years after AVR for aortic stenosis. Six patients with significant left sided valve regurgitation were excluded from further analysis: they had significantly lower St. Jude valve gradient and left ventricular ejection fraction (LVEF) and larger mass index (LVMi) than 37 without.

RESULTS

In the 37 patients without left sided valve regurgitation peak and mean gradients were inversely related to St. Jude valve geometric orifice area (GOA) indexed for either body surface area or left ventricular end-diastolic dimension (LVEDD). The gradients correlated directly with LVEDD but not with LVEF or LVMi. Eleven patients with hypertension had higher peak gradients (31+/-13 versus 22+/-8 mmHg, p<0.05), lower LVEF, and higher LVEDD and LVMi than 26 without. Peak gradient was greater than 35 mmHg in five hypertensive patients with normal LVEF but lesser than 30 mmHg in six with impaired LVEF. Supranormal LVEF and severe size mismatch identified the remaining patients (N=3) with peak gradient above 35 mmHg. In a multilinear regression analysis GOA indexed for LVEDD, hypertension, and LVEF were independently related to peak gradient.

CONCLUSION

High gradients of the standard St. Jude bileaflet disc valve 10 years after AVR was primarily related to systemic hypertension and mismatch between valve and left ventricular cavity size. Hypertension and left sided valve regurgitation, but not St. Jude valve gradient or size mismatch, were the dominant determinants of left ventricular hypertrophy and impaired function.

The design and implementation of the immune epitope database and analysis resource

Epitopes are defined as parts of antigens interacting with receptors of the immune system. Knowledge about their intrinsic structure and how they affect the immune response is required to continue development of techniques that detect, monitor, and fight diseases. Their scientific importance is reflected in the vast amount of epitope-related information gathered, ranging from interactions between epitopes and major histocompatibility complex molecules determined by X-ray crystallography to clinical studies analyzing correlates of protection for epitope based vaccines. Our goal is to provide a central resource capable of capturing this information, allowing users to access and connect realms of knowledge that are currently separated and difficult to access. Here, we portray a new initiative, "The Immune Epitope Database and Analysis Resource." We describe how we plan to capture, structure, and store this information, what query interfaces we will make available to the public, and what additional predictive and analytical tools we will provide.

The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage

Cytotoxic T cells (CTLs) perceive the world through small peptides that are eight to ten amino acids long. These peptides (epitopes) are initially generated by the proteasome, a multi-subunit protease that is responsible for the majority of intra-cellular protein degradation. The proteasome generates the exact C-terminal of CTL epitopes, and the N-terminal with a possible extension. CTL responses may diminish if the epitopes are destroyed by the proteasomes. Therefore, the prediction of the proteasome cleavage sites is important to identify potential immunogenic regions in the proteomes of pathogenic microorganisms (or humans). We have recently shown that NetChop, a neural network-based prediction method, is the best method available at the moment to do such predictions; however, its performance is still lower than desired. Here, we use novel sequence encoding methods and show that the new version of NetChop predicts approximately 10% more of the cleavage sites correctly while lowering the number of false positives with close to 15%. With this more reliable prediction tool, we study two important questions concerning the function of the proteasome. First, we estimate the N-terminal extension of epitopes after proteasomal cleavage and find that the average extension is relatively short. However, more than 30% of the peptides have N-terminal extensions of three amino acids or more, and thus, N-terminal trimming might play an important role in the presentation of a substantial fraction of the epitopes. Second, we show that good TAP ligands have an increased chance of being cleaved by the proteasome, i.e., the specificity of TAP has evolved to fit the specificity of the proteasome. This evolutionary relationship allows for a more efficient antigen presentation.

Selection of proteins for human MHC class II presentation

We investigated the predicted function of proteins eluded from human MHC class II molecules. Peptides that are presented by MHC class II were obtained from the SYFPEITHI database and the corresponding proteins were found in the SWISSPROT database. The functions of these proteins were predicted using the protfun server. Our analysis showed that human proteins presented by MHC class II molecules are likely to be in the cell envelope, be a receptor or involved in immune responses. Presented proteins from bacteria and virus, on the other hand, are more likely to be involved in regulatory functions, translation, transcription as well as replication. These results can lead to better understanding the autoimmunity and the response to infections.

Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach

MOTIVATION

Prediction of which peptides will bind a specific major histocompatibility complex (MHC) constitutes an important step in identifying potential T-cell epitopes suitable as vaccine candidates. MHC class II binding peptides have a broad length distribution complicating such predictions. Thus, identifying the correct alignment is a crucial part of identifying the core of an MHC class II binding motif. In this context, we wish to describe a novel Gibbs motif sampler method ideally suited for recognizing such weak sequence motifs. The method is based on the Gibbs sampling method, and it incorporates novel features optimized for the task of recognizing the binding motif of MHC classes I and II. The method locates the binding motif in a set of sequences and characterizes the motif in terms of a weight-matrix. Subsequently, the weight-matrix can be applied to identifying effectively potential MHC binding peptides and to guiding the process of rational vaccine design.

RESULTS

We apply the motif sampler method to the complex problem of MHC class II binding. The input to the method is amino acid peptide sequences extracted from the public databases of SYFPEITHI and MHCPEP and known to bind to the MHC class II complex HLA-DR4(B1*0401). Prior identification of information-rich (anchor) positions in the binding motif is shown to improve the predictive performance of the Gibbs sampler. Similarly, a consensus solution obtained from an ensemble average over suboptimal solutions is shown to outperform the use of a single optimal solution. In a large-scale benchmark calculation, the performance is quantified using relative operating characteristics curve (ROC) plots and we make a detailed comparison of the performance with that of both the TEPITOPE method and a weight-matrix derived using the conventional alignment algorithm of ClustalW. The calculation demonstrates that the predictive performance of the Gibbs sampler is higher than that of ClustalW and in most cases also higher than that of the TEPITOPE method.

Coronavirus 3CLpro proteinase cleavage sites: possible relevance to SARS virus pathology

Background

Despite the passing of more than a year since the first outbreak of Severe Acute Respiratory Syndrome (SARS), efficient counter-measures are still few and many believe that reappearance of SARS, or a similar disease caused by a coronavirus, is not unlikely. For other virus families like the picornaviruses it is known that pathology is related to proteolytic cleavage of host proteins by viral proteinases. Furthermore, several studies indicate that virus proliferation can be arrested using specific proteinase inhibitors supporting the belief that proteinases are indeed important during infection. Prompted by this, we set out to analyse and predict cleavage by the coronavirus main proteinase using computational methods.

Results

We retrieved sequence data on seven fully sequenced coronaviruses and identified the main 3CL proteinase cleavage sites in polyproteins using alignments. A neural network was trained to recognise the cleavage sites in the genomes obtaining a sensitivity of 87.0% and a specificity of 99.0%. Several proteins known to be cleaved by other viruses were submitted to prediction as well as proteins suspected relevant in coronavirus pathology. Cleavage sites were predicted in proteins such as the cystic fibrosis transmembrane conductance regulator (CFTR), transcription factors CREB-RP and OCT-1, and components of the ubiquitin pathway.

Conclusions

Our prediction method NetCorona predicts coronavirus cleavage sites with high specificity and several potential cleavage candidates were identified which might be important to elucidate coronavirus pathology. Furthermore, the method might assist in design of proteinase inhibitors for treatment of SARS and possible future diseases caused by coronaviruses. It is made available for public use at our website: .

