Profile of Stephen P. Goff

One gets the sense from virologist Stephen P. Goff that his achievements are the result of good timing and good company. With a woodworking father who restored antique clocks, an elder brother who studied phage genetics with James Watson at Harvard University, and Nobel Prize-winning mentors who saw the possibilities of manipulating DNA, perhaps Goff is right.

Stephen P. Goff and his wife, Marian Carlson.

Stephen Goff, Higgins Professor of Biochemistry and Molecular Biophysics at the Columbia University Medical Center since 1990, and an investigator with the Howard Hughes Medical Institute since 1993, was elected to the National Academy of Sciences in 2006.

His career can be measured in nearly 300 publications, with almost 50 in the Nature journals, Science, Cell, and PNAS.

As a student, Goff made pivotal contributions to the development of recombinant DNA technology and its promise for gene therapy. As a graduate student, he studied SV40 gene structure and function. As a fellow and in his own laboratory, he explored the life cycle of retroviruses. Much of his work defined the viral enzymes that later became the targets of drugs in modern-day combination therapies against HIV.

In addition to his natural talent at the laboratory bench, Goff has a knack for being in the right place at the right time. He was a graduate student at Stanford University when researchers realized that a great many cancers are the result of mutations in protooncogenes—genes activated by mutation or during their acquisition by retroviral genomes. While a postdoctoral fellow at the Massachusetts Institute of Technology (MIT), he cloned and characterized one of the earliest known oncogenes, v-abl, in the context of the Abelson murine leukemia virus and its corresponding mouse protooncogene, c-abl. Years later, when the human version of the gene was identified as the cause of chronic myelogenous leukemia (CML), his work provided part of the rationale for the search that identified a therapeutical kinase inhibitor known as imatinib (Gleevec). Since its approval by the US Food and Drug Administration, Gleevec has revolutionized the treatment of CML and has energized searches for other oncogene-specific inhibitors.

In recent years, Goff combined his knowledge of retroviral proteins with emerging technologies to identify cellular proteins that interact with and sabotage retroviral replication. This growing list of future drug targets includes the zinc finger proteins ZAP and ZFP809 as well as eIF3f, the subject of Goff's PNAS Inaugural Article in 2009 (1).

Wind-Up Clocks and Catboats

Goff was born in 1951 in Providence, Rhode Island, and was raised on the waterfront of the Coles River in Swansea, Massachusetts. He grew up in a house built by his father, a contractor and boat builder who worked at the legendary Herreshoff boatyard in nearby Bristol, Rhode Island. The family spent as much time as possible on the water, often in a gaff-rigged catboat.

“My dad had an amazing workshop right on the water in Narragansett Bay with lathes, saws, and woodworking tools,” Goff said. “When he got older, he became interested in fixing 100-plus-year-old clocks. He, my brother Chris, and I would take clocks apart and put them back together, which was probably the start of my love for puzzles.”

In 1969, Goff went to Amherst College, where he studied chemistry and nurtured a passion for arcane computer programs—assemblers and compilers that convert one code into another. Along with attending to coursework and hobbies, Goff made a habit of reading academic papers on various topics that caught his interest, from physics to biology. One such paper (2), by Paul Berg at Stanford University, described a procedure for creating one of the earliest recombinant DNAs and united many of Goff's interests.

“I became tremendously excited by the idea that researchers had suddenly become able to control DNA like a computer language—that DNA had become programmable,” Goff said.

Unbelievably Lucky

After graduating summa cum laude from Amherst College in 1973 with a bachelor's degree in biophysics, Goff hoped to enroll in the biochemistry graduate program at Stanford University but almost was not admitted.

“I was so disappointed to hear I had been put on a waiting list, but then I got this last-minute miraculous call saying ‘You're in,’” Goff said. “I was unbelievably lucky to get into Stanford, and then in the next year to join Paul Berg's lab just as recombinant DNA was hitting, and hitting at Stanford like nowhere else.”

