Discovering a tiny gene’s role in big diseases

Nearly five years ago, scientists completed one of the largest international projects in research history, tremendous in its scope and importance. They determined the sequence of the nearly 30,000 genes in the human genome. Although the Human Genome Project introduced the concept of ‘completeness’ to human biology for the first time, it was just the first step toward the eventual goal of using genomics to diagnose, treat and prevent disease. Staff reporter AMBIKA BHUSHAN reports on new genome research and microbiology techniques at the Yale School of Medicine.

Now, armed with a basic physical map of the human genome and novel advances in molecular biology, Yale scientists and others across the country are working on discovering the functions of each human gene.

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“We already have a physical map to work with,” said Tian Xu, vice chairman of the Department of Genetics at the School of Medicine. “But we have to encode the functions of that map.”

Xu’s lab is responsible for having determined the function of 1,000 of the approximately 5,000 genes for which functions are currently known. He said his goal is to map 10,000 genes over the next three years. His lab’s method for analyzing gene function, he said, is more efficient than the Nobel Prize-winning “knock-out” technique, which introduces specific mutations into individual genes to disrupt their normal function in the cell. It makes use of transposons, mobile genetic elements that can alter gene function and provide a straightforward means to identify mutant genes. Come the move to West Campus, scientists will set up a laboratory Xu called Mouse Clinic, dedicated to mutating mammalian genes using this technique.

But the puzzle of genomic functionality is not as simple as “one-gene-one-function.” Far from having consistent or singular functions in cells, genes interact with other genes in complex pathways, are continuously influenced by the environment and even appear to have different functions in different contexts, Xu said.

For instance, while some diseases, like sickle cell anemia, are clearly inherited in the form of faulty genes, many diseases, such as diabetes, heart disease and Alzheimer’s, which have a strong environmental component, have a more complex genetic basis, said Daniel DiMaio, vice chairman of Genetics.

“There’s a spectrum: All diseases have some genetic basis, but some diseases are more clearly genetic,” Xu said.

Speaking in such indefinites is necessary, considering many common diseases have not been mapped to the genes that help cause them.

Understanding disease genes — genes that cause or are implicated in disease — is not only crucial to understanding how diseases develop but also to how they can be reversed and prevented.

Here at Yale, a team headed by Erol Fikrig, chief of Infectious Diseases, is making headway on just that. The group recently characterized the several hundred genes that impact the West Nile virus infection, a potentially serious illness spread by infected mosquitoes.

In his study, which was published earlier this month, Fikrig and his team used RNA interference, a technique that uses small fragments of interfering RNA to systematically “knock out” individual genes to determine their functions. Testing the entire human genome, the group found 305 genes that impacted the virus’s ability to enter, survive or replicate in the cell to create disease, he said.

About 30 percent of the genes involved in West Nile infection also appear to play a role in Dengue fever, a mosquito-transmitted disease prevalent in tropical areas, Fikrig said.

Theoretically, some of these genes could be targets for new therapeutics if scientists can figure out a way to turn off their expression without interfering with other bodily processes, he said.

“Now that we have a dictionary for these genes, we can block these genes or the pathways associated with these genes, or modulate them to develop new drugs,” Fikrig said.

Fikrig said the team is now working on determining the individual functions of and interactions between the 305 genes, a task that will help them to understand which genes would potentially be effective targets.

figure out, Map out, Stamp out

While drugs may be able to change the way our genes function, can faulty disease genes themselves be changed?

Research conducted by Yale scientists earlier this month suggests that we may indeed be able to alter our genetic destinies — at least in the case of some inherited diseases.

Headed by Joanna Chin from the lab of Peter Glazer, chair of Therapeutic Radiology and professor of genetics at the medical school, the study corrected a specific defect within a human gene that causes the blood disorder thalassemia. The disease weakens the body’s ability to produce hemoglobin, an oxygen-carrying molecule found in red blood cells.

The team designed a set of DNA fragments that bound in vivo to specific locations along the genome, creating a triple helix of DNA. Once bound, these fragments triggered the cell’s own repair machinery to permanently correct the defective DNA by making the appropriate sequence change.

“Because the sequences [of the synthetic and natural DNA] are aligned just right, it triggers the cell to realize something is wrong and try to fix it,” Glazer said.

Since in genetic disorders like thalassemia, every cell carries a copy of the disease-conferring gene, it is laborious to correct every faulty red blood cell, he said. Glazer’s team got around this by conducting this process on hematopoietic progenitor cells, which give rise to red blood cells.

Though the procedure cannot stop defective hematopoietic cells contained in the body from producing faulty red blood cells, the corrected red blood cells have a survival advantage over the faulty blood cells. The process of generating blood cells is more robust when the hemoglobin gene is correct, and the healthy blood cells also last longer in the blood stream, Glazer explained.

The technique — the first of its kind to be applied to human stem cells — improves upon the traditional method of gene therapy, he said, because “it modifies the natural gene in its natural place.” In comparison, conventional therapy, which involves inserting a synthetic gene into the genome via a virus, usually causes the gene to insert into the wrong part of the genome. This can interrupt cellular processes or activate genes that are normally suppressed, he said.

The lab is now working on developing an even more efficient procedure for sequence change, and testing the technique on mice. The mouse serves as an effective analogue to the human, because many of the genetic pathways important for disease development in humans are evolutionarily conserved.

Seeing Small, Thinking Big

Since the days of the Human Genome Project, much headway has been made on genomic technologies that are accelerating scientists’ understanding of how the human genome functions.

Scientists hope to eventually use genomic technologies to personalize medicine, DiMaio said, by using information about a person’s genetic makeup to diagnose, treat or prevent disease. For instance, as rapid DNA sequencing becomes more affordable, scientists are now talking about sequencing patients to individualize drug therapy.

“It’s not inconceivable to say that in another five years, sequencing every gene in a single patient will be possible in an affordable way,” DiMaio said.

Currently drugs treat all patients as if they have the same genetic makeup and respond identically to drugs. This means that subsets of patients who respond differently are effectively “lost,” he said.

But sequencing individual patients will allow doctors to separate subgroups of patients based on their genes that respond most similarly to drugs.

“Ultimately, rather than treating patients as a large group,” he said, “we want to be able to profile any patient that comes in the door.”

Contact Ambika Bhushan at ambika.bhushan@yale.edu.

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