Predictable changes in left ventricular mass and function during ten years after valve replacement for aortic stenosis

BACKGROUND AND AIM OF THE STUDY

Left ventricular (LV) hypertrophy is the underlying basis for longevity after aortic valve replacement (AVR) for aortic stenosis (AS). However, a detailed account of changes in LV mass and function in the long term after AVR and identification of the determinants of such changes have not yet been presented.

METHODS

Ninety-one unselected consecutive adult patients with AS underwent AVR and were followed up to 10 years, at which time 41 survivors without new mitral disease underwent repeat measurement of LV mass index (LVMi), ejection fraction (LVEF), fast filling fraction (LVFFF), and end-diastolic volume index (LVEDVi). A subgroup comprising 49 patients was also assessed at eight days, three months, and 1.5 years postoperatively. All measurements were analyzed in a longitudinal regression model for repeated measures.

RESULTS

LVMi fell from 202 +/- 58 g/m2 (n = 91) via 150 +/- 45 g/m2 (n = 39) at 1.5 years to 139 +/- 40 g/m2 (n = 41) at 10 years in all patients, and to 124 +/- 31 g/m2 (n = 29) in non-hypertensive patients. The LVMi falls were paralleled by improvements in LVEF and LVEDVi. LVFFF was not correlated to LVMi before the 10-year study. The longitudinal model indicated progressive reduction of LVMi to 1.5 years, but no change thereafter. The predictor variables were preoperative LVMi and end-systolic dimension index (high values of both related to high postoperative LVMi), hypertension, and male gender. The model for LVEF indicated a rapid increase to three months, followed by a slight decrease to 1.5 years and further to 10 years, predicted by preoperative LVEF and LVFFF. LVFFF fell sharply by three months, had recovered somewhat at 1.5 years and fully at 10 years, positively related to preoperative LVFFF and inversely to end-systolic chamber radius:wall thickness ration and small-sized prosthetic valves. LVEDVi converged from extreme values over time predicted by preoperative LVEF, but rose with hypertension and coronary artery disease. Hemodynamic function of the prosthetic aortic valve at any of the measurement times had no impact.

CONCLUSION

Changes in LV mass and function up to 10 years after AVR for AS were highly predictable. Poorer outcomes were related to preoperative excessive hypertrophy and indices of underlying irreversible myocardial disease and further compromised by hypertension and, to a lesser extent, coronary artery disease. The hemodynamic function of the aortic prosthetic valve did not seem to play a role.

Definition of supertypes for HLA molecules using clustering of specificity matrices

Major histocompatibility complex (MHC) proteins are encoded by extremely polymorphic genes and play a crucial role in immunity. However, not all genetically different MHC molecules are functionally different. Sette and Sidney (1999) have defined nine HLA class I supertypes and showed that with only nine main functional binding specificities it is possible to cover the binding properties of almost all known HLA class I molecules. Here we present a comprehensive study of the functional relationship between all HLA molecules with known specificities in a uniform and automated way. We have developed a novel method for clustering sequence motifs. We construct hidden Markov models for HLA class I molecules using a Gibbs sampling procedure and use the similarities among these to define clusters of specificities. These clusters are extensions of the previously suggested ones. We suggest splitting some of the alleles in the A1 supertype into a new A26 supertype, and some of the alleles in the B27 supertype into a new B39 supertype. Furthermore the B8 alleles may define their own supertype. We also use the published specificities for a number of HLA-DR types to define clusters with similar specificities. We report that the previously observed specificities of these class II molecules can be clustered into nine classes, which only partly correspond to the serological classification. We show that classification of HLA molecules may be done in a uniform and automated way. The definition of clusters allows for selection of representative HLA molecules that can cover the HLA specificity space better. This makes it possible to target most of the known HLA alleles with known specificities using only a few peptides, and may be used in construction of vaccines. Supplementary material is available at http://www.cbs.dtu.dk/researchgroups/immunology/supertypes.html.

Selecting Informative Data for Developing Peptide-MHC Binding Predictors Using a Query by Committee Approach

Strategies for selecting informative data points for training prediction algorithms are important, particularly when data points are difficult and costly to obtain. A Query by Committee (QBC) training strategy for selecting new data points uses the disagreement between a committee of different algorithms to suggest new data points, which most rationally complement existing data, that is, they are the most informative data points. In order to evaluate this QBC approach on a real-world problem, we compared strategies for selecting new data points. We trained neural network algorithms to obtain methods to predict the binding affinity of peptides binding to the MHC class I molecule, HLA-A2. We show that the QBC strategy leads to a higher performance than a baseline strategy where new data points are selected at random from a pool of available data. Most peptides bind HLA-A2 with a low affinity, and as expected using a strategy of selecting peptides that are predicted to have high binding affinities also lead to more accurate predictors than the base line strategy. The QBC value is shown to correlate with the measured binding affinity. This demonstrates that the different predictors can easily learn if a peptide will fail to bind, but often conflict in predicting if a peptide binds. Using a carefully constructed computational setup, we demonstrate that selecting peptides with a high QBC performs better than low QBC peptides independently from binding affinity. When predictors are trained on a very limited set of data they cannot be expected to disagree in a meaningful way and we find a data limit below which the QBC strategy fails. Finally, it should be noted that data selection strategies similar to those used here might be of use in other settings in which generation of more data is a costly process.

Regression of left ventricular hypertrophy during 10 years after valve replacement for aortic stenosis is related to the preoperative risk profile

BACKGROUND

Previous studies have suggested that regression of hypertrophy may be the underlying determinant of longevity and left ventricular function after valve replacement (AVR) for aortic stenosis (AS). The potential for hypertrophy regression could therefore be related to the preoperative risk profile.

METHODS

Ninety-one consecutive patients with AS had a "project" Doppler-echo and radionuclide ventriculography in addition to the standard investigation programme prior to AVR with a disc valve (19-29mm, n=82), a caged ball valve (26-29mm, n=8), or a stented porcine valve (26mm, n=1); 49 (group A) were selected for a serial follow-up study while 42 served as controls (group B). Forty-two group A patients took part in a 1.5-year examination while 47 (26 group A, 21 group B) patients were studied at 10 years.

RESULTS

Groups A and B were comparable as regards all pre- and intra-operative data including left ventricular mass index (LVMi). A previously developed preoperative prognostic index (PI) separated the patients into groups with low (n=23), intermediary (n=19) and high risk (n=49) with 10-year survivals of 87%, 58% and 43% (P<0.01). LVMi dropped from 202+/-58g/m(2)preoperatively to 152+/-45g/m(2)(P<0.0001) at 1.5 years, and 139+/-40g/m(2)(P<0.0001) at 10 years (three and six patients, respectively, with paravalvular leak or mitral regurgitation excluded). PI correlated with preoperative (r=0.51, P<0.001), 1.5-year (r=0.46, P<0.01), and 10-year LVMi (r=0.41, P<0.01). Also preoperative left ventricular ejection fraction correlated with the three LVMi measurements. Patients with systemic hypertension had higher LVMi at 1.5 years (193+/-42, n=6 vs 144+/-42, n=33, P<0.05) and 10 years (175+/-39, n=12 vs 124+/-31g/m(2), n=29, P<0.001). Patients with low, intermediary or high PI, excluding those with hypertension, had 1.5-year LVMi of 110+/-35 (n=8), 134+/-43 (n=9) and 164+/-33g/m(2)(n=16; P<0.01), respectively, and 10-year LVMi of 116+/-25 (n=17), 126+/-27 (n=6), and 146+/-41g/m(2)(n=6; P<0.05), respectively. There was no relation between LVMi at 1.5 or 10 years and peak or mean Doppler gradient, prosthetic valve size, or valve size index.

