Second year BMS student and Ott Lab graduate student Camille Simoneau passed her qualifying exam on July 26, making her an official PhD candidate! Congrats, Camille!
News Category: Ott Lab in the News
Philip Ansumana Hull moves on to Bristol-Meyers Squibb
On June 22nd, Philip Ansumana Hull successfully defended his thesis and earned his PhD. His thesis work focused on immune aging, T cell biology, and T cell metabolism. This included identifying a novel evolutionary conserved SIRT1-FoxO1 axis that regulates CD8+ memory T cell metabolism and cytotoxicity. His last day in the Ott Lab was July 31st, and he is now off to work for Bristol-Meyers Squibb.
Congratulations, Ansu, and good luck at your new job!
Juan Torres presents research
Ott Lab summer intern Juan Torres presented the research he did with postdoc Nathan Meyers on August 1st. Juan’s presentation was entitled “Using Liver Stem Cells to Develop a 3D Model for Studying Hepatitis C”. Juan will return to UCLA in the fall to complete his undergraduate studies.
Great job, Juan!
Kristoffer Leon presents at the 2018 American Academy of Neurology Annual Meeting
Kristoffer Leon presented his talk “Pediatric Brainstem Encephalitis Outbreak Investigation with Metagenomic Next-Generation Sequencing” during the Contemporary Clinical Issues Plenary Session at the 2018 American Academy of Neurology Annual meeting in Los Angeles, CA. The abstract was named a 2018 Abstract of Distinction to recognize top scientific achievement in the field.
Complimentary access to the 2018 plenary sessions can be viewed here.
An Anti-Aging Protein Could Be Targeted to Rejuvenate Immune Cells
Aging proteins have long been shown to protect against age-related diseases, such as cancer, neurodegeneration, and cardiovascular disease. A study by researchers at the Gladstone Institutes now reveals that one such protein could also be targeted to rejuvenate cells in the immune system.
The protein in question is called SIRT1, more commonly known for being activated by red wine. In the new study, published in the Journal of Experimental Medicine, the scientists found that it is also involved in how cells in the immune system develop with age.
They wanted to find out how this anti-aging protein affects a specific category of immune cells known as cytotoxic T cells. These cells are highly specialized guardians of the immune system and their role is to kill cells infected by a virus, damaged cells, or cancer cells.
“Over the course of a person’s life, with repeated exposure to bacteria and viruses, these T cells mature and eventually lose a protein called CD28,” said Gladstone Senior Investigator Melanie Ott, senior author of the new study. “And as these cells get older, they become more toxic to their environment.”
This aging process is accelerated by persistent viral infections, such as HIV and CMV (human cytomegalovirus). In fact, HIV-infected patients accumulate mature cytotoxic T cells at a much younger age than an uninfected person.
“A higher number of mature cytotoxic T cells in the body has been associated with age-related, autoimmune, and inflammatory diseases,” added Ott, who is also a professor in the Department of Medicine at UC San Francisco. “We wanted to come up with a way to counteract this phenomenon.”
What Happens in Aging Cells
When a young (or naive) T cell is in a resting state, it uses oxygen to “breathe.” Once it is activated to defend the body against a bacteria or virus, it shifts into enhanced glycolysis and uses sugar to get an immediate boost in energy. This is useful to jump into action, but it isn’t sustainable for long-term performance.
“You can think of it like a 60-meter sprint runner who needs a quick boost of energy to finish the race, in comparison to a marathon runner who needs different energy sources to keep going for a long period of time,” said Ott.
As the cells age and lose CD28, they can shift into glycolysis much more quickly if breathing is inhibited. They also lose the anti-aging protein SIRT1. This becomes a problem, as it makes them more toxic to the cells around them.
In the new study, Ott and her team finally explain how this all happens.
“We studied human T cells, isolated from blood donors of all ages, to compare mature cytotoxic T cells with naive ones,” said Philip Ansumana Hull, graduate student in Ott’s lab and one of the first authors of the study.
They found that naive T cells have a high concentration of SIRT1. This stabilizes an entire mechanism that prevents the cells from entering glycolysis to use sugar as an energy source, and limits their toxic effects.
