Better explicating the strengths and shortcomings of these models will help refine projections and improve transparency in the years ahead.
Image credit: Witsawat.S.
To bakers, yeast is important for leavening dough. To geneticist Philip Hieter, yeast can help unravel human disease. Hieter, a professor at the University of British Columbia’s Michael Smith Laboratories and member of the National Academy of Sciences, believes that model organisms, such as yeast, represent the future of genetics, as discoveries made using such organisms are increasingly linked to human disorders.
Philip Hieter. Image courtesy of Philip Hieter.
Hieter, born in 1952, grew up in Garden City, New York, with two older brothers and an older sister. As an undergraduate at The Johns Hopkins University in the early 1970s, Hieter worked in the laboratory of Carl Levy, who worked to isolate ribonuclease enzymes from soil in an early effort at RNA sequencing.
A year after graduating, Hieter attended a seminar given by Philip Leder, a molecular biologist at the National Institutes of Health in Bethesda, Maryland. Leder and his colleagues had just cloned mouse antibody genes using bacteriophage cloning vectors, and were studying the phenomenon of genetic recombination that endows the immune system with a rich array of antibodies. “The talk blew my mind,” Hieter says.
Inspired, Hieter arranged to work as a graduate student in Leder’s laboratory. Mentored by postdoctoral scholar John Seidman (“a wizard,” Hieter says), Hieter cloned the κ and λ light-chain genes that encode human antibodies. “Cloning the first gene took forever,” Hieter says, but once he cloned the κ gene (1), the λ gene soon followed (2). Hieter, Seidman, and immunologist Stan Korsmeyer worked together to investigate the nature of B-cell leukemias, blood cancers that affect immune system cells (3). The work led to Hieter’s doctoral dissertation (4) and the 1981 Council of Graduate Schools/University Microfilms International Dissertation Prize.
About a year before Hieter’s graduation, Leder suggested that he start exploring options for a postdoctoral fellowship. Hieter talked to NIH colleagues, and learned of Ronald Davis at Stanford University. Davis had been developing yeast as a model organism for genetic studies, and had developed techniques for inserting yeast genes into Escherichia coli bacteria (5), allowing for DNA transformation markers and gene replacement in yeast.
Hieter moved to Stanford, California, in 1982 to begin his postdoctoral fellowship. As an East Coast native, he was impressed with his new setting. “Stanford looked like a country club,” he says. “Everyone seems to have a smile on their face all the time.” Hieter found himself in the company of Nobel laureates such as Paul Berg and Arthur Kornberg, and mingling with their graduate students in shared laboratories. “The weather was amazing, but the science was incredible,” Hieter says.
Hieter intended to continue working on mammalian cells, but soon discovered that the simple yeast genome provided a good model system for eukaryotic cells. He also discovered that his own training in bacterial genetics was almost entirely lacking, unlike other postdoctoral scholars. His peers helped him get up to speed. “I saw for the first time the power of genetics,” Hieter says.
Chromosomal Elements
Interested in chromosomal elements such as centromeres, which are structures that facilitate the segregation of chromosomes at mitosis, and origins of replication, DNA sequences that initiate genome replication, Hieter developed a visual assay (6) for determining the stability of yeast chromosomes. He also cloned and sequenced yeast centromeres (7), laying the foundation for his later work as an independent researcher.
Hieter met regularly with Nobel laureate Leland Hartwell, who was on sabbatical at Stanford. Hartwell had discovered the genes responsible for regulating the cell-division cycle in yeast (8). “We would have talks sitting around fountains at the Stanford Medical Center,” Hieter says. “I was amazed by the beauty of his work.”
Midway through his fellowship at Stanford, Hieter received a call from Johns Hopkins. The Molecular Biology and Genetics Department was hiring five new faculty members, and invited Hieter to apply. Hieter hadn’t expected to be in the job market so early, but found himself drawn back to Johns Hopkins. “The scientific atmosphere of the department was exciting,” he says.
Hieter continued his work on chromosome stability, introducing an artificial chromosome into yeast (9) and then testing mutations to see what genes affected the segregation of chromosomes during mitosis. In 1990, Hieter’s group published a collection of 138 mutants, defining about 50 genes that caused mis-segregation of chromosomes (10). Hieter further identified genes that encoded proteins for the kinetochore (11), a structure to which spindles attach to separate chromatids during mitosis. He also explored the genes that arrested the cell cycle after the chromosomes had been replicated but before they initiated segregation into daughter cells (12). Hieter and his group found that the cell-division cycle mutants they had been studying were subunits of a mechanism called the anaphase promoting complex (13). When cells detect that chromosomes have successfully aligned during the metaphase of mitosis, the chemical brake on anaphase promoting complex is released, allowing chromosome separation and the anaphase stage of mitosis to proceed. “It’s a checkpoint,” Hieter says, “a mechanism for cells ensuring that metaphase is complete before you start anaphase.”
