RESEARCH BRIEFS

Personal Genome Project Off and Running

HMS professor of genetics George Church has been working toward an affordable genome for 30 years. With next-generation sequencing platforms coming of age, he is finally close to that goal. He is ramping up the Personal Genome Project (PGP)—an effort to sequence the genomes of 100,000 individuals—against the backdrop of plummeting platform costs.

On Oct. 6, a California company called Complete Genomics (with Church as an adviser and collaborator) announced that it could sequence a complete human genome for just $5,000. Church plans to sequence only a portion of the PGP participants’ genomes, so the price tag should be lower for each volunteer. He is focusing on the protein-coding regions, or exons, which are thought to contain most of the information relevant to human disease.

Using an exon-capture method developed by former HMS postdoc Jay Shendure and HMS lecturer Gregory Porreca (see Focus, Oct. 26, 2007), Church has already started to sequence the genomes of 10 volunteers, dubbed the PGP-10. On Oct. 20, these individuals received their first batch of data, which (in most cases) included more than 10 percent of the protein-coding regions of the genome.

“As someone who actually deals with patients who have genetic disorders, I can tell you that it makes sense to target the protein-coding regions,” said clinical geneticist Joseph Thakuria, medical director of the PGP and an attending physician at Massachusetts General Hospital. “In the overwhelming majority of cases, the pathogenic mutation resides in an exon.”

Thakuria sifted through the first batch of PGP-10 data and pulled out sequences associated with disease in the scientific literature. He also scanned Affymetrix data from each participant, identifying single nucleotide polymorphisms of interest. He shared the findings—which included few surprises—with the PGP-10 during individual consultations.

Following these meetings, nine of the 10 volunteers decided to release their data to the public through the PGP website. Due to technical problems, one volunteer did not receive his exon information. He will decide whether or not to release the data after reviewing it.

The PGP website is accessible to anyone with an Internet connection. “It’s truly an open source model,” said Church. He and colleagues are now selecting the next batch of volunteers.

Last April, Harvard University’s Institutional Review Board gave Church permission to scale his project to 100,000 people from a screen of 350,000 potential participants. As the database grows, it will serve as a powerful resource for researchers probing the genetic basis of diseases and other traits. Researchers will also have access to a biobank of reprogrammed fibroblasts from PGP participants. Each volunteer will provide a skin biopsy that will serve as a source of adult stem cells for future experiments.

For more information on the Personal Genome Project, visit www.personalgenomes.org.

—Alyssa Kneller

Conflict Disclosure: Several DNA-sequencing companies have licensed Church lab patents or software. Church also serves in scientific advisory roles for DNA-sequencing companies and direct-to-consumer genomics. For a full list of Church’s technology-transfer and commercial scientific advisory roles, visit http://arep.med.harvard.edu/gmc/tech.html.

Funding Sources: The PGP has received grants for biomedical research from The Broad Institute of Harvard and MIT. The PGP has received financial support in the form of unrestricted gifts from Google, COUQ Foundation, and Orbimed. Relevant grants for technology development (restricted to non-human-subjects related activities) include those from the Department of Energy (DOE GTL) and the National Institutes of Health (NIH NHGRI CEGS). The PGP has received unrestricted royalty donations via Harvard and George Church from Applied Biosystems, Agencourt, Helicos, Lynx (Solexa / Illumina), and Complete Genomics Inc.

Knockdown of Gene Pairs Widens View of Cellular Systems

Despite the rise of systems biology, many geneticists continue to probe genes in isolation. They even use cutting-edge RNA interference (RNAi) technology to knock down one gene at a time. This approach often yields a narrow view of cellular systems.

Now, researchers at HMS, the Institute for Cancer Research, and the Institut de Biologia Molecular de Barcelona have widened the lens, using RNAi to systematically knock down pairs of genes in fruit fly cells. The findings appear in the Oct. 17 Science.

“Data from our novel double-RNAi screens provide panoramic views of cellular processes,” said senior author Norbert Perrimon, a Howard Hughes investigator and an HMS professor of genetics. “By using this approach to expose interactions between genes, researchers may accelerate the pace of discovery in systems biology and advance personalized medicine.”

