Identification of candidate genes for drug discovery by differential display

The Wnt antagonist secreted frizzled-related protein-1 controls osteoblast and osteocyte apoptosis

Mechanisms controlling human bone formation remain to be fully elucidated. We have used differential display-polymerase chain reaction analysis to characterize osteogenic pathways in conditionally immortalized human osteoblasts (HOBs) representing distinct stages of differentiation. We identified 82 differentially expressed messages and found that the Wnt antagonist secreted frizzled-related protein (sFRP)-1 was the most highly regulated of these. Transient transfection of HOBs with sFRP-1 suppressed canonical Wnt signaling by 70% confirming its antagonistic function in these cells. Basal sFRP-1 mRNA levels increased 24-fold during HOB differentiation from pre-osteoblasts to pre-osteocytes, and then declined in mature osteocytes. This expression pattern correlated with levels of cellular viability such that the pre-osteocytes, which had the highest levels of sFRP-1 mRNA, also had the highest rate of cell death. Basal sFRP-1 mRNA levels also increased 29-fold when primary human mesenchymal stem cells were differentiated to osteoblasts supporting the developmental regulation of the gene. Expression of sFRP-1 mRNA was induced 38-fold following prostaglandin E2 (PGE2) treatment of pre-osteoblasts and mature osteoblasts that had low basal message levels. In contrast, sFRP-1 expression was down-regulated by as much as 80% following transforming growth factor (TGF)-beta1 treatment of pre-osteocytes that had high basal mRNA levels. Consistent with this, treatment of pre-osteoblasts and mature osteoblasts with PGE(2) increased apoptosis threefold, while treatment of pre-osteocytes with TGF-beta1 decreased cell death by 50%. Likewise, over-expression of sFRP-1 in HOBs accelerated the rate of cell death threefold. These results establish sFRP-1 as an important negative regulator of human osteoblast and osteocyte survival.

Functional Genomics Conference: From Identifying Proteins to Faster Drug Discovery

The massive effort to sequence the human, mouse, rat, nematode (Caenorhabditis elegans), fruit fly (Drosophila), zebra fish, yeast (Saccharomyces cerevisiae), fungal (Candida albicans and Aspergillus fumigatus) and several bacterial genomes has produced a flood of sequence data. Of the more than 100,000 human genes and thousands from other organisms, many partial sequences and several completed microbial genomes are available in both public and private databases. However, elucidation of function has been achieved for only a very small portion and an even smaller percentage have been validated as drug targets. Many companies interested in identifying new drug targets also see this bounty of opportunity as a major challenge. The raw sequence data say little about the importance of the gene and nothing about its potential as a target for drug discovery. Since 1994, a new term, 'functional genomics', has entered our lexicon. Functional genomics, which in effect is 'high-throughput biology', was originally focused on understanding gene function by studying the genes of simpler organisms, such as the nematode, C. elegans. As the genes from a number of organisms are highly conserved across species, it is believed that studying these basic systems can yield valuable insights for drug companies interested in targeting therapeutics for the higher organisms. More recently, the approach to functional genomics has expanded to include study of gene function in organisms to be targeted for therapeutic intervention. This new approach was the theme of the Functional Genomics Conference: From Identifying Proteins to Faster Drug Discovery held in Washington DC on March 10 and 11, 1998. The organisers (NMHCC) hoped that the breadth of the conference topics would reflect the complexities of the modern drug discovery process and covered technologies from gene chips, bioinformatics, disease models, protein discovery and expression, target validation, high-throughput screening for genes of unknown function, to integration of the drug discovery process. The two day conference placed emphasis on cutting edge technology solutions and the development of high-throughput tools to address the emerging opportunities in genome-based drug discovery.

T lymphocyte activation gene identification by coregulated expression on DNA microarrays

High-capacity methods for assessing gene function have become increasingly important because of the increasing number of newly identified genes emerging from large-scale genome sequencing and cDNA cloning efforts. We investigated the use of DNA microarrays to identify uncharacterized genes specifically involved in human T cell activation. Activation of human peripheral blood T lymphocytes induced significant changes in hundreds of transcripts, but most of these were not unique to T cell activation. Variation of experimental parameters and analysis techniques allowed better enrichment for gene expression changes unique to T cell activation. Best results were achieved by identification of genes that were most highly coregulated with the T-cell-specific transcript interleukin 2 (IL2) in a "compendium" of experiments involving both T cells and other cell types. Among the genes most highly coregulated with IL2 were many genes known to function during T cell activation, together with ESTs of unknown function. Four of these ESTs were extended to novel full-length clones encoding T-cell-regulated proteins with predicted functions in GTP metabolism, cell organization, and signal transduction.

Tachycardia-induced primate model of heart failure in cardiovascular drug discovery

Congestive heart failure (CHF) is a complex, multifactoral disease involving genetic and environmental factors that represents a large unmet medical need. There are currently many animal models of CHF that have provided some insight into the etiology of this disease. However, due to the complex interactions of environmental and genetic components of this disease most animal models are somewhat limited. Nonhuman primates offer a unique opportunity to investigate the genetic aspects of this complex disease due to their close genetic and phenotypic similarity to humans. Here we describe a novel tachycardia-induced primate model of CHF characterized by depressed global function that progresses to a symptomatic stage consistent with clinical data. No animal model, including this one, can exactly mimic the clinical pathophysiology of CHF. However, this tachycardia-induced primate model of CHF has similarities to the dynamic state of CHF in humans and affords the opportunity to evaluate changes in gene expression using genomic and proteomic technologies throughout the progression of the disease.

Identification of genes regulated by muscarinic acetylcholine receptors: application of an improved and statistically comprehensive mRNA differential display technique

In order to identify genes that are regulated by muscarinic acetylcholine receptors, we developed an mRNA differential display technique (DD) approach. By increasing redundancy and by evaluating optimised reagents and conditions for reverse transcription of total RNA, PCR and separation of PCR products, we generated a DD protocol that yields highly consistent results. A set of 64 distinct random primers was specifically designed in order to approach a statistically comprehensive analysis of all mRNA species in a defined cell population. This modified DD protocol was applied to total RNA of HEK293 cells stably expressing muscarinic m1 acetylcholine receptors and cells stimulated with the receptor agonist carbachol were compared to identical but non-stimulated cells. In 81 of 192 possible PCR experiments, 38 differential bands were identified. Sequence analysis followed by northern blot analyses confirmed differentially expressed genes in 19 of 23 bands analysed. These represented 10 distinct immediate-early genes that were up-regulated by m1AChR activation: Egr-1, Egr-2, Egr-3, NGFi-B, ETR101, c- jun, jun -D, Gos-3 and hcyr61, as well as the unknown gene Gig-2. These data show that this improved DD protocol can be readily applied to reliably identify differentially expressed genes.

Functional genomics: from genes to new therapies

The application of genomics in pharmaceutical R&D is presently one of the central issues in the industry. The evolution of functional genomics approaches and their integration into a technology platform for therapeutic discovery is a challenging and complex process. In this review, the authors describe how functional genomics will offer significant opportunities in the search for causal and disease-modifying therapies for better treatment of society's most outstanding medical needs.