CONCLUSIONS

Left ventricular hypertrophy regression for patients who survived up to 10 years after AVR for AS is dependent on the preoperative risk profile indicating that irreversible myocardial disease is the underlying factor. Systemic hypertension is an important factor in its own right.

Reliable prediction of T-cell epitopes using neural networks with novel sequence representations

In this paper we describe an improved neural network method to predict T-cell class I epitopes. A novel input representation has been developed consisting of a combination of sparse encoding, Blosum encoding, and input derived from hidden Markov models. We demonstrate that the combination of several neural networks derived using different sequence-encoding schemes has a performance superior to neural networks derived using a single sequence-encoding scheme. The new method is shown to have a performance that is substantially higher than that of other methods. By use of mutual information calculations we show that peptides that bind to the HLA A*0204 complex display signal of higher order sequence correlations. Neural networks are ideally suited to integrate such higher order correlations when predicting the binding affinity. It is this feature combined with the use of several neural networks derived from different and novel sequence-encoding schemes and the ability of the neural network to be trained on data consisting of continuous binding affinities that gives the new method an improved performance. The difference in predictive performance between the neural network methods and that of the matrix-driven methods is found to be most significant for peptides that bind strongly to the HLA molecule, confirming that the signal of higher order sequence correlation is most strongly present in high-binding peptides. Finally, we use the method to predict T-cell epitopes for the genome of hepatitis C virus and discuss possible applications of the prediction method to guide the process of rational vaccine design.

[St Jude's bi-leaflet aortic valve prosthesis throughout two decades. Quality profile and risk factors]

INTRODUCTION

The St Jude standard aortic bi-leaflet disc valve is still the most widespread. With almost 20 years of follow-up, the present material may describe the quality profile of the valve and the relevant risk factors throughout the remainder of most patients' lives.

MATERIAL AND METHODS

A 100% complete follow-up was conducted of 694 adult patients who had an aortic valve replacement with the St Jude valve during 1980-1993. The Cox regression analysis was used to identify independent risk factors.

RESULTS

Survival was 79%, 58%, 39%, and 37% at 5, 10, 15, and 18 years, respectively. Only 12% of the deaths (0.60%/patient-year) were valve-related with a 15-year freedom of 91%. Embolism (1.18%/patient-year) and anticoagulant-related bleeding (2.24%/patient-year) were the dominant complications with 15-year freedoms of 80% and 72%. Valve thrombosis was noted in two patients (0.04%/patient-year) who were off anticoagulation. Mechanical failure was not observed. Endocarditis (0.42%/patient-year) had a 15-year freedom of 92% compared with 72% and 54%, respectively, for major valve (2.33%/patient-year) and all valve-related complications together (4.33%/patient-year) and 96% for aortic valve reoperation (0.36%/patient-year). Age of the patient and heart-related variables were identified as independent risk factors for mortality and valve-related complications.

CONCLUSION

With a follow-up of almost two decades showing a low incidence of valve-related deaths, acceptable thrombogenicity, and absence of mechanical failure, the St Jude bi-leaflet aortic disc valve sets the standard for contemporary mechanical valves.

On-pump versus off-pump coronary artery bypass: independent risk factors and off-pump graft patency

OBJECTIVE

Current knowledge on off-pump coronary artery bypass (OPCAB) generally stems from single surgeons' experience or from series where OPCABs constituted a minor fraction of coronary operations. The present center decided to venture as far into OPCAB as possible during 1999. The present series thus represents the average surgeon's experience.

METHODS

During 1999, 533 patients underwent coronary artery bypass grafting using cardiopulmonary bypass (CPB) in 368 and OPCAB in 165 including the circumflex artery (CX) area in 91. Coronary arteriography was performed before discharge in the first 103 OPCAB patients.

RESULTS

The CPB and OPCAB groups differed as regards left ventricular ejection fraction (53+/-13 versus 57+/-11, P < 0.0001) and frequency of triple-vessel or left main stem disease (84 versus 32%, P < 0.0001) but were comparable as regards diabetes (12%), prior myocardial infarct (57%), unstable angina (21%), and previous heart surgery (3%). Using multivariate analyses, 30-day mortality (1.3%), P-creatine kinase myocardial band (CKMB) > 80 microg/l (11.1%), re-sternotomy for bleeding (4.5%) or dehiscense (1.7%), transitory cerebral ischemia and stroke (1.7%), supraventricular tachycardia (27.4%), and hospital stay (mean 8 days) were unrelated to off- versus on-pump surgery as well as to OPCAB in triple-vessel disease. CX branches < or = 1mm, > or = 5 distal anastomoses, prior heart surgery, right coronary artery (RCA) branches < or = 1.5mm, 8-21 days old myocardial infarct, female gender, and preoperative acute arrhythmia (among others) were identified as independent risk factors for mortality or increased CKMB in all 533 patients. The latter five risk factors were reproduced in the OPCAB group isolated. The patency in the 103 OPCABs was 95.3, 91.8, and 85.3% in the left anterior descending artery (LAD), CX, and RCA, respectively. Patency was inversely related to diameter of the grafted vessel in the LAD and CX areas, unlike the RCA area.

CONCLUSIONS

The results after beating heart surgery were good also in patients with triple-vessel disease, but specific gains relative to on-pump surgery could not be shown. The independent risk factors in the OPCAB group may indicate relative contraindications for OPCAB grafting.

[Coronary artery bypass without use of the heart-lung-machine]

INTRODUCTION

Off pump coronary artery bypass via sternotomy (OPCAB) and via a small left anterior thoracotomy (MIDCAB) on the anterior coronary arteries of the heart was introduced at the present center in 1997. Starting this year we decided to increase OPCAB and MIDCAB to constitute at least 50% of CAB procedures including the posterior aspect of the heart.

METHODS

From January 1st through April 16th 1999 we performed 152 CAB procedures: 108 CABG, 6 MIDCAB, 13 OPCAB (on the anterior cornary arteries) and 25 OPCAB-Cx (including the circumflex artery). OP procedures were done using OCTOPUS-II to expose and stabilize the arteriotomies, and control angiography was performed before discharge.

RESULTS

Off pump CAB was performed in 2% of the first 50 CAB patients, 36% of the next 50 and 50% of the last 52. The CABG and OPCAB-Cx groups were comparable as regards degree of coronary artery disease and number of distal anastomoses, but differed as regards poor left ventricular function and unstable preoperative status. Early mortality was 1.9% in the CABG group and 0% in the OP groups. Control angiograms in the OP groups showed a patency from 92 to 100%.

CONCLUSIONS

In this short preliminary series, it was possible to increase the fraction of OP procedures to nearly 50% with good results.

Mutational spectrum in the cardioauditory syndrome of Jervell and Lange-Nielsen

Jervell and Lange-Nielsen syndrome (JLNS) is an autosomal recessive syndrome characterised by profound congenital sensorineural deafness and prolongation of the QT interval on the electrocardiogram, representing abnormal ventricular repolarisation. In a study of ten British and Norwegian families with JLNS, we have identified all of the mutations in the KCNQ1 gene, including two that are novel. Of the nine mutations identified in this group of 10 families, five are nonsense or frameshift mutations. Truncation of the protein proximal to the recently identified C-terminal assembly domain is expected to preclude assembly of KCNQ1 monomers into tetramers and explains the recessive inheritance of JLNS. However, study of a frameshift mutation, with a dominant effect phenotypically, suggests the presence of another assembly domain nearer to the N-terminus.

