Prediction of survival in follicular lymphoma based on molecular features of tumor-infiltrating immune cells.

Background: Patients with follicular lymphoma may survive for periods of less than 1 year to more than 20 years after diagnosis. We used gene-expression profiles of tumor-biopsy specimens obtained at diagnosis to develop a molecular predictor of the length of survival.

Methods: Gene-expression profiling was performed on 191 biopsy specimens obtained from patients with untreated follicular lymphoma.

Clinical implications of macrolide therapy in chronic sinopulmonary diseases.

Macrolides have broad antibacterial spectrum and proven efficacy in the management of respiratory tract infections. Over the past decade there has been progressive interest in these agents for their potential role as tissue modifying, anti-inflammatory agents. Increasingly, the effect of macrolides on numerous cell types has been documented.

Candidate epitope identification using peptide property models: application to cancer immunotherapy.

Peptides derived from pathogens or tumors are selectively presented by the major histocompatibility complex proteins (MHC) to the T lymphocytes. Antigenic peptide-MHC complexes on the cell surface are specifically recognized by T cells and, in conjunction with co-factor interactions, can activate the T cells to initiate the necessary immune response against the target cells. Peptides that are capable of binding to multiple MHC molecules are potential T cell epitopes for diverse human populations that may be useful in vaccine design.

Evaluating the efficiency of targeted designs for randomized clinical trials.

Purpose: Genomic technologies make it increasingly possible to identify patients most likely to benefit from a molecularly targeted drug. This creates the opportunity to conduct targeted clinical trials with eligibility restricted to patients predicted to be responsive to the drug.

Experimental Design: We evaluated the relative efficiency of a targeted clinical trial design to an untargeted design for a randomized clinical trial comparing a new treatment to a control.

Iterative class discovery and feature selection using Minimal Spanning Trees.

Background: Clustering is one of the most commonly used methods for discovering hidden structure in microarray gene expression data. Most current methods for clustering samples are based on distance metrics utilizing all genes. This has the effect of obscuring clustering in samples that may be evident only when looking at a subset of genes, because noise from irrelevant genes dominates the signal from the relevant genes in the distance calculation.

Plasminogen activator inhibitor-1 impairs alveolar epithelial repair by binding to vitronectin.

The pathogenesis of pulmonary fibrosis is thought to involve alveolar epithelial injury that, when successfully repaired, can limit subsequent scarring. The plasminogen system participates in this process with the balance between urokinase-type plasminogen activator (uPA) and plasminogen activator inhibitor-1 (PAI-1) being a critical determinant of the extent of collagen accumulation that follows lung injury. Because the plasminogen system is known to influence the rate of migration of epithelial cells, including keratinocytes and bronchial epithelial cells, we hypothesized that the balance of uPA and PAI-1 would affect the efficiency of alveolar epithelial cell (AEC) wound repair.

Localization of plasminogen activator activity within normal and injured lungs by in situ zymography.

During inflammatory lung injury, the fibrinolytic activity that is normally present within bronchoalveolar lavage (BAL) fluid (BALF) is often suppressed due to increased levels of inhibitors, including plasminogen activator inhibitor (PAI)-1. Despite this suppression, BALF frequently contains fibrin degradation products, indicating persistence of fibrinolytic activity within the lung. To address this discrepancy and determine the sites where plasminogen activation is occurring, we developed an in situ zymographic technique for frozen sections of lung tissue that localizes plasminogen activator activity at the cellular level.

In silico simulation of inhibitor drug effects on nuclear factor-kappaB pathway dynamics.

NF-kappaB is a transcription factor family that activates numerous genes that are related to cell survival, apoptosis, and cell migration. Its persistent activity is associated with tumor formation, growth, metastasis, and drug resistance in many cancer types, including lymphoma, colon cancer, and breast cancer. Current therapeutic efforts for inhibiting this central "switch" include using small molecules to block a selected target in this pathway.

Genomewide conserved epitope profiles of HIV-1 predicted by biophysical properties of MHC binding peptides.

We propose a new method for predicting MHC binding of peptides using biophysical parameters of the constituent amino acids. Unlike conventional matrix-based methods, our method does not assume independent binding of the individual side chains and uses a model that simultaneously represents all the residues. The model discovers the quantified 9-mer "property model" within the longer peptides that are most common among binders.

A powerful combination: the use of positional scanning libraries and biometrical analysis to identify cross-reactive T cell epitopes.

Studies on the elucidation of the specificity of the T cell receptor (TCR) at the antigen and peptide level have contributed to the current understanding of T cell cross-reactivity. Historically, most studies of T cell specificity and degeneracy have relied on the determination of the effects on T cell recognition of amino acid changes at individual positions or MHC binding residues, and thus they have been limited to a small set of possible ligands. Synthetic combinatorial libraries (SCLs), and in particular positional scanning synthetic combinatorial libraries (PS-SCLs) represent collections of millions to trillions of peptides which allow the unbiased elucidation of T cell ligands that stimulate clones of both known and unknown specificity.

Expansion and functional relevance of high-avidity myelin-specific CD4+ T cells in multiple sclerosis.