In the years before Goff's arrival, enzymologist Arthur Kornberg and the biochemistry faculty at Stanford University had discovered and purified enzymes—DNA polymerases, endonucleases, and ligases—that would enable the field to manipulate DNA molecules almost at will.

“We had access to the most powerful DNA technologies in the world before many senior researchers elsewhere,” Goff said.

A leader in Kornberg's department since its founding, Berg had studied the aminoacylation of tRNAs in the 1960s. In the study that had first caught Goff's eye, however, Berg successfully joined DNAs from two species—the DNA genome of the SV40 virus, which infects monkey cells, and a DNA plasmid capable of replication in the common gut bacterium, Escherichia coli (2). This technique eventually won Berg the Nobel Prize in 1980. Such hybrid DNA molecules, coupled with screening concepts from faculty members David Hogness and Ron Davis, later permitted the isolation of virtually unlimited quantities of any gene segment from any organism.

Inducing bacteria to reproduce foreign genes launched an industry that now uses bacteria to mass produce drugs such as insulin and antibodies. At the time, however, Berg wanted to introduce replicating DNAs into mammalian cells, and it was Goff who gave it a try.

One of Goff's “first serious papers,” published in Cell in 1976 (3), described a hybrid virus composed of SV40 DNA that included regulatory sequences known to trigger DNA replication and an inert chunk of bacteriophage DNA. The hybrid successfully replicated with the aid of a helper virus in African green monkey kidney cells.

“It was the obvious thing to try, but when it worked, it represented one of the earliest recombinant DNAs introduced into mammalian cells, and in that sense laid the groundwork for gene therapy,” Goff said.

As Goff prepared to graduate from Stanford University in 1977, he met with MIT scientist David Baltimore, who had shared the Nobel Prize 2 years before for the discovery of the viral enzyme reverse transcriptase.

“I wrote a fellowship proposal in a week and was invited to go to MIT the next summer,” said Goff, recalling how he had hoped that his wife and classmate at Stanford University, Marian Carlson, would also find a good laboratory in Boston.

The couple celebrated when Carlson found a position in yeast genetics in David Botstein's laboratory, just across the street from Baltimore's facility at MIT. Carlson, currently a professor of genetics and development and microbiology at Columbia University, joined her husband in April 2009 as a member of the National Academy of Sciences.

As a postdoctoral fellow, Goff switched his focus to match that of Baltimore's: the Moloney and Abelson murine retroviruses.

“I found retroviruses intriguing because their integration into host genomes represented a deliberate, orderly, and fearsome survival strategy—not an accident, as in the rare cases of integration of SV40 DNA,” Goff said. “We learned that it was made possible by a viral enzyme—the integrase—that was essential for virus replication. Integrase allowed the virus to make permanent changes in the host genome of an infected cell and in the germline of that species forever after.”

Goff's early work at MIT included cloning the complete and fully functional genomes of the Moloney and Abelson viruses. He also developed a rapid high-throughput screen for virus replication that scored reverse transcriptase activity in raw culture medium. The system is still widely used today. Even after Goff joined the Department of Biochemistry and Molecular Biophysics at Columbia University in 1981, he continued to target these viral genomes with a series of mutations that defined the functional domains of reverse transcriptase (4–8), integrase (9–12), and the viral gene products contained within the Gag and Pol precursor proteins (13–25).

His work has described many details of the retroviral life cycle. In this process, the viruses enter the cell; use reverse transcriptase to convert their RNA genome into a DNA genome; and then use integrase to stitch the viral DNA into the host cell's genetic material, forming the provirus. The host cell's machinery then expresses the proviral DNA and assembles immature viral particles. Finally, the precursor proteins are cleaved by the viral protease to form the next generation of infectious virions.

“When HIV came along in 1983 and was identified as a retrovirus, many of us in the field thought we didn't have the facilities and skills to work with such a human pathogen,” Goff said. “Then, Baltimore made a pitch to his retrovirologist colleagues that we should dedicate at least 10% of our time to HIV, and I took that to heart.”