Long-term results after aortic valve replacement in patients with congestive heart failure. Homografts vs prosthetic valves

OBJECTIVES

The aim of this study was to assess the influence of valve substitute (homograft vs prosthetic valve) on the long-term survival and late valve-related complication rates following aortic valve replacement in patients with aortic valve disease and congestive heart failure.

BACKGROUND

The effect of choice of valve substitute on outcome after aortic valve replacement in patients with pre-operative heart failure is unknown. The superior haemodynamic profile of homografts may be of particular benefit.

METHODS

We retrospectively analysed pre-operative, operative and follow-up data on 518 adults in functional classes III and IV, who, over the 25 years 1969-1993, had their initial aortic valve replacement at Harefield hospital. Follow-up conducted during 1996 to April 1997 and totalling 4439 patient-years was 96.1% complete. Using multivariate analysis, independent risk factors for different complications and mortality were defined.

RESULTS

Overall 5-, 10- and 20-year survival was 80+/-2%, 62+/-2% and 30+/-3%, respectively, with no significant difference between valve types. However, homografts (n=381) independently reduced the rate of serious complications and cardiac death, whereas mechanical valves were an independent adverse risk factor for late mortality. The rates of anticoagulant-related bleeding and thromboembolism were increased by mechanical valves, whereas primary tissue failure was the main complication of homografts.

CONCLUSIONS

Long-term outcome of homograft aortic valve replacement in patients with congestive heart failure is acceptable, with a reduced rate of serious complications and cardiac death. Further improvements would be expected if the rate of primary tissue failure could be reduced.

Prediction of protein secondary structure at 80% accuracy

Secondary structure prediction involving up to 800 neural network predictions has been developed, by use of novel methods such as output expansion and a unique balloting procedure. An overall performance of 77.2%-80.2% (77.9%-80.6% mean per-chain) for three-state (helix, strand, coil) prediction was obtained when evaluated on a commonly used set of 126 protein chains. The method uses profiles made by position-specific scoring matrices as input, while at the output level it predicts on three consecutive residues simultaneously. The predictions arise from tenfold, cross validated training and testing of 1032 protein sequences, using a scheme with primary structure neural networks followed by structure filtering neural networks. With respect to blind prediction, this work is preliminary and awaits evaluation by CASP4.

Short-term results after aortic valve replacement with stentless xenografts in elderly patients

OBJECTIVE

Our aim was to chart the short-term results of the first 75 of our patients who had undergone first-time aortic valve replacement (AVR) with stentless xenografts.

DESIGN

Our study included a complete follow-up (mean/max. 1.5/3.7 years) of the first 75 patients (42 males, 33 females; mean age 74, range 61-84 years) who underwent a first AVR with stentless xenografts.

RESULTS

Forty-three percent of patients were in functional class II and 57% in classes III-IV preoperatively. Coronary artery bypass grafting (CABG) was performed in 33 patients. Early mortality (< or = 30 days) was 6.7%, with no significant relation to CABG or age. Crude survival was 81% (95% confidence interval, CI: 71-91 %) at 3 years. Using a multivariate analysis, we identified a low left ventricular ejection fraction as a predictor of early and late mortality. Late survival (early mortality excluded) was comparable with the survival of a matched Danish background population. There were six embolic events (all cerebral: 3 minor, 1 major, 2 fatal), while two patients underwent redo-AVR because of either endocarditis (fatal) or aortic regurgitation caused by malaligned commissures. There were no other valve-related complications. Cumulative freedom was 89% (95% CI: 79-99%) for embolism and 86% (95% CI: 76-96 %) for all complications at 3 years. At the end of the study, 64% of the survivors were in functional class I, 34% were in class II and 2% in class III.

CONCLUSIONS

Considering the age composition of our patients, and compared with international results, our early mortality rates were acceptable. The absence of late excess mortality compared with the background population and the functional status at end-of-study may indicate the potential haemodynamic advantages of stentless aortic valves, at least in the short term.

Changes in left ventricular function and mass during serial investigations after valve replacement for aortic stenosis

BACKGROUND AND AIM OF THE STUDY

The potential for left ventricular hypertrophy regression and associated functional improvements may well be the underlying mechanism of results in general after valve replacement for aortic stenosis. The study aim was to investigate preoperative predictors and the time course of such ventricular changes.

METHODS

Forty-six patients (mean age 61 years; range: 24-82 years) with aortic stenosis were prospectively followed with serial investigations (Doppler echocardiography, radionuclide ventriculography) at eight days (n = 43), three months (n = 42) and 18 months (n = 39) after valve replacement with a mechanical valve (19-29 mm). The postoperative course of left ventricular ejection fraction (EF), fast filling fraction, mass index and end-diastolic volume index (EDVi) was analyzed in an independent increments statistical model for repeated measurements.

RESULTS

EF rose marginally, from 59+/-15% preoperatively to 64+/-16% (p <0.05) at 18 months, independently related to preoperative EF (p = 0.0001) and fast filling fraction (p = 0.0001). Changes in fast filling fraction were similarly predicted by the preoperative starting point (p = 0.003) and by preoperative left ventricular systolic radius:wall thickness ratio (p = 0.0002) with an inverse relation (the larger the chamber and the poorer its contractility, the lower the postoperative fast filling fraction). Mass index was independently related to the time point of postoperative measurement, indicating continuing regression of hypertrophy, from 200+/-66 g/m2 preoperatively to 148+/-49 g/m2 at 18 months (p <0.0001), when only 18% of the patients had normal mass index. Mass index was also independently related to preoperative left ventricular end-systolic dimension index (p = 0.0008) with a constant influence, and systolic wall stress (p = 0.0009) which was modified by time: the influence of wall stress was significant at eight days, weak at three months, and pronounced at 18 months. Left ventricular EDVi after surgery was inversely related to preoperative EF modified by time. Associated coronary artery disease, size of the prosthetic valve, and peak gradient across the valve (mean 15 mmHg; range: 7-26 mmHg at 18 months) did not influence any of the four target variables.

CONCLUSION

We conclude that left ventricular response to valve replacement for aortic stenosis is predictable. A significant reduction in hypertrophy occurs during the first 18 postoperative months, but to a normal ventricular mass in only a minority of patients. Insufficient regression of hypertrophy was related to indices of irreversible myocardial disease, which also prevented functional ventricular improvement despite successful valve replacement and a hemodynamically well functioning valve.

Using sequence motifs for enhanced neural network prediction of protein distance constraints

Correlations between sequence separation (in residues) and distance (in Angstrom) of any pair of amino acids in polypeptide chains are investigated. For each sequence separation we define a distance threshold. For pairs of amino acids where the distance between C alpha atoms is smaller than the threshold, a characteristic sequence (logo) motif, is found. The motifs change as the sequence separation increases: for small separations they consist of one peak located in between the two residues, then additional peaks at these residues appear, and finally the center peak smears out for very large separations. We also find correlations between the residues in the center of the motif. This and other statistical analysis are used to design neural networks with enhanced performance compared to earlier work. Importantly, the statistical analysis explains why neural networks perform better than simple statistical data-driven approaches such as pair probability density functions. The statistical results also explain characteristics of the network performance for increasing sequence separation. The improvement of the new network design is significant in the sequence separation range 10-30 residues. Finally, we find that the performance curve for increasing sequence separation is directly correlated to the corresponding information content. A WWW server, distanceP, is available at http://www.cbs.dtu.dk/services/distanceP/.