In 1992, Hieter tasked a graduate student with cloning the human versions of the genes he had identified as crucial cell-division cycle mutants in yeast. “We started to clone human orthologs of genes we were studying and map them to human chromosomes (14), and then hopefully make a link to human disease gene mutations,” he says. A collaboration with Francis Collins and Yossi Shiloh aimed to gain insights into ataxia telangiectasia mutated gene function immediately after it was positionally cloned, by studying the yeast ortholog (15). Hieter expanded this concept to a community-wide resource to link human and yeast geneticists, by creating a database that cross-referenced the human disease gene genetic map with the biology of yeast genes being studied by yeast researchers (16).
Focus on Cancer
Over the past decade, Hieter and his group have translated the lessons learned from the yeast model system into discoveries relevant to human cancer. “How do you find candidate genes for any human disease?” he asks. “If you know the biology of the human disease, you can guess a pathway and then go to the model organism and define all the genes in that pathway. You then can ask directly: Are the corresponding human genes mutated in patients or not?”
The disease that most chromosome stability researchers were focusing on was cancer. Tumor cells often have altered numbers of chromosomes, suggesting that some cancers may harbor mutations in chromosome separation processes. Since moving to the University of British Columbia in 1997, Hieter has focused on chromosome stability genes, and his group systematically identified in yeast around 700 genes responsible for maintaining genome stability (17). In a collaboration with Hieter, cancer researcher Bert Vogelstein used the list of yeast genes to identify mutations in colon cancer cells in the corresponding human genes in a painstaking gene-resequencing process. They found a set of cohesin genes consistently mutated in tumor cells (18).
Synthetic Lethality
Hieter has been using a concept called “synthetic lethality” to use yeast genetics to identify drug targets for human cancers. Synthetic lethality holds that pairs of mutations exist in cells that, individually, have little or no impact on cell function but are fatal together. Synthetic lethality helps identify related genes because searching for genes synthetically lethal with a kinetochore mutant likely leads to other kinetochore genes. The process can also generate highly specific drug targets. “If the reference mutation is a cancer somatic mutation and the disruption of the second gene specifically kills a cell carrying this mutation but not a cell with the normal gene, it’s a perfect drug target,” Hieter says. Expanding the concept further, Hieter has identified highly conserved networks (19) of genes in mammalian cells that can be knocked out through several approaches.
In 2009, Hieter attended a meeting of the American Society of Human Genetics. One presentation described an effort to identify the gene responsible for a rare disease by directly comparing the genomes of four patients. A subsequent presentation by geneticist David Altshuler expounded on the problem in identifying human disease genes. Altshuler had also been looking at large cohorts of patients to identify genetic variants that were possibly causative of disease. “His point was that finding the gene is just the beginning,” Hieter says. “It’s not the end of the story.” The next task, Altshuler argued, is understanding the biological processes associated with the disease gene’s function. “The way it almost always works is there’s someone who’s already working on the function of the gene in a model system,” Hieter says. “I had a big smile on my face.”
Amid the rapid development in 2010 of next-generation sequencing, which dramatically lowered the cost of sequencing genomes, scientists began identifying rare disease genes, with Canadian scientists identifying around 200 genes over a four-year period. Hieter and colleagues across Canada launched the Rare Disease Models and Mechanisms Network, a registry of researchers working on model organisms and the genes in which they specialize. When clinicians identify a rare disease gene, the network helps match them up with a model organism researcher who can help elucidate the gene’s function. Since January 2015, the network has made around 40 awards. Hieter serves as the network’s principal investigator. “Very proud of that one,” he says.
On occasion, Hieter meets at conferences with families of people with rare diseases. “The families are incredibly gratified to know that their kid has a mutation in a specific gene and that links them to other families that are dealing with very big issues with their very sick kids,” Hieter says. “They can work as a group to try to do something about the disease.”
Hieter’s Inaugural Article (20) unifies many of the themes of his career. Investigating gene overexpression, he and his colleagues identified 245 genes in yeast that, when overexpressed, lead to chromosome instability. Comparing those genes with human counterparts, the team found two human genes that, when overexpressed, destabilized chromosomes.
Hieter and his colleagues then applied synthetic lethality to gene overexpression. The researchers looked for genes in yeast that, when knocked out, would kill only cells with the overexpressed genes and not cells with normal gene expression. Using samples of rhabdomyosarcoma, a muscle cancer, the researchers inhibited the enzyme histone deacetylase. In the cancer cells with overexpressed genes, the inhibitor proved lethal.
“I want to continue pushing the idea of synthetic lethality and synthetic dosage lethality in yeast as a filter to define a small set of candidate cancer drug targets that are highly connected within genetic networks, and take that to the level of small-molecule inhibitors,” Hieter says, and acknowledges that the work is still too early for him to hope that he’ll ever see the final result in the clinic. “The approach has great promise, and has a good chance of leading to novel therapies,” he says. “There’s no way of telling where the big breakthroughs in cancer treatment will happen.”
Footnotes
This is a Profile of a recently elected member of the National Academy of Sciences to accompany the member’s Inaugural Article on page 9967 in issue 36 of volume 113.
References
Profile of Philip Hieter
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