In a typical RNAi screen, researchers begin with a library of small interfering RNAs (siRNAs) targeting specific genes. Each siRNA disrupts the gene’s ability to produce a particular protein. Scientists place the siRNAs on thousands of cells, with just one gene being targeted in each well of cells. Then they watch the cells and record changes.

But this approach fails to capture some key players because many genes are redundant. Cells can mask their distress when they lose a single gene by turning to fail-safes with the same function. Perrimon’s approach overcomes this obstacle.
“If you take one part out of a plane engine, it still works, but if you take out that part plus its fail-safe, then you’re in trouble,” explained corresponding author Chris Bakal, a postdoctoral researcher in the Perrimon lab.

Bakal began with a traditional RNAi screen for genes that play a role in a cell’s stress response, generating a list of genes that help the cell decide whether to die, move, or take some other action in a stressful environment. Bakal noticed that some key players—genes identified by other labs via a different method—were missing from the list.

He selected 12 of these suspects, including the tumor-suppressor gene PTEN, for further study. Bakal knocked down PTEN and used the resulting cells to perform another massive RNAi screen. So he performed the screen in the context of a defective tumor suppressor. The stress response results were very different from the original screen. He performed similar double-knockdown screens with the 11 other suspects. In total, he tested 17,724 different combinations in the same cell type.

“A given gene behaved differently, depending on the genetic context,” said Bakal. “Our approach highlights the connections between genes, telling a more complete story.”

Bakal says researchers can use this approach to map cellular systems and make predictions about the behavior of particular genes, which has direct implications for personalized medicine.

—Alyssa Kneller

For Students: Contact Norbert Perrimon at perrimon@receptor.med.harvard.edu for further information on this and other lab projects.

Conflicts of interest: The authors declare no conflicts of interest.

Funding Sources: Genome Canada, the European Union, and the Leukemia and Lymphoma Society

Genetic Switch Found For Growth of Common Childhood Tumor

Researchers have discovered a mechanism for the rapid growth seen in infantile hemangioma, the most common childhood tumor.

Made up of proliferating blood vessels, hemangiomas affect up to 10 percent of children of European descent, with girls more frequently afflicted than boys. The growths appear within days of birth—most often as a single blood-red lump on the head or face—then grow rapidly in the ensuing months. The development of infantile hemangioma slows later in childhood, and most tumors disappear entirely by the end of puberty.

Though the tumors are benign, they can cause disfigurement and clinical complications. The study offers hope for the most severe of these cases, pointing to a potential, noninvasive treatment.

The findings, from a collaboration of scientists at HSDM, HMS, Children’s Hospital Boston, and the de Duve Institute at the Catholique University of Louvain in Brussels, appeared online Oct. 19 in Nature Medicine.

The researchers looked at tissue isolated from nine distinct hemangioma tumors, finding that the endothelial cells that lined the affected blood vessels were all derived from the same abnormal cell. Like other tumors, hemangiomas are caused by the abnormal proliferation of tissue. Since no other type of cell within the tissue displayed the same self-replicating tendency, the scientists concluded that the endothelial cells were the source of the tumors’ growth.

Looking further, the team discovered that these cells behaved as if they were activated by a hormone called vascular endothelial growth factor (VEGF). The hormone usually binds to a specific receptor that prevents VEGF from signaling the cell to proliferate. The researchers found that at least two gene mutations were capable of setting off a chain of events that ultimately stymied these receptors, enabling VEGF to trigger unchecked growth in the endothelial cells.

The findings open up new treatment options, according to study leader Bjorn Olsen, dean for research and professor of developmental biology at HSDM and the Hersey professor of cell biology at HMS. First author Masatoshi Jinnin is a research fellow in developmental biology at the Dental School.

“What the data suggest,” Olsen said, “is that any therapy that is directed against vascular endothelial growth factor—anti-VEGF therapy—is the rational therapy to use in these tumors.”

Anti-VEGF therapies have already been approved for other conditions, including certain types of cancer. The next step for Olsen’s team is to get approval to test the therapies in clinical trials.

—Veronica Meade-Kelly

For Students: Contact Bjorn Olsen at bjorn_olsen@hms.harvard.edu for further information about this and other lab projects.

Conflicts of interest: The authors declare no conflicts of interest.

Funding Sources: The John B. Mulliken Foundation, the National Institutes of Health

top