Standard aortic St. Jude valve at 18 years: performance profile and determinants of outcome

BACKGROUND

The standard St. Jude disc valve has been in use for 20 years and remains the dominant mechanical valve of today. With nearly 19 years of follow-up, the present large series could indicate the performance profile and its determinants in the very long term.

METHODS

A detailed follow-up was performed to a maximum of 18.6 years in 694 patients aged 15 to 83 years who undervent aortic valve replacement (AVR) with the standard St. Jude valve during 1980 to 1993. The Cox regression analysis was used to identify independent determinants of outcome in the aortic stenosis (n = 490) and regurgitation (n = 204) groups.

RESULTS

Overall survival was 58%, 39%, and 37% at 10, 15, and 18 years, respectively. Only 12% of deaths (0.60%/ patient-year) were related to the valve with a 15-year freedom of 91%. Embolism (1.18%/patient-year) and anticoagulant-related bleeding (2.24%/patient-year) were the dominant complications with 10-year/15-year freedoms of 90%/80% and 85%/72%, respectively. Only 24% of bleeding events were classified as major. Valve thrombosis occurred in 2 patients (0.04%/patient-year): 1 did not receive vitamin K antagonist treatment and International Normalized Ratio was below target level in the other. There were no mechanical failures. Endocarditis (0.42%/patient-year) and paravalvular leak (0.42%/ patient-year) occurred with 15-year freedoms of 92% and 96%, respectively, with a relation between the latter (but not the former) and preoperative endocarditis in the regurgitation group. Freedom from serious complications (2.33%/patient-year) and all complications joined (4.33%/ patient-year) were 72% and 54%, respectively, at 15 years with a 96% freedom from redo AVR (0.36%/patient-year). Age- and heart-related variables were independent risk factors for mortality, thromboembolism, bleeding, serious complications, and all complications joined. Small valve (19 and 21 mm) adversely affected serious and all complications in the regurgitation group.

CONCLUSIONS

With a follow-up approaching 2 decades and exhibiting a low rate of valve-related deaths, acceptable low thrombogenicity, and absence of mechanical failure, the standard aortic St. Jude disc valve sets the standard for contemporary mechanical valves.

Recurrence of uterine intravenous leiomyomatosis with intracardiac extension. Diagnostic considerations and surgical removal

A 28-year-old woman (gravida 2, para 2) was admitted 20 months after a hysterectomy because of fibromyoma. The hysterectomy specimen had shown intravenous leiomyomatosis. The patient presented with unspecific abdominal symptoms, serologic signs of hepatic and renal failure and clinical right-sided heart failure. Progression despite treatment with a gonadotropin-releasing hormone analogue promoted transferral to the present centre. Abdominal ultrasonography, phlebography and transoesophageal echocardiography showed a left pelvic mass and a seemingly free-floating tumour extending from the left main iliac vein via the inferior caval vein to the right ventricle. During a combined cardiac and distal caval approach using extracorporeal circulation, a 45 cm massive leiomyoma was removed successfully. Seven weeks later the left pelvic tumour was removed radically together with left oophorectomy. At control 12 months later the patient was well and without any remaining symptoms.

Stoichiometry of monoclonal antibody neutralization of T-cell line-adapted human immunodeficiency virus type 1

In order to study the stoichiometry of monoclonal antibody (MAb) neutralization of T-cell line-adapted human immunodeficiency virus type 1 (HIV-1) in antibody excess and under equilibrium conditions, we exploited the ability of HIV-1 to generate mixed oligomers when different env genes are coexpressed. By the coexpression of Env glycoproteins that either can or cannot bind a neutralizing MAb in an env transcomplementation assay, virions were generated in which the proportion of MAb binding sites could be regulated. As the proportion of MAb binding sites in Env chimeric virus increased, MAb neutralization gradually increased. Virus neutralization by virion aggregation was minimal, as MAb binding to HIV-1 Env did not interfere with an AMLV Env-mediated infection by HIV-1(AMLV/HIV-1) pseudotypes of CD4(-) HEK293 cells. MAb neutralization of chimeric virions could be described as a third-order function of the proportion of Env antigen refractory to MAb binding. This scenario is consistent with the Env oligomer constituting the minimal functional unit and neutralization occurring incrementally as each Env oligomer binds MAb. Alternatively, the data could be fit to a sigmoid function. Thus, these data could not exclude the existence of a threshold for neutralization. However, results from MAb neutralization of chimeric virus containing wild-type Env and Env defective in CD4 binding was readily explained by a model of incremental MAb neutralization. In summary, the data indicate that MAb neutralization of T-cell line-adapted HIV-1 is incremental rather than all or none and that each MAb binding an Env oligomer reduces the likelihood of infection.

Performance profile of the Starr-Edwards aortic cloth covered valve, track valve, and silastic ball valve

OBJECTIVE

The Starr-Edwards aortic ball valve has passed 30 years of clinical follow-up. A detailed account of the long-term performance from a large series could thus give valuable guidance in managing patients who are still alive, depict the total remaining life-span after aortic valve replacement (AVR) for the average patient, and set a record yet to be matched by modern disc valves.

METHODS

A detailed follow-up to a maximum of 31.1 years was performed for 717 patients who underwent their first AVR during 1965-1993 with a Starr-Edwards silastic ball valve (N = 355), a cloth covered valve (N = 164) or a track valve (N = 198) with a total of 7254 patient-years at risk.

RESULTS

Patients who received a silastic ball valve were older (average 60 vs. 58 years), had more endocarditis (9%) and more secondary kidney failure (24%) preoperatively than the other patients. The three valve types did not differ as regards long-term survival or freedom from complications and only 15% of late deaths were related to the valve. For the silastic ball valve cumulative freedoms at 10 and 25 years were 59 and 20% from all deaths (crude survival), 85 and 80% from thromboembolism, 87 and 70% from bleeding, 98 and 94% from endocarditis, 96 and 95% from redo AVR and 68 and 51% from all valve related complications joined. There were no instances of structural failure apart from wear of the cloth covering the cage struts of the cloth covered valves. Incidences of haemolysis (0.10%/patient-year) and valve thrombosis (0.06%/patient-year) were low for the silastic ball valve. Analysis of relative survival for the silastic ball valve indicated excess mortality relative to a matched background population only during 1st and 13th postoperative year. Apart from heart related factors and age, independent incremental risk factors for mortality and the various complications included, not valve type, but valve size index (valve size divided by body surface area) < or = 13 mm/m2.

CONCLUSIONS

The Starr-Edwards aortic ball valves, not least the currently available silastic ball valve, are durable through the remaining life time of the patients and able to secure near normal age and sex specific survival provided valve and patient size mismatch is avoided.

MatrixPlot: visualizing sequence constraints

MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot.

AVAILABILITY

MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot.

CONTACT

gorodkin@cbs.dtu.dk

Primary aortic valve replacement with allografts over twenty-five years: valve-related and procedure-related determinants of outcome

OBJECTIVES

Allografts offer many advantages over prosthetic valves, but allograft durability varies considerably.

