Viruses aren’t thought of as living beings. Rather, they are collections of genetic instructions that hijack the replication machinery of living cells to perpetuate themselves.
A specific type of virus called a retrovirus does this by integrating a DNA copy of its RNA genome into the host cell’s DNA. This capability has proven to be useful in modern medicine.
Retroviruses form the foundations for many forms of gene therapy, serving as delivery vehicles that insert corrective genes into patient’s cells. These delivery vehicles are called viral “vectors.” Scientists are studying retroviruses in the laboratory to see if their natural features can be adapted to make viral vectors that more precisely integrate genes into the genome to increase the safety of gene therapy.
New research by Parmit Singh, PhD, a Dana-Farber scientist working in the Cancer Immunology and Virology lab of Alan Engelman, PhD, and in collaboration with the laboratory of Paul Lesbats at the University of Bordeaux in France, has revealed mechanistic details of how a virus called Prototype Foamy Virus (PFV) integrates into a host cell’s DNA.
Dana-Farber’s basic science laboratories are at the forefront of discovering biological mechanisms like these that can lead to new and unexpected therapeutic advances. This study, published in Nucleic Acids Research, uncovers possible ways to tune both when and where a virus integrates into an infected cell’s genome, providing clues that may help in the design of safer viral vectors for gene therapy.
“This kind of basic research is important because Prototype Foamy Virus is being studied as a possible tool for gene therapy,” says Singh. “Understanding how and where the virus inserts its genetic material could help design safer and more precise viral vectors for gene therapy in the future.”
New Dana-Farber findings suggest that viral vectors can be engineered to adjust not only when but also where viral DNA integrates. This opens the door to designing safer tools for gene therapy.
Small mutation, big change
Prototype Foamy Virus (PFV), which does not cause human illness, has evolved to integrate its DNA into cells during mitosis, the stage of cell division when chromosomes are reorganized. The key player in the process is a viral protein called Gag. Gag helps PFV latch onto the host cell’s chromatin, the material that builds chromosomes, to begin viral integration.
The researchers studied both the normal, wild-type version of PFV and a mutant PFV that contains an engineered Gag protein. The wild-type PFV latches during the early stage of mitosis, when chromosomes are tightly packed.
The altered Gag protein, however, changed the timing of viral latching onto chromatin. Instead of binding early, the mutant PFV attached to chromatin less strongly at the later stage of mitosis, when chromosomal DNA is looser or decondensed. This delay in binding also changed where the virus inserted its DNA.
Specifically, wild type PFV integrates into gene-rich regions of chromosomes, and into regions that replicate early during cell division. Mutant PFV integrates into gene-poor regions and into regions that replicate late during cell division.
Interestingly, scientists have observed a similar shift in viral integration patterns with HIV-1 capsid mutants, suggesting there may be strategies for integration that are shared across retroviruses. In the future, Singh and colleagues are interested in testing whether the integration site selection of other viruses from the Orthoretrovirinae subfamily also correlates with chromosomal replication timing.
“Understanding where retroviruses insert their genetic material is crucial because it can affect how the virus impacts cellular physiology,” says Singh. “Our research shows that PFV integration depends on both the replication timing of chromosomes and how host chromosomes are arranged in 3D space.”
Implications for gene therapy
These findings suggest that viral vectors can be engineered to adjust not only when but also where viral DNA integrates. This opens the door to designing safer tools for gene therapy.
“These viral vectors can be altered to tune the timing — and perhaps the location of viral DNA insertion — toward potentially safer regions of the genome,” says Singh.
Written by: Beth Dougherty