Constructing ‘beautiful, basic science’

Scripps Florida scientists build ribosome assembly process; discover key targets of new anticancer drug candidates

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JUPITER, Fla.—Targeted toward discovering new treatments to fight breast cancer and other malignancies, scientists at the Florida campus of The Scripps Research Institute (TSRI) have solved a puzzle surrounding ribosomes. They have done so by confirming that the ribosome assembly process is potentially a new fertile target for anticancer drugs, and detailed the essential function of a key component of that process in a study published in the March 16 issue of the Journal of Cell Biology.
Ribosomes are ancient molecular machines that produce proteins in cells, are required for cell growth in all organisms and accomplish strikingly complex tasks with apparent ease, according to lead researcher Katrin Karbstein, associate professor in the TSRI cancer biology department. But defects in the assembly process and its regulation can lead to serious biological problems, including cancer.
“This study confirms that ribosome assembly is a good therapeutic target in cancer,” Karbstein stated in a news release. “Whether or not we have pinpointed the best molecule remains to be shown, but this is a vindication of our basic research. There should be effort devoted to exploring this pathway.”
“In my view, (Karbstein) is the best biochemist in her field and clearly a rising star,” Prof. Thomas Kodadek, chair of the TSRI department of cancer biology, tells DDNews. “As you may know, this work is an extension of her beautiful, basic science of how the ribosome assembles. As such, it provides a nice case study in how a firm understanding of the biochemical details of a system can contribute to something highly practical, like identification of a drug target. We would like to think that the translational environment here at Scripps was conducive to getting Katrin to think along these lines.”
Ribosome assembly—which involves about 200 essential proteins known as "assembly factors" in addition to the four RNA molecules and 78 ribosomal proteins that are part of the mature ribosome—has become a fruitful area of research in recent years because of the importance of ribosome assembly for cell growth, Karbstein stated.
The new study highlights the molecules casein kinase 1δ (CK1δ) and CK1ε, which are essential for human ribosome assembly. The expression of CK1δ is elevated in several tumor types, as well as Alzheimer’s and Parkinson’s disease—and CK1δ inhibitors have shown promise in some preclinical animal studies.
Karbstein and her group—working closely with three labs across the state of Florida, including the laboratory of William Roush at Scripps Florida—used Hrr25, the yeast equivalent of casein kinase 1δ (CK1δ) and CK1ε, as a research model.
Biochemical experiments showed that Hrr25 is necessary for ribosome assembly and that the molecule normally adds a phosphate group to an assembly factor called Ltv1, allowing it to separate from other subunits and mature, she said. If Hrr25 is inactivated or a mutation blocks the release of Ltv1, the assembly process is doomed.
“Inhibiting Hrr25 and the subsequent release of Ltv1 blocks the formation of other subunits that are required for maturation—and the subsequent production of proteins,” according to Homa Ghalei, the first author of the study and a member of the Karbstein lab.
In additional experiments on human breast cancer cells, the researchers showed that CK1δ/CK1ε inhibitors no longer induce programmed cell death (apoptosis) and prevent cancer cells from growing when Ltv1 is removed.
“This clearly establishes that the antiproliferative potency of these inhibitors is in large part due to blocking ribosome assembly,” Karbstein said.
“Previous work had implicated CK1d in 40S ribosome assembly,” Karbstein tells DDNews. “We had a hunch about what exactly it was doing and followed up on that.”
Karbstein is applying for grants to “follow up on this work specifically, and have funding to better understand the mechanism of other potential drug target candidates. Nevertheless, this is currently by far the best target,” she says. “Our work addresses the role of CK1d in physiological and pathological states. All cancers that overexpress CK1 delta should be targets. Our current work involves triple-negative breast cancer cells, but it is likely that other cancers might be similarly susceptible to CK1d inhibitors.”
In addition, “Parkinson's disease is also linked to increased expression of CK1d and ribosomes,” she says. “We have not explored this route, but it is very conceivable that CK1 inhibitors might provide therapeutic benefit in these cases, as well. We have mostly approached this problem from a basic science perspective. You first need to understand a pathway before exploiting its vulnerabilities, and our recent work is a vindication of that. We and others have learned a lot about the mechanism of ribosome assembly.”
Many others “have developed a catalog of assembly factors,” she says, including the Ross Hannan lab in Australia, which has developed a drug (CX-5461) currently in Phase 1 trials that blocks the first step in ribosome assembly, the transcription of rRNA.
In April, Karbstein was taking the next step by applying for two research grants, she said.
The short-term goals of this research are “to establish ribosome assembly as the prime target for CK1 delta inhibitors, and the assembly pathways as a viable drug target,” Karbstein says. “A basic science goal is to better understand the regulation of ribosome assembly; a translational goal would be to see our discoveries used in the clinic.”
In addition to Karbstein and Ghalei, other authors of the study, “Hrr25/CK1d-Directed Release of Ltv1 From Pre-40S Ribosomes Is Necessary For Ribosome Assembly And Cell Growth”, are Joanne R. Doherty, Yoshihiko Noguchi and William R. Roush of TSRI; Franz X. Schaub and John L. Cleveland of the Moffitt Cancer and Research Institute and M. Elizabeth Stroupe of Florida State University.

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