Multiple sclerosis (MS) is an autoimmune disease in which myelin-specific T cells are believed to play a crucial pathogenic role. Nevertheless, so far it has been extremely difficult to demonstrate differences in T cell reactivity to myelin Ag between MS patients and controls. We believe that by using unphysiologically high Ag concentrations previous studies have missed a highly relevant aspect of autoimmune responses, i.

The plasminogen activation system reduces fibrosis in the lung by a hepatocyte growth factor-dependent mechanism.

Mice deficient in the plasminogen activator inhibitor-1 gene (PAI-1-/- mice) are relatively protected from developing pulmonary fibrosis from bleomycin administration. We hypothesized that one of the protective mechanisms may be the ability of the plasminogen system to enhance hepatocyte growth factor (HGF) effects, which have been reported to be anti-fibrotic in the lung. HGF is known to be sequestered in tissues by binding to extracellular matrix components.

Curvilinear, geometric and phylogenetic modeling of basicranial flexion: is it adaptive, is it constrained?

Prior work has shown that the degree of basicranial flexion among primates is determined by relative brain size, with anatomically modern humans possibly having a less flexed basicranium than expected for their relative brain size. Basicranial flexion has also been suggested to be adaptive in that it maintains a spheroid brain shape, thereby minimizing connections between different parts of the brain. In addition, it has been argued that the degree of flexion might be constrained such that increases in relative brain size beyond that seen in Australopithecus africanus were accommodated by mechanisms other than basicranial flexion.

A random variance model for detection of differential gene expression in small microarray experiments.

Motivation: Microarray techniques provide a valuable way of characterizing the molecular nature of disease. Unfortunately expense and limited specimen availability often lead to studies with small sample sizes. This makes accurate estimation of variability difficult, since variance estimates made on a gene by gene basis will have few degrees of freedom, and the assumption that all genes share equal variance is unlikely to be true.

Application of support vector machines for T-cell epitopes prediction.

Motivation: The T-cell receptor, a major histocompatibility complex (MHC) molecule, and a bound antigenic peptide, play major roles in the process of antigen-specific T-cell activation. T-cell recognition was long considered exquisitely specific. Recent data also indicate that it is highly flexible, and one receptor may recognize thousands of different peptides.

A strategy for detection of known and unknown SNP using a minimum number of oligonucleotides applicable in the clinical settings.

Detection of unknown single nucleotide polymorphism (SNP) relies on large scale sequencing expeditions of genomic fragments or complex high-throughput chip technology. We describe a simplified strategy for fluorimetric detection of known and unknown SNP by proportional hybridization to oligonucleotide arrays based on optimization of the established principle of signal loss or gain that requires a drastically reduced number of matched or mismatched probes. The array consists of two sets of 18-mer oligonucleotide probes.

Using DNA microarrays for diagnostic and prognostic prediction.

DNA microarrays are a potentially powerful technology for improving diagnostic classification, treatment selection and prognostic assessment. There are, however, many potential pitfalls in the use of microarrays that result in false leads and erroneous conclusions. Effective use of this technology requires new levels of interdisciplinary collaboration with statistical and computational scientists.

Molecular diagnosis of primary mediastinal B cell lymphoma identifies a clinically favorable subgroup of diffuse large B cell lymphoma related to Hodgkin lymphoma.

Using current diagnostic criteria, primary mediastinal B cell lymphoma (PMBL) cannot be distinguished from other types of diffuse large B cell lymphoma (DLBCL) reliably. We used gene expression profiling to develop a more precise molecular diagnosis of PMBL. PMBL patients were considerably younger than other DLBCL patients, and their lymphomas frequently involved other thoracic structures but not extrathoracic sites typical of other DLBCLs.

Evaluation of normalization methods for microarray data.

Background: Microarray technology allows the monitoring of expression levels for thousands of genes simultaneously. This novel technique helps us to understand gene regulation as well as gene by gene interactions more systematically. In the microarray experiment, however, many undesirable systematic variations are observed.

Distinguishing right from left colon by the pattern of gene expression.

Distinct epidemiological and clinicopathological characteristics of colorectal carcinomas (CRCs) based on their anatomical location suggest different risk factors and pathways of transformation associated with proximal and distal colon carcinogenesis. These differences may reflect distinct biological characteristics of proximal and distal colonic mucosa, acquired in embryonic or postnatal development, that determine a differential response to uniformly distributed environmental factors. Alternatively, the differences in the epidemiology of proximal and distal CRCs could result from the presence of different procarcinogenic factors in the ascending versus descending colon, acting on cells with either similar or distinct biological characteristics.

Reduction in fibrotic tissue formation in mice genetically deficient in plasminogen activator inhibitor-1.

Mice with homozygous deletion of the plasminogen activator inhibitor-1 gene (PAI-1(-/-)) are relatively protected from bleomycin-induced pulmonary fibrosis. At least part of the protective effect appears to occur during the latter stages of the pathological process when fibrotic tissue is being deposited. To investigate the effect of PAI-1 deficiency on fibrosis, we studied the accumulation of fibrotic tissue within subcutaneously implanted polyvinyl alcohol sponges.