METHODS

From 1969 through 1993, 618 patients aged 15 to 84 years underwent their first aortic valve replacement with an aortic allograft. Concomitant surgery included aortic root tailoring (n = 58), replacement or tailoring of the ascending aorta (n = 56), and coronary artery bypass grafting (n = 87). Allograft implantation was done by means of a "freehand" subcoronary technique (n = 551) or total root replacement (n = 67). The allografts were antibiotic sterilized (n = 479), cryopreserved (n = 12), or viable (unprocessed, harvested from brain-dead multiorgan donors or heart transplant recipients, n = 127). Maximum follow-up was 27.1 years.

RESULTS

Thirty-day mortality was 5.0%, and crude survival was 67% and 35% at 10 and 20 years. Ten- and 20-year rates of freedom from complications were as follows: endocarditis, 93% and 89%; primary tissue failure, 62% and 18%; and redo aortic valve replacement, 81% and 35%. Multivariable Cox analyses identified several valve- and procedure-related determinants: rising allograft donor age and antibiotic-sterilized allograft for mortality; donor more than 10 years older than patient for endocarditis; rising donor age minus patient age, rising implantation time (from harvest to aortic valve replacement), and donor age more than 65 years for tissue failure; and rising donor age minus patient age, young patient age, rising implantation time, and subcoronary implantation preceded by aortic root tailoring for redo aortic valve replacement. Estimated 10- and 20-year rates of freedom from tissue failure for a 70-year-old patient with a viable valve from a 30-year-old donor and no other risk factors were 91% and 64%; the figures were 71% and 20% if the donor age was 65 years. The rates of freedom from tissue failure for a 30-year-old patient with a 30-year-old donor were 82% and 39%; the figures were 49% and 3% with a 65-year-old donor. Beneficial influences of a viable valve were largely covered by short harvest time (no delay for allografts from brain dead organ donors or heart transplant recipients) and short implantation time.

CONCLUSIONS

Primary allograft aortic valve replacement can give acceptable results for up to 25 years. The late results can be improved by the use of a viable allograft, by matching patient and donor age, and by more liberal use of free root replacement with re-implantation of the coronary arteries rather than tailoring the root to accommodate a subcoronary implantation.

Myocardial structure as a determinant of pre- and postoperative ventricular function and long-term prognosis after valve replacement for aortic stenosis

BACKGROUND

Long-term results after aortic value replacement for aortic stenosis can be correlated to a cardiac-related pre-operative risk profile. This predictability indicates that there is a common basis in subtle or overt structural abnormalities of left ventricular myocardium.

METHODS AND RESULTS

Forty-nine patients aged 24-82 (mean 61) years, with aortic stenosis had a full wall thickness transmural biopsy of the left ventricular antero-lateral free wall during aortic valve replacement. Echocardiography and radionuclide ventriculography were performed prior to, and 18 months (n = 41) after, the operation. Postoperative follow-up to a maximum of 7.7 years was 100% complete. Pre-operatively, all patients had an increase in both the left ventricular mass index (202 +/- 67 g.m-2) and the muscle cell diameter (41 +/- 8 microns); other morphological data included a muscle cell nucleus volume of 752 +/- 192 microns3, a muscle cell mass index of 163 +/- 54.m-2, and a fibrous tissue mass index of 39 +/- 16 g.m-2. Patients with a pre-operative episode of clinical left ventricular failure (n = 19) had significantly greater morphological variables than those without. Pre-operative ejection fraction and other measures of systolic function correlated inversely with the morphological data, except for the fibrous tissue mass index; diastolic function indices correlated inversely with all the morphological variables. At the 18-month re-study, the same general picture was noted, but with an underlying strengthening, especially of the muscle cell mass index. Overall, the mass index dropped to 152 +/- 51 g.m-2 (P < 0.0001), but in 17% of the patients it became normal; the mass index at 18 months was directly correlated to morphological variables. A high muscle cell nucleus volume was identified as an independent predictor of early and late mortality.

CONCLUSIONS

Abnormalities of the hypertrophied left ventricular muscle cell and the degree of muscle hypertrophy are, to some degree, underlying determinants of pre-operative symptomatology, pre- and postoperative ventricular function, and early and late mortality after valve replacement for aortic stenosis. Incomplete hypertrophy impaired results, was related to pre-operative myocardial structural abnormalities.

[Mortality and worsening of prognosis for patients with aortic stenosis while on the waiting list]

In a prospective study, 99 consecutive patients with an operative indication due to severe aortic stenosis (AS) were put on a surgical waiting list. The waiting time to aortic valve replacement (AVR) averaged 6.3 months (0.5-19 months). There were 58 men and 41 women with a mean age of 61 years (21-82 years). The patients were divided into three groups: group 1 (N = 81) with an uneventful stay on the waiting list; group 2 (N = 11) with significant worsening of a prognostic index; and group 3 (N = 7) with patients who died during the waiting time. The waiting list death rate was 13.5%/patient-year compared with a post-AVR death rate of 4.9% patient-year (p < 0.05) with a mean post-AVR follow-up of 5.7 years. According to a prognostic index (Cox regression model) at inclusion, group 2 patients had a predicted 7-year post-AVR survival probability of 72%, but only of 61% according to their prognostic index immediately preoperatively; their observed 7-year post-AVR survival was 60%. Logistic regression analysis identified high age, short duration of symptoms, signs of severe hypertrophy and strain in the ECG, female gender, and deranged left ventricular diastolic function (related to severely increased left ventricular muscle mass) as independent predictors of prognostic worsening and death while on the waiting list. The predictive models did not allow sufficiently accurate identification of the patients at risk during the waiting period. The consequences of a surgical waiting period averaging 6 months are serious for AS patients. The death rate is high and a subgroup worsens its prognostic profile with a significantly reduced post-AVR long-term survival as the result.

NetOglyc: prediction of mucin type O-glycosylation sites based on sequence context and surface accessibility

The specificities of the UDP-GalNAc:polypeptide Nacetylgalactosaminyltransferases which link the carbohydrate GalNAc to the side-chain of certain serine and threonine residues in mucin type glycoproteins, are presently unknown. The specificity seems to be modulated by sequence context, secondary structure and surface accessibility. The sequence context of glycosylated threonines was found to differ from that of serine, and the sites were found to cluster. Non-clustered sites had a sequence context different from that of clustered sites. Charged residues were disfavoured at position -1 and +3. A jury of artificial neural networks was trained to recognize the sequence context and surface accessibility of 299 known and verified mucin type O-glycosylation sites extracted from O-GLYCBASE. The cross-validated NetOglyc network system correctly found 83% of the glycosylated and 90% of the non-glycosylated serine and threonine residues in independent test sets, thus proving more accurate than matrix statistics and vector projection methods. Predictions of O-glycosylation sites in the envelope glycoprotein gp120 from the primate lentiviruses HIV-1, HIV-2 and SIV are presented. The most conserved O-glycosylation signals in these evolutionary-related glycoproteins were found in their first hypervariable loop, V1. However, the strain variation for HIV-1 gp120 was significant. A computer server, available through WWW or E-mail, has been developed for prediction of mucin type O-glycosylation sites in proteins based on the amino acid sequence. The server addresses are http://www.cbs.dtu.dk/services/NetOGlyc/ and netOglyc@cbs.dtu.dk.