As the cells age, they lose SIRT1, which changes their basic metabolism. They can then rapidly shift into glycolysis and start producing more toxic proteins called cytokines, which could lead to inflammatory diseases.
One Mechanism to Fight Both Aging and Aggressive Tumors
Based on a better understanding of the crucial role played by SIRT1 in the aging of T cells, the researchers identified two potential new drug targets.
First, new drugs could be developed to strengthen SIRT1 to rejuvenate mature cytotoxic T cells or keep them from progressing too quickly into a highly toxic state.
“This could postpone the development of age-related diseases,” said Mark Y. Jeng, the study’s other first author and former graduate student in Ott’s lab. “It could also help people with a weaker immune system fight infections or better respond to immune vaccination, such as seniors or chronically-infected patients.”
Alternatively, drugs could be used to obtain the opposite effect and encourage the T cells to be more toxic. By temporarily making young T cells more aggressive and behave like mature cells, they could, for example, support an aggressive anti-tumor response or other immune therapeutic approaches.
Publication: Jeng MY, Hull PA, Fei M, Kwon H-S, Tsou C-L, Kasler H, et al. Metabolic reprogramming of human CD8+ memory T cells through loss of SIRT1. J Exp Med. 2017 Nov 30. em.20161066; DOI: 10.1084/jem.20161066
Ibs Ali was awarded the ASM Graduate Research Fellowship
Ibs Ali was awarded the Robert D. Watkins Graduate Research Fellowship from the American Society for Microbiology. It also means that you will be supported to travel to the ASM Microbe meeting, and provide you with access to career advancement workshops provided by ASM. Congratulations, Ibs!
Melanie Ott Presented with DiNA Award 2017
Congratulations, Melanie for being honored for your work with the Promoting Underrepresented Minorities Advancing in the Sciences (PUMAS) internship program by the California Life Sciences Association (CLSA). PUMAS supports educational activities that enhance diversity in biomedical research. Established in 2014 by Melanie Ott and Kathy Ivey at the Gladstone Institutes, the program encourages students from historically underrepresented backgrounds, who are currently attending a community college, to pursue undergraduate and graduate degrees in science, technology, engineering, or mathematics (STEM).
Each summer, qualified students are matched with a scientific mentor to gain hands-on biomedical research experience in a Gladstone laboratory. To date, 24 interns have gone through the PUMAS program, and three have since returned to Gladstone as research associates.
The PUMAS program is funded by the National Heart, Lung, and Blood Institute of the National Institutes of Health.
Gladstone is an independent, nonprofit life science research organization that uses visionary science and technology to overcome disease. To ensure their work does the greatest good, Gladstone researchers focus on conditions with profound medical, economic, and social impact—unsolved diseases. Gladstone has an academic affiliation with the University of California, San Francisco.
Cancer Drug Can Reactivate HIV
SAN FRANCISCO, CA—August 24, 2017
People living with HIV must take a combination of three or more different drugs every day for the rest of their lives. Unfortunately, by following this strict treatment plan, they can suffer from side effects ranging from mild dizziness to life-threatening liver damage. However, if they stop taking the drugs, the virus hiding inside their cells can spontaneously resurface.
In fact, the latent HIV, which can hide in cells for many years, is a critical barrier to a cure. Researchers are exploring two main strategies to tackle this problem––reactivate and destroy the latent virus (called “shock and kill”) or find a way to silence it for good.
In an effort to tackle both strategies, a team of scientists at the Gladstone Institutes studies drugs that disrupt latency and could eventually be used to treat infected patients. They recently discovered how a new drug called JQ1, which is currently in early-phase human cancer trials, can reactivate latent HIV.
The Key Is the Short Form
“Our discovery was born out of frustration,” explained Gladstone Senior Investigator Melanie Ott, whose study was published today in the journal Molecular Cell. “We already knew that the drug JQ1 targets a protein called BRD4, but our experiments were not yielding consistent results. Then, we started looking at different forms of the protein and, unexpectedly, found that a short form was the key to silencing HIV.”
By identifying this new role for the short form of BRD4, Ott’s team could finally explain a mechanism that controls HIV latency. They showed that the drug JQ1 