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Genomics and Infectious Disease
Summary: Joseph DeRisi is applying the latest genomic technology, such as DNA microarrays, to detect unknown viruses and explore the genetic machinery of malaria, to develop new treatments.
My laboratory uses a wide variety of approaches to study infectious diseases. This includes use of genomic technologies and bioinformatics for the study of P. falciparum and the investigation of diseases of unknown etiology. Both of these research targets are served by a core interest in developing new technologies for biomedical applications.
Malaria
The majority of the world's infectious disease burden can be attributed to just a handful of pathogens. Among these, Plasmodium falciparum ranks as the most vicious and arguably one of the most neglected afflictions known to humankind. This protozoan parasite is the causative agent of the most deadly form of human malaria: more than 1 million people will perish every year, in addition to a far greater number who will suffer repeated debilitating infections. Beyond the immediate human toll, the burden of malaria has a profoundly negative impact on socioeconomic development in those regions where the disease is endemic. The global eradication campaigns initiated in the middle of the last century failed miserably, and more recent programs to slow the increasing rates of infection have had only modest effects. These efforts have been severely hampered by the emergence of drug-resistant strains of P. falciparum. Indeed, the mainline defense of many nations (chloroquine) has become useless. Although vector control is an immediate and crucial component of malaria prevention, there is also a dire need for new, cheap antimalarial therapeutics.
In addition to seeking to advance fundamental understanding of Plasmodium molecular physiology and genomics, my laboratory is pursuing the discovery and development of new malaria therapeutics. Although the causative agent of malaria has been known for more than a century, our knowledge of malaria molecular biology is shockingly sparse when compared to knowledge of a model organism such as Saccharomyces cerevisiae, which has a comparable genome size. We believe that pushing the frontiers of Plasmodium biology will yield insights that will ultimately aid both drug and vaccine development.
Drug discovery. Our drug discovery efforts are twofold. First, in collaboration with Kip Guy (University of California, San Francisco/St. Jude Children's Research Hospital, Memphis), we have exploited the "privileged" scaffold approach by developing and testing novel compounds in the quinoline series. These compounds, especially the 4-aminoquinoline series, have a proven track record of success against malaria and have several desirable characteristics, including cheap synthetic routes, bioavailability, excellent toxicity profiles, and a reasonable metabolic half-life. We seek to discover new compounds in this series that bypass chloroquine drug resistance, yet retain the pharmacokinetic and medicinal chemical properties of cholorquine.
As a parallel approach to directed synthesis, we have implemented medium-throughput screens utilizing both private and commercially available compound libraries to discover novel classes of antimalarial small molecules. All compounds are tested at multiple concentrations against a variety of P. falciparum strains in a whole-cell growth assay, and promising leads are then pursued by traditional medicinal chemical approaches.
As with our genomic data, we are publishing on the Web and making freely available the results of our synthesis and screening efforts, including negative data. We hope that this effort will be the kernel of a larger effort to create a public database of antimalarial compounds and screening data. This open-source approach to drug discovery is intended to reduce unnecessary duplication of effort, which is common in this area.
Plasmodium genomics. Our laboratory seeks to discover and dissect fundamental regulatory mechanisms that govern Plasmodium development. As a first step in this process, we have developed an expression-profiling platform based on long (70mer) oligonucleotide arrays. These arrays are produced in-house, using robotics and software of my own design, and allow us the freedom to execute large numbers of expression experiments at modest cost.
To facilitate our expression experiments, we have pioneered the development of multiliter bioreactor techniques for growing large quantities of parasites, thus enabling us to conduct high-time-resolution experiments. Our first large-scale effort was to profile the intraerythrocytic developmental life cycle (IDC) of P. falciparum. Sampling from the bioreactor on the hour, every hour, for more than 50 hours produced a detailed portrait of the malarial transcriptome. This portrait revealed a continual cascade of gene expression, whereby the vast majority of genes are induced once, and only once, per life cycle. The biochemical functionalities represented in the transcriptome are well ordered and are reminiscent of a "just-in-time" assembly process. Such a tightly regulated and well-ordered cascade implies that small perturbations in gene regulation may cause catastrophic failure for the parasite. We are now seeking both the transcriptional determinants of this cascade and the post-transcriptional modifiers, including decay processes and kinase-signaling pathways. These efforts may ultimately identify novel therapeutic targets and spawn new avenues toward drug development.
The Virus Chip
A second focus of our lab is the pursuit of viral agents associated with diseases of unknown etiology. In collaboration with Don Ganem (HHMI, University of California, San Francisco), we have developed a screening system that is able to detect essentially all known sequenced viruses and potentially new, previously undiscovered viruses. Although we have evaluated the system in a controlled setting, we have also used the virus chip to identify the etiological agent of SARS (severe acute respiratory syndrome), as part of the global emergency effort initiated by the Centers for Disease Control and Prevention and the World Health Organization.
Through retrospective studies of adult and pediatric populations, we are evaluating the virus chip as a realistic alternative to currently used viral diagnostics. Patients hospitalized with unexplained critical respiratory illness suffer from a high mortality rate (>30 percent). This highlights the need for a new generation of panviral diagnostics, and we believe the greatly expanded scope of our technology will lead to a better understanding of the circulating flora of infectious respiratory disease and the disease spectra associated with each pathogen and, ultimately, to better antiviral development.
In parallel with the development of the virus chip itself, we are also developing the bioinformatic algorithms to critically evaluate results from clinical samples, with the goal of providing automated analysis of virus chip data.
Of primary interest for this project are diseases of unknown etiology, such as fulminant hepatitis (non-A, -B, -C, and -E), presumed encephalitis, AIDS-related lymphomas, and other cancers. Recently, in collaboration with Robert Silverman (Lerner Research Institute, Cleveland), we have used the virus chip to discover a novel gamma retrovirus (XMRV) associated with prostate cancer. This virus is found in the prostate tissue of patients who are homozygous for mutations in the antiviral defense enzyme RNaseL. Although this discovery does not prove causation, we are pursuing the possible link between infection with this virus and oncogenesis.
Last updated: September 10, 2008
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