TSRI Researchers Develop New Method to ‘Fingerprint’ HIV

Now scientists at The Scripps Research Institute (TSRI) have developed a method to analyze the glycan shield on HIV’s protective outer glycoprotein, developed as a potential HIV vaccine candidate. With this method, scientists can rapidly create a “fingerprint” of the glycans on the glycoprotein to tell if they are on the right track in developing an effective vaccine.

“The ability to identify the glycan fingerprint on HIV’s glycoprotein will help us develop a vaccine that matches what is found on the virus,” said James Paulson, Cecil H. and Ida M. Green Chair of Chemistry at TSRI and co-chair of the Department of Molecular Medicine, who led the study published today in the journal Nature Communications.

Breaking Down HIV’s Defenses

With the new method, scientists can finally see which types of glycans make up the glycoprotein—and whether the glycoprotein has any vulnerable holes.

The glycans cover the glycoprotein machinery that HIV uses to enter host cells. The human immune system wants to produce antibodies that bind to the glycoprotein to stop infection, but the glycans block immune cells from seeing their targets and developing useful antibodies.

At TSRI, several research teams are designing HIV vaccines that prompt the body to create rare “broadly neutralizing” antibodies that can actually get around the glycan, or sugar, shield. To do this, they need to introduce the immune system to HIV-like glycoproteins and teach the immune system where the holes in the glycan shield are.

For the new study, the researchers developed a way to figure out the composition of sugars on the glycoprotein. They used enzymes to break the glycoprotein into smaller peptide chunks. Next, the team used a technique called mass spectrometry to analyze these peptides and see if they fell into one of three categories: high-mannose glycans (a type with a specific kind of sugar), complex-type glycans (which are more mature glycans) or sites with no glycans.

While previous HIV studies had distinguished between high-mannose and complex-type glycans, this was the first time scientists could also see the number of glycan-free sites. In fact, the new method has already revealed that the glycoprotein does not have as many holes as many researchers had predicted.

The new method also saves time. Previous studies using mass spectrometry had required researchers to manually analyze the peptide results—a process that could take months. By teaming up with the laboratory of TSRI Professor John Yates, the researchers in this study successfully used a computer algorithm to rapidly analyze results instead.Study first author Liwei Cao, a research associate in the Paulson laboratory, said speed will come in handy as scientists sort through many HIV vaccine candidates to find the right ones to prevent a wide range of ever-evolving HIV strains.

The next step in this research is to analyze the glycan composition and glycan-free sites on the natural, or “native,” form of HIV, not just an HIV-like vaccine candidate. “Then we can see if the fingerprints match up,” Paulson said. If they do match, the researchers will know they are on a path to developing a vaccine that can induce useful antibodies.

This new method could also be helpful against viruses with a similar glycoprotein shield, such as influenza, Paulson explained. In fact, the new study included a side project where the researchers successfully tested their method on an influenza protein.

In addition to Paulson, Cao and Yates, authors of the study, “Global site-specific N-glycosylation analysis of HIV envelope glycoprotein,” were Jolene K. Diedrich, Lin He, Sung-Kyu Robin Park, Ching Yao Su, Claire M. Delahunty, Raiees Andrabi, Javier Guenaga, Erik Georgeson and Michael Kubitz of TSRI; and Daniel W. Kulp, Matthias Pauthner, Devin Sok, Sergey Menis, Yumiko Adachi, Dennis R. Burton and William R. Schief of TSRI and the International AIDS Vaccine Initiative (IAVI) Neutralizing Antibody Center and Consortium.

The study was supported by the National Institutes of Health (grants R01AI113867, UM1 AI100663 and P41 GM103533) and IAVI._________About The Scripps Research InstituteThe Scripps Research Institute (TSRI) is one of the world's largest independent, not-for-profit organizations focusing on research in the biomedical sciences. TSRI is internationally recognized for its contributions to science and health, including its role in laying the foundation for new treatments for cancer, rheumatoid arthritis, hemophilia, and other diseases. An institution that evolved from the Scripps Metabolic Clinic founded by philanthropist Ellen Browning Scripps in 1924, the institute now employs more than 2,500 people on its campuses in La Jolla, CA, and Jupiter, FL, where its renowned scientists—including two Nobel laureates and 20 members of the National Academies of Science, Engineering or Medicine—work toward their next discoveries. The institute's graduate program, which awards PhD degrees in biology and chemistry, ranks among the top ten of its kind in the nation. In October 2016, TSRI announced a strategic affiliation with the California Institute for Biomedical Research (Calibr), representing a renewed commitment to the discovery and development of new medicines to address unmet medical needs. For more information, see www.scripps.edu.