Complement-mediated enhancement of HIV-1 infection in peripheral blood mononuclear cells

We investigated if complement-mediated enhancement of HIV infection occurs in peripheral blood mononuclear cells (PBMC). In 7 experiments, we evaluated the effect of human complement on HIVIIIB infection in vitro. We measured HIV antigen production on day 4 and found that pre-incubation of HIV with complement led to enhanced production of antigen with a median enhancement of 2.5-fold (range 1.1-6.8). This complement-mediated increase in antigen production was statistically significant (p < 0.02). Complement-mediated enhancement of HIV infection was also tested in CD4 cells enriched from PBMC, and CD4 cells persistently gave higher levels of infection enhancement than PBMC. Thus, CD4 cells appear to be sufficient for complement-mediated enhancement of HIV infection to occur. In addition, we tested if it was possible to detect complement-mediated enhancement of primary HIV isolates in PBMC. We tested 3 isolates and found only a minor effect on antigen production (median enhancement 1.2-fold, range 0.6-1.5). Furthermore, addition of HIV-specific antibodies in combination with complement resulted in enhanced antigen production in 2/3 sera tested. However, the combination of complement and antibodies resulted in only a minor increase in enhancement of HIV infection compared to that obtained with complement alone. Finally, we found evidence of complement-mediated enhancement of HIV infection in resting PBMC. In conclusion, we demonstrated that complement-mediated enhancement of HIV infection does occur in vitro in PBMC.

O-GLYCBASE Version 3.0: a revised database of O-glycosylated proteins

O-GLYCBASE is a revised database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the sequence databases. Entries include information about species, sequence, glycosylation sites and glycan type and is fully cross-referenced. Compared to version 2.0 the number of entries has increased by 20%. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through the WWW at http://www.cbs.dtu. dk/databases/OGLYCBASE/

Left ventricular systolic and diastolic function in aortic stenosis. Prognostic value after valve replacement and underlying mechanisms

AIMS

The aims of the study were to examine the prognostic value of pre-operative left ventricular systolic and diastolic function on early, and late mortality after valve replacement for aortic stenosis, and to identify possible underlying mechanisms.

METHODS AND RESULTS

Ninety-one prospectively recruited consecutive patients with a mean age of 61 years underwent valve replacement for aortic stenosis with concomitant coronary artery bypass grafting in 32 and a minimum postoperative observation period of 5.4 years. There were six early (< or = 30 days postoperatively) and 19 late deaths, and 18 deaths from specific causes (cardiac and prosthetic valve related). Early mortality occurred exclusively among patients with a combined subnormal left ventricular systolic function (subnormal ejection fraction or peak ejection rate, or supranormal time-to-peak ejection--duration of systole ratio) and a subnormal fast filling fraction. In Cox regression models on crude mortality and specific deaths, a subnormal ejection fraction and a fast filling fraction of < or = 45% were the only independent risk factors. Patients with none of these risk factors had normal sex- and age-specific survival, those with any one factor had an early, and those with both factors a massive early and a late excess mortality, with 5-year crude survival of 92%, 77%, and 50%, respectively (P < 0.0001). Systolic wall stress was without prognostic value. Further analyses indicated that impairment of left ventricular function occurred with increasing muscle mass over two phases: (1) diastolic dysfunction characterized by a pattern of severe relative concentric hypertrophy; (2) the addition of systolic dysfunction characterized by a more dilated, less concentric chamber geometry. Coronary artery disease seemed to provoke the latter development sooner.

CONCLUSIONS

Impaired systolic and diastolic left ventricular function, irrespective of afterload, were decisive independent pre-operative risk factors for early as well as late mortality after aortic valve replacement for aortic stenosis. The adverse influence of concentric hypertrophy was the main underlying mechanism. Operative intervention, before impairment of diastolic and systolic function, should be advocated.

IsK and KvLQT1: mutation in either of the two subunits of the slow component of the delayed rectifier potassium channel can cause Jervell and Lange-Nielsen syndrome

The Jervell and Lange-Nielsen syndrome (JLNS) comprises profound congenital sensorineural deafness associated with syncopal episodes. These are caused by ventricular arrhythmias secondary to abnormal repolarisation, manifested by a prolonged QT interval on the electrocardiogram. Recently, in families with JLNS, Neyroud et al. reported homozygosity for a single mutation in KVLQT1 , a gene which has previously been shown to be mutated in families with dominantly inherited isolated long QT syndrome [Neyroud et al . (1997) Nature Genet ., 15, 186-189]. We have analysed a group of families with JLNS and shown that the majority are consistent with mutation at this locus: five families of differing ethnic backgrounds were homozygous by descent for markers close to the KVLQT1 gene and a further three families from the same geographical region were shown to be homozygous for a common haplotype and to have the same homozygous mutation of the KVLQT1 gene. However, analysis of a single small consanguineous family excluded linkage to the KVLQT1 gene, establishing genetic heterogeneity in JLNS. The affected children in this family were homozygous by descent for markers on chromosome 21, in a region containing the gene IsK . This codes for a transmembrane protein known to associate with KVLQT1 to form the slow component of the delayed rectifier potassium channel. Sequencing of the affected boys showed a homozygous mutation, demonstrating that mutation in the IsK gene may be a rare cause of JLNS and that an indistinguishable phenotype can arise from mutations in either of the two interacting molecules.

Protein distance constraints predicted by neural networks and probability density functions

We predict interatomic Calpha distances by two independent data driven methods. The first method uses statistically derived probability distributions of the pairwise distance between two amino acids, whilst the latter method consists of a neural network prediction approach equipped with windows taking the context of the two residues into account. These two methods are used to predict whether distances in independent test sets were above or below given thresholds. We investigate which distance thresholds produce the most information-rich constraints and, in turn, the optimal performance of the two methods. The predictions are based on a data set derived using a new threshold which defines when sequence similarity implies structural similarity. We show that distances in proteins are predicted more accurately by neural networks than by probability density functions. We show that the accuracy of the predictions can be further increased by using sequence profiles. A threading method based on the predicted distances is presented. A homepage with software, predictions and data related to this paper is available at http://www.cbs.dtu.dk/services/CPHmodels/.

Gene therapy of T helper cells in HIV infection: mathematical model of the criteria for clinical effect

This paper presents a mathematical analysis of the criteria for gene therapy of T helper cells to have a clinical effect on HIV infection. The analysis indicates that for such a therapy to be successful, it must protect the transduced cells against HIV-induced death. The transduced cells will not survive as a population if the gene therapy only blocks the spread of virus from transduced cells that become infected. The analysis also suggests that the degree of protection against disease-related cell death provided by the gene therapy is more important than the fraction cells that is initially transduced. If only a small fraction of the cells can be transduced, transduction of T helper cells and transduction of haematopoietic progenitor cells will result in the same steady-state level of transduced T helper cells. For gene therapy to be efficient against HIV infection, our analysis suggests that a 100% protection against viral escape must be obtained. The study also suggests that a gene therapy against HIV infection should be designed to give the transduced cells a partial but not necessarily total protection against HIV-induced cell death, and to avoid the production of viral mutants insensitive to the gene therapy.

Impact of size mismatch and left ventricular function on performance of the St. Jude disc valve after aortic valve replacement

BACKGROUND

The hemodynamic function of the St. Jude valve may change relative to changes in left ventricular function after aortic valve replacement for aortic stenosis. From theoretical reasons one may hypothesize that prosthetic valve hemodynamic function is related to left ventricular failure and mismatch between valve size and patient/ventricular chamber size.

