Genomics in Action: Kyungjae Myung, Ph.D.
Fantastic Molecular Voyage: Understanding Genome Instability
Kyungjae Myung won't just tell you about unstable genomes, he'll show you one.
Exploring genomes - frequently human, but often mouse and yeast genomes as well - fills his day as a National Human Genome Research Institute (NHGRI) investigator in the Genetics and Molecular Biology Branch and head of the Genome Instability Section.
Dr. Myung — known as "KJ" among his colleagues — is a Korean-born and educated scientist who came to NHGRI in 2002 to study genome instability, which is both a characteristic of and, in some cases, a trigger for many genetic diseases, including cancer. Dr. Myung's interest in the field was initially piqued by trying to understand how cells repair DNA damage caused by ultraviolet radiation, such as sunlight.
"I was fascinated," explains Dr. Myung. "DNA damage happens in people's cells every day. There can be around 10,000 different sites where an individual's DNA can be damaged just in one day, though the damage is seldom actually transmitted."
Ultraviolet radiation inflicts fairly minor changes to DNA, often affecting just one or two of the approximately three billion base pairs in the human genome. At NHGRI, Dr. Myung focuses on how a cell mends larger-scale DNA damage — such as a break in one or both strands of the DNA — that can occur by oxidative stress or exposure to ionizing radiation, such as x-rays. This more extensive damage, known as gross chromosomal rearrangement, includes deletions, in which a chunk of chromosome is lost; translocations, in which part of one chromosome attaches to another; and inversions, in which a segment of DNA is broken and then reattached in the opposite orientation.
When DNA breaks, a team of enzymes arrives at the site of damage and halts replication until the damage is repaired. But in many cancers, as well as some other diseases, one or several members of the repair crew are either absent or do not function properly. The result is that DNA damage accumulates, leading to mutations. The mutations either kill the cell, or, worse, they may survive to produce a population of abnormal cells that sometimes cause cancer.
Dr. Myung discovers and studies proteins that help repair DNA. One of these is the enhanced level of genome instability 1 (ELG1) protein. In a healthy cell, ELG1 levels are low. But when DNA is damaged, ELG1 is produced in higher quantities and migrates to the damage.
"That's what I will show you," says Dr. Myung, excitedly launching a movie clip on his computer. "Seeing is believing!" On a grainy, gray backdrop, he points out the dark gray ovals marking the boundaries of three human cells. Inside each cell is another dark gray circle reflecting its nucleus, and the DNA is inside the nucleus. There are also a couple of bright green fluorescent dots inside the nucleus - this is the ELG1 protein labeled with a fluorescent tag. The time-lapse movie shows first just a few green dots, but then a swarm of green dots converge on the broken DNA.
What interests Dr. Myung is not so much the consequence of genomic instability — tumors or cell death — but how the cells repair such damage and prevent it from happening altogether.
He uses yeast to identify the genes and their encoded proteins that keep the cell free of DNA damage. The yeast genome contains just over 12 million base pairs of DNA packaged within 16 chromosomes. Yeast has approximately 6,000 genes in all, approximately 1,000 of which are essential for survival. To explore the yeast genome for genes of interest, Dr. Myung has used two approaches.
He designed a novel method to screen all of the 5,000 non-essential genes in the yeast genome to figure out which ones, when eliminated, cause the genome to become unstable. In doing so, he and his colleagues found 10 genes that have not previously been known to play a role in protecting and repairing the DNA. If any one of these genes are eliminated, the yeast genome suffers damage. Dr. Myung chose to focus on two of the 10 genes — radiation sensitive 5 (RAD5) and the gene mentioned above, called ELG1.
He also looked at all 6,000 genes in the yeast genome and asked: If you have too much of the protein encoded by any one of these genes, can you increase the level of DNA damage? He found 13 genes that fit the bill; the first one he chose to investigate is mutator phenotype 1 (MPH1).
Together, these two screens discovered genes involved in DNA repair that have provided the foundation of all his current and future research, says Dr. Myung. Having fished out these interesting genes in yeast, he plans to find their counterparts in humans, then knock out those same genes in mice and see whether tumors arise.
To date, Dr. Myung and his colleagues have discovered two human counterparts to RAD5 — a gene called SNF2 histone linker PHD RING Helicase (SHPRH) and another called helicase-like transcription factor (HLTF). Both have links to cancer. Though little is known about the gene, mutations in SHPRH have been encountered in several cancers. For the past 10 years, other researchers have noted that HLTF seems to be turned off in many colorectal cancers, but before Dr. Myung's discovery, no one had figured out that HLTF is involved in DNA repair.
When DNA damage occurs, a protein called proliferating cell nuclear antigen (PCNA) encircles the DNA and blocks replication of the damaged region, thereby ensuring that it is not passed to the next generation. But before PCNA can alert repair crews to the damaged site, it must first be chemically modified — Dr. Myung discovered that this is the role of HLTF and SHPRH.
"That's the signal that 'Oh, we have damage in DNA and we need to repair it,'" says Dr. Myung. "If a cell has damaged DNA and dies, that's great because it was abnormal and you want to eliminate it. But if it barely survives, then that's a problem because it carries damaged DNA and makes the genome unstable. Now you have created something really dangerous."
To test his hypothesis, Dr. Myung engineered mice lacking both Hltf and Shprh — these animals should have more DNA damage and eventually produce more tumors than a mouse that had both genes. It will be another year before he has the results of these studies.
The ELG1 protein also has links to cancer. Some patients with neurofibromatosis are also cancer prone: these individuals have a deletion in their DNA that disrupts not only the neurofibromin 1 gene that causes their disease, but also the ELG1 gene. "These patients are probably cancer prone because they have a defect in their DNA repair pathway," explained Dr. Myung.
Dr. Myung is also investigating whether cells that lack ELG1 are more susceptible to DNA damage in the presence of carcinogens and other harmful agents. He has reduced the levels of ELG1 in mice by half and found that the animals develop cancers.
To illustrate his point, Dr. Myung reveals another movie. This one shows what happens in cells that produce too little ELG1. A 48-hour, time-lapse clip shows DNA replicating, after which the cell divides. But another pair of cells doesn't divide-instead they fuse together and then separate making two, three, and four cells. But in one of the cells is a glowing green chunk- part of a chromosome. "That could be a broken piece of chromosome, a type of genome instability. And then, see they survive, they didn't die - those could be precursors to cancer."
Of the 13 genes that Dr. Myung uncovered among the genes that produce too much protein, he chose to study MPH1. When high levels of MPH1 are produced, DNA damage increases. MPH1 is the yeast counterpart of the Fanconi anemia gene FANCM. This condition is characterized by, among other things, increased risk of tumors. While Fanconi anemia is well-understood clinically, it is poorly understood at the molecular level. Dr. Myung is planning to use MPH1 as a genetic tool to probe the Fanconi anemia pathway in yeast and then humans. "So, hopefully,we're going to be able to finally solve the almost 80-year mystery of Fanconi anemia."
Dr. Myung speculates that regions of certain chromosomes may be more susceptible to damage than others. He hopes to use ELG1, which naturally marks damaged regions of DNA, to zoom in on the sites on each human chromosome that are vulnerable to DNA damage; essentially mapping the unstable regions of the human genome.
"Fundamental molecular mechanisms in organisms-from yeast to human-have been maintained through evolution to preserve genetic information," Dr. Myung said. "Simple model organisms such as yeast provide clues to help us understand the mechanisms important for suppressing genome instability. Follow up studies of the mammalian counterparts of yeast genes will help us figure out what causes the genome instabilities that we see in many genetic disorders, including cancers."
Last Reviewed: March 14, 2012