Goff soon confirmed that his detailed knowledge of the life cycle of Moloney could be quickly applied to HIV. His later studies heralded viral protease as the target of drugs such as indinavir (Crixivan), ritonavir (Norvir), and nelfinavir (Viracept). “The field needed to understand the life cycle to know where to attack,” Goff said. “There are some 15 or 20 drugs now that target various steps in the HIV life cycle, and we feel very good about having helped with the basic science that led to the development of these drugs.”

Endless Entertainment

In the 1980s, Stanley Fields, then at the State University of New York at Stony Brook, demonstrated the power of the yeast two-hybrid system, a technology that swept through the scientific community and especially through the halls of nearby Columbia University. The system enabled researchers to “fish” quickly among the thousands of proteins in a cell for those critical components that specifically bound to a given “bait” protein. In Goff's case, the system proved invaluable in identifying cellular proteins that affect the replication of invading retroviruses. Among these was cyclophilin A, which bound to the HIV-1 Gag protein and was later identified as a major regulator of retroviral replication in primate evolution. From 1993 on, Goff's laboratory performed many more screens of cDNA libraries and discovered additional host proteins that affect retroviral replication, some with dramatic potency (26–31).

Although the yeast two-hybrid screen identified many host proteins capable of binding to viral proteins, binding was not a strong indicator that the proteins played a critical role in virus replication. Goff sensed the need for a more functional screen. He encouraged his laboratory to develop screens for true virus resistance in animal cells, in strict analogy to the screens for phage resistance that had been so powerful in the 1960s. These screens revealed many dominant-acting genes that induced resistance to retrovirus replication. Among the most important of these, one that Goff's laboratory described in a 2002 paper in Science (32), was ZAP—a CCCH-type zinc finger protein that degrades the RNAs of many viral genomes, including those of retroviruses, alphaviruses, Ebola, and others.

As Goff continued to screen cDNA libraries, he kept thinking about a then 30-year-old mystery in genetics: What made embryonic stem cells uniquely resistant to retroviral infections? Goff knew that retroviruses successfully integrated into the genomes of mouse stem cells as proviruses but were silenced before their genomes could be transcribed into mRNA.

Rudy Jaenisch demonstrated in the 1980s that such silencing depends on a “silencing complex” present in the nucleus of embryonic stem cells. This complex binds a specific sequence element, known as the primer binding site, in the retroviral genome. The complex was present at such low levels that its makeup had remained mysterious for 30 years.

“In 2007, a very dedicated and talented postdoc in my lab, Dan Wolf, purified the complex, and by mass spectrometry showed that it included TRIM28, a protein known to help block the transcription of many genes,” Goff said. TRIM28, however, was present in differentiated cells as well, so it could not be the embryonic stem cell-specific virus-repressing factor. Goff and Wolf then identified Zfp809, a member of the large family of zinc finger proteins, as the key factor that linked TRIM28 to the proviral DNA to be silenced (33).

Goff believes that TRIM28/ZFP809 silencing is not only a stem cell-specific defense mechanism but a key to the silencing of many retroviral genomes, including that of HIV-1, in its cellular reservoirs.

Goff continues to screen libraries for host genes that affect retrovirus replication. He recently identified a protein fragment—the N-terminal 91 amino acids of the eukaryotic initiation factor 3 subunit f (N91-eIF3f)—as yet another core player in human gene expression that also potently blocks retroviral replication. Like zinc fingers, N91-eIF3f drastically reduces viral mRNA levels but through a different mechanism.

Of his many accomplishments, Goff is most proud of helping to launch the careers of his many trainees. His research, he says, has “generated a large enough number of genes to entertain our incoming students and postdocs for years to come.”

“The next generation of scientists and their offspring, in turn, will be making contributions beyond our wildest imaginations,” he said. “This is the motivation for all we do today.”