Publications

Acute human immunodeficiency virus (HIV) infection is associated with the rapid development of neutralization escape mutations. The degree to which viral evolution persists in chronic infection has not been well characterized, nor is it clear if all patients develop high-level neutralization antibody escape. We therefore measured neutralizing antibody responses against autologous and heterologous viruses in a cohort of acutely and chronically infected subjects (n = 65). Neutralizing antibody responses against both autologous virus and heterologous viruses were lower among individuals with acute infection than among those with chronic infection. Among chronically infected individuals, there was a negative correlation between the level of neutralizing antibodies against autologous virus and the level of viremia. In contrast, there was a positive correlation between the level of neutralizing antibodies against a panel of heterologous viruses and the level of viremia. Viral evolution, as defined by the presence of higher neutralizing titers directed against earlier viruses than against contemporaneous viruses, was evident for subjects with recent infection but absent for those with chronic infection. In summary, neutralizing antibody responses against contemporaneous autologous viruses are absent in early HIV infection but can be detected at low levels in chronic infection, particularly among those controlling HIV in the absence of therapy. HIV replication either directly or indirectly drives the production of increasing levels of antibodies that cross-neutralize heterologous primary isolates. Collectively, these observations indicate that although HIV continuously drives the production of neutralizing antibodies, there may be limits to the capacity of the virus to evolve continuously in response to these antibodies. These observations also suggest that the neutralizing antibody response may contribute to the long-term control of HIV in some patients while protecting against HIV superinfection in most patients.

Pharmacogenomics (PGx), the use of genetic information to individualize drug therapy, is an immediate and important application of the Human Genome Project. The advent of PGx presents challenges to the U.S. Food and Drug Administration (FDA) in pursuing its mandate of protecting public health and safety. The authors conducted a review of academic, industry, and government literature using a technology diffusion framework to identify issues faced by the FDA relevant to the application of PGx. Two hundred and ten articles were reviewed. Key issues were categorized as rationale and structure for PGx regulation, regulation of PGx-based testing technologies, regulation of applications in clinical settings, regulation of data, and regulation of product life cycles. This review identifies issues faced by the FDA with respect to PGx, which the FDA is addressing through several initiatives. It also illustrates the complex issues involved in developing, implementing, and adopting new technologies.

The clinical course of idiopathic pulmonary fibrosis (IPF) is variable; however, the long-term survival in IPF is poor. Prednisone has been the mainstay of therapy since its release for clinical use in 1948. Recently, prednisone combined with azathioprine or cyclophosphamide has been used. A number of other drug combinations have been tried with prednisone (e.g., methotrexate, colchicine, penicillamine, or cyclosporine) but have failed or are not well tolerated by the patient. Few high quality, prospective, controlled clinical trials have been performed. Thus, there is no good evidence to support the routine use of any specific therapy in the management of IPF. Additional large clinical trials are needed to confirm the potential usefulness of the newer agents (e.g., IFN-gamma1b, pirfenidone, N-acetylcysteine, coumadin, bosentan, or etanercept). This article examines the body of evidence supporting the current therapies and reviews the newer agents being tested in patients with IPF.

In the American Thoracic Society/European Respiratory Society consensus classification, idiopathic interstitial pneumonias are classified into seven clinicopathologic entities. The classification is largely based on histopathology, but depends on the close interaction of clinician, radiologist, and pathologist. An accurate diagnosis can be very difficult, especially when deciding between idiopathic pulmonary fibrosis and fibrotic nonspecific interstitial pneumonia; better diagnostic markers are needed. The prognosis of idiopathic pulmonary fibrosis is very poor, with median survival of 2-4 yr after the diagnosis, yet the course of individual patients is highly variable. Predicting prognosis in the individual patient is challenging but various clinical and radiologic variables have been identified. According to several recent clinical trials, the natural history of this disease may involve periods of relative stability punctuated by acute exacerbations of disease that result in substantial morbidity or death. Nonspecific interstitial pneumonia is characterized by a distinct histopathologic appearance and a better prognosis than idiopathic pulmonary fibrosis. However, there is still confusion and controversy over the relationship between idiopathic pulmonary fibrosis and fibrotic nonspecific interstitial pneumonia.

Congenital diaphragmatic hernia (CDH) is a common birth defect with a high mortality and morbidity. There have been few studies that have assessed copy number changes in CDH. We present array comparative genomic hybridization data for 29 CDH patients to identify and map chromosome aberrations in this disease. Three patients with 15q26.1-15q26.2 deletions had heterogeneous breakpoints that overlapped with the critical 4 Mb region previously delineated for CDH, confirming 15q26.1-15q26.2 as a critical region for CDH. The three other most compelling CDH-critical regions for genomic deletions based on these data and a literature review are located at chromosomes 8p23.1, 4p16.3-4pter, and 1q41-1q42.1. Based on these recurrent deletions at 15q26.1-15q26.2, we hypothesized that loss-of-function mutations in a gene or genes from this region could cause CDH and sequenced six candidate genes from this region in more than 100 patients with CDH. For three of these genes (CHD2, ARRDC4, and RGMA), we identified missense changes and that were not identified in normal controls; however, none of these alterations appeared unambiguously causal with CDH. These data suggest that CDH caused by chromosome deletions at 15q26.2 may arise because of a contiguous gene deletion syndrome or may have a multifactorial etiology. In addition, there is evidence for substantial genetic heterogeneity in CDH and diaphragmatic hernias can be non-penetrant in patients who have deletions involving CDH-critical regions.