METHODS

Forty patients aged 24 to 82 years who survived aortic valve replacement for aortic stenosis with a standard St. Jude disc valve (mean size, 23.5 mm; range, 19 to 29 mm) were followed up prospectively with Doppler echocardiography and radionuclide left ventriculography preoperatively and 9 days, 3 months, and 18 months after the operation with assessment of intravascular hemolysis at 18 months. Follow-up to a maximum of 7.4 years (mean, 6.3 years) was 100% complete.

RESULTS

Left ventricular muscle mass index decreased from 198 +/- 62 g.m-2 preoperatively to 153 +/- 53 g.m-2 at 18 months (p < 0.001), paralleled by a significant increase in left ventricular ejection fraction, peak ejection rate, and peak filling rate; only 18% of the patients had normal left ventricular muscle mass index and only 32% normal ventricular function (normal left ventricular ejection fraction, peak ejection rate, peak filling rate, early filling fraction, and late filling fraction during atrial contraction) at 18 months. Prosthetic valve peak Doppler gradient dropped from 20 +/- 6 mm Hg at 9 days to 17 +/- 5 mm Hg at 18 months (p < 0.05). Reduction of left ventricular muscle mass index was unrelated to peak gradient and size of the valve. Peak gradient at 18 months rose with valve orifice diameter of 17 mm or less (by 6 mm Hg), orifice diameter/body surface area of 9 mm.m-2 or less (by 5 mm Hg), left ventricular enddiastolic dimension (by 23 mm Hg per 10 mm increase), and impaired ventricular function (by 3 mm Hg). All but 2 patients (5%) had intravascular hemolysis; none had anemia. Two patients with moderate paravalvular leak had the highest serum lactic dehydrogenase levels; 4 patients with trivial leak had higher serum lactic dehydrogenase levels than those without leak. Serum lactic dehydrogenase levels rose with moderate paravalvular leak, impaired ventricular function, and valve orifice diameter. Six patients with trivial or moderate paravalvular leak had a cumulative 7-year freedom from bleeding and thromboembolism of 44% +/- 22% compared with 87% +/- 5% for those without leak (p < 0.05).

CONCLUSIONS

The peak gradient of the St. Jude aortic valve dropped marginally over the first 18 postoperative months in association with incomplete left ventricular hypertrophy regression and marginal improvement of ventricular function. Mismatch between valve size and ventricular cavity size or patient size and impaired function of a dilated ventricle significantly compromised the performance of the St. Jude valve. Probably explained by platelet destruction or activation, paravalvular leak was related to bleeding and thromboembolic complications.

O-GLYCBASE version 2.0: a revised database of O-glycosylated proteins

O-GLYCBASE is an updated database of information on glycoproteins and their O-linked glycosylation sites. Entries are compiled and revised from the literature, and from the SWISS-PROT database. Entries include information about species, sequence, glycosylation sites and glycan type. O-GLYCBASE is now fully cross-referenced to the SWISS-PROT, PIR, PROSITE, PDB, EMBL, HSSP, LISTA and MIM databases. Compared with version 1.0 the number of entries have increased by 34%. Revision of the O-glycan assignment was performed on 20% of the entries. Sequence logos displaying the acceptor specificity patterns for the GalNAc, mannose and GlcNAc transferases are shown. The O-GLYCBASE database is available through WWW or by anonymous FTP.

M-mode echocardiography in aortic stenosis. Clinical correlates and prognostic significance after valve replacement

To relate preoperative findings at M-mode echocardiography to preoperative clinical and haemodynamic status and to identify possible echocardiographic risk factors for mortality after aortic valve replacement (AVR), 250 patients with AVR for aortic stenosis (AS) were studied. In follow-up averaging 3.2 years there were 22 early (< 30 days) and 23 late deaths. Rising NYHA function class and cardiothoracic index, and left ventricular (LV) failure were related to rising LV end-diastolic and end-systolic diameter index (EDDI, ESDI), and to increasing LV muscle mass index and decreasing fractional shortening (FS). High peak-to-peak systolic aortic valve gradient and LV end-systolic pressure were related to small dimensions of LV with increased FS and posterior wall thickness (PWTh). EDDI < or = 20 mm/m2 and increasing PWTh were independent risk factors for early mortality. Patients with EDDI < or = 20 mm/m2 had normal or supranormal FS. PWTh was the only independent risk factor in long-term survival: 5-year rates being 81 +/- 6%, 94 +/- 3% and 85 +/- 7% for PWTh < or = 13, 14-17 and > or = 18 mm, respectively (p = 0.03). Prevalence of concomitant coronary artery disease (CAD) rose with decreasing PWTh. Angina pectoris in non-CAD patients was related to very high PWTh. Subnormal EDDI was associated with poor surgical outcome, and dilated, poorly contracting LV with congestive heart failure prior to AVR. The degree of LV hypertrophy seemed to be the dominant risk factor, but confounders included myocardial ischaemia due to CAD in low-grade hypertrophy or to hypertrophy per se. A hypothetically confounding factor is the reversibility potential of moderate or severe LV hypertrophy following AVR.

Mortality and worsening of prognostic profile during waiting time for valve replacement in aortic stenosis

In a prospective study 99 consecutive patients with operative indication due to severe aortic stenosis (AS) were put on a surgical waiting list. The waiting-time to aortic valve replacement (AVR) averaged 6.3 months (0.5-19 months). There were 58 men and 41 women with a mean age of 61 years (21-82 years). The patients were divided into three groups: group I (n = 81) with an uneventful stay on the waiting list (including one patient who declined the AVR offer); group II (n = 11) with significant worsening of a prognostic index; and group III (n = 7) with patients who died during the waiting-time. The waiting-list death rate was 13.5 +/- 5.0% patient-year-1 compared with a post-AVR death rate of 4.9 +/- 0.9%. patient-year-1 (p < 0.05) with a mean post-AVR follow-up of 5.7 years. According to their prognostic index at inclusion, group II patients had a predicted (by a Cox model) 7-year post-AVR survival probability of 72%, but only of 61% according to their prognostic index immediately preoperatively; their observed 7-year post-AVR survival was 60%. Logistic regression analysis identified high age, short duration of symptoms, severe hypertrophy and strain in the ECG, female sex, and deranged left-ventricular diastolic function (related to severely increased left-ventricular muscle mass) as independent predictors of death on the waiting-list and prognosis worsening. From a clinical viewpoint, the predictive models did not allow sufficiently accurate identification of the patients at risk during the waiting-time. The consequences of a surgical waiting-time averaging 6 months are serious for AS patients. The death rate is high and a subgroup worsen their prognostic profile, with significantly reduced post-AVR long-term survival as the result.

Relationship between protein structure and geometrical constraints

We evaluate to what extent the structure of proteins can be deduced from incomplete knowledge of disulfide bridges, surface assignments, secondary structure assignments, and additional distance constraints. A cost function taking such constraints into account was used to obtain protein structures using a simple minimization algorithm. For small proteins, the approximate structure could be obtained using one additional distance constraint for each amino acid in the protein. We also studied the effect of using predicted secondary structure and surface assignments. The constraints used in this approach typically may be obtained from low-resolution experimental data. When using a cost function based on distances, half of the resulting structures will be mirrored, because the resulting structure and its mirror image will have the same cost. The secondary structure assignments were therefore divided into chirality constraints and distance constraints. Here we report that the problem of mirrored structures, in some cases, can be solved by using a chirality term in the cost function.