New research has uncovered how HIV evades the body’s innate immune system in the first few days after exposure. Like a petty thief, it lucks out.

When the virus breaks into a cell, it leaves traces of itself inside the cell’s cytoplasm. Those traces, like fingerprints on a doorknob, would normally be detected by molecular guards that patrol the cell and sound alarms if they sense an invader. But the cell’s built-in cleaning crew-specifically, a molecule called TREX1-cleans up those traces before the guards find them. This gives HIV the cover it needs to establish an infection.

The work, from the Program in Cellular and Molecular Medicine and the Immune Disease Institute (affiliated with both Children’s Hospital Boston and Harvard Medical School) and published in the September 26 advance online Nature Immunology, may lead to therapeutics that prevent HIV transmission.

“There is a short window of time that lasts a week or two when HIV is just in T cells and macrophages in the genital mucosa,” said principal investigator Judy Lieberman, professor of pediatrics at HMS. “That’s the window of opportunity.” After that, the virus has disseminated into the body. “By then, it’s too late.”

During that slim window, the HIV virus has penetrated the cell membrane and injected viral RNA into the cytoplasm. The viral RNA begins a process called reverse transcription; it translates its RNA into DNA. Fully-formed pieces of viral DNA slip into the cell’s nucleus and replicate, creating new copies of the virus that spread and cause infection.

The tool HIV uses for reverse transcription, however, is “very sloppy,” says first author Nan Yan, research fellow in pediatrics at IDI. It makes fragments of DNA that never make it into the nucleus. Rather, they accumulate in the cytoplasm. Normally these fragments are detected by sensors in the cytoplasm that patrol for foreign DNA and RNA and trigger the cell to produce interferons, the body’s anti-viral defense mechanism.

But T cells and macrophages don’t produce interferon in response to an HIV infection. This observation was first reported in 1991, by Anne Goldfeld, professor of medicine at IDI. At that time, said Lieberman, “people didn’t really know about these cytoplasmic sensors, which is partly why for a long time nobody really asked why HIV doesn’t follow this path.”

In their new work, cell culture studies of the early stages of HIV infection showed that TREX1 binds to the viral DNA fragments and clears them from the cytoplasm. The cells never detect the foreign DNA and therefore never produce interferon-beta.

TREX1, however, isn’t acting out of turn. “TREX1 may have evolved to remove self DNA,”-DNA from the host’s body-“to prevent it from being detected as foreign and triggering an autoimmune reaction,” said Jonathan Kagan, HMS assistant professor of pediatrics at Children’s Hospital Boston. “If we activated innate immunity to our own DNA, we would be riddled with autoimmune diseases. Our own system for preventing autoimmunity is exploited by HIV to prevent innate immunity.”

Lieberman and Yan created cells lacking the TREX1 cleanup-crew and infected them with HIV. Instead of being cleaned up, fragments of HIV DNA accumulated in the cytoplasm. In turn, the cells activated an innate immune reaction and produced interferon-beta. Interferon-beta stopped HIV infection by blocking viral DNA expression and cell-to-cell spreading of the virus, said Yan. Similarly, human immune cells treated with gene-silencing RNA to suppress TREX1 also produced interferon-beta in response to HIV infection.

“It is an elegant discovery,” said Laurie Glimcher, Irene Heinz Given Professor of Immunology, Harvard School of Public Health. “It could lead to therapeutics that block the TREX1 pathway and, hence, HIV transmission during early infection, preventing the virus from setting up shop.”

Lieberman and Yan are applying these findings to their work on a potential anti-HIV microbicide. The microbicide, which is still in development, delivers gene-silencing RNA specifically into T cells and macrophages, the cells HIV uses as a gateway. If that technology can be used to shut down the TREX1 cleanup crew in these cells, said Lieberman, it could trigger the body’s alarm systems and unleash an immune response to stop HIV infection before it starts.

One part of that work involves moving from cell culture tests to in vivo studies of the early phases of HIV infection in mice with human immune systems, called humanized mice. “We would like to see if knocking down TREX1 blocks HIV transmission in humanized mice,” said Lieberman. “Sexual transmission of HIV in these mice is amazingly similar to what happens in humans.”

Please see the post on the Children’s Hospital Boston Vector blog here.

Nan Yan, Ashton D Regalado-Magdos, Bart Stiggelbout, Min Ae Lee-Kirsch, Judy Lieberman.  “The cytosolic exonuclease TREX1 inhibits the innate immune response to human immunodeficiency virus type 1”. Nature Immunology 11:1005-1013, 2010, Epub Sept 26, 2010.