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The Skaggs Institute
for Chemical Biology

Scientific Report 2006

Training in Molecular and Experimental Medicine

E. Beutler

There has been widespread national concern about the fact that discoveries in the laboratory are translated to clinical practice slowly, if at all. The main cause of delay is a regulatory network that impedes translation, but even if this problem were overcome, we need a cadre of young scientists trained in the study of human disease, the mechanisms that underlie the diseases, and their treatment. The Skaggs Institute for Chemical Biology is helping to achieve this goal by supporting the training of young scientists in the Department of Molecular and Experimental Medicine at Scripps Research.

Yueh-Luen Lee is studying the mechanisms by which the S-phase checkpoint is operated in mammalian cells. Genome instability is a hallmark of the malignant phenotype and a driving force for tumorigenesis. The S-phase checkpoint is a principal defense mechanism to maintain genome stability. Mutations in checkpoint genes contribute to many types of lymphoid malignant neoplasms, particularly in the context of ataxia telangiectasia, which has a defect in the gene for ATM and impairs the S-phase checkpoint.

The detailed mechanism by which the S-phase checkpoint is operated in mammalian cells remains unclear. Dr. Lee’s preliminary data suggest an important role for the regulatory subunit Dbf4 of the kinase Cdc7. The phosphorylation modification of Dbf4 in response to DNA damage and the mechanism by which Dbf4/Cdc7 participates in the S-phase checkpoint will be investigated. These studies may clarify molecular pathways that link damage signal transduction through Dbf4/Cdc7 to the effector proteins to regulate the S-phase checkpoint. They will help to elucidate the overall mechanism of the S-phase checkpoint in mammalian cells and shed light on the cellular mechanisms that control genome stability and prevent cancer.

Jaroslav Truksa is studying the regulation of the transcription of hepcidin, an antimicrobial peptide that plays a key role in iron metabolism. He is investigating the molecular mechanisms that lead to hepcidin upregulation after stimulation with IL-6, bone morphogenetic protein 9, or iron. He has developed a luciferase reporter system suitable for use in both cell culture systems and in vivo imaging, footprinting, and electrophoretic mobility shift assays to disclose the pathways that regulate hepcidin expression. Better understanding of hepcidin regulation could provide new drug targets that could be useful in treatment of patients with anemia of chronic disease and patients with hemochromatosis.

Zhengyi Ye is studying transthyretin amyloid. Most transthyretin is synthesized in the liver and choroid plexus and secreted into the blood stream and cerebrospinal fluid. The main function of transthyretin is to transport thyroid hormone and retinal binding protein–vitamin A complex. Low levels of transthyretin in the cerebrospinal fluid are common among patients who have Alzheimer’s disease. Amyloid beta (Aβ) peptides in human brain are the pathologic hallmark of Alzheimer’s disease, and some in vitro studies suggest that transthyretin interacts with Aβ and prevents the fibril formation. In a mouse model of Alzheimer’s disease, transthyretin was upregulated in the brain, a finding that may account for the less severe phenotypes in the mouse model compared with human patients. One of Dr. Ye’s projects is to further study the interaction between Aβ and transthyretin by using surface plasmon resonance. His data suggest that recombinant human transthyretin only interacts with the Aβ fibril and that transthyretin aggregates and monomer have much higher interaction with Aβ fibril than tetramer does. Mouse tetramer transthyretin also binds to Aβ fibril with much higher affinity than human tetramer transthyretin does. He is addressing the question of whether the binding of transthyretin to the Aβ fibril prevents the cytotoxic effects of the fibril. He will be working on transthyretin expression in patients with Alzheimer’s disease by using real-time polymerase chain reaction.

Wei Zhang is studying the action of pleiotrophin, a secreted, highly conserved cytokine. Pleiotrophin has recently been found to be an angiogenic factor when applied directly to ischemic myocardium and when expressed by cancer cells. The mechanisms through which pleiotrophin signals are of major importance. Pleiotrophin signals through its receptor, receptor protein tyrosine phosphatase (RPTP) β/ζ. The interaction of RPTPβ/ζ with pleiotrophin inactivates the intrinsic tyrosine phosphatase activity of RPTPβ/ζ. β-Catenin, β-adducin, and Fyn are substrates of RPTPβ/ζ, and the tyrosine phosphorylation levels of these proteins are decreased through pleiotrophin signaling. Dr. Zhang has found that anaplastic lymphoma kinase is also a substrate of RPTPβ/ζ and is activated by pleiotrophin. Anaplastic lymphoma kinase is not a direct receptor of pleiotrophin but interacts with and is dephosphorylated by RPTPβ/ζ. He also found that, on the contrary, the kinase activity of Fyn is decreased by pleiotrophin stimulation. By using an established MCF-7/EGFR-RPTPβ/ζ chimera receptor cell line, more experiments will be conducted to define the mechanisms through which pleiotrophin-RPTPβ/ζ signaling regulates different cell functions such as proliferation, differentiation, and angiogenesis through the aforementioned substrates.


Ernest Beutler, M.D. Professor
Chairman, Department of Molecular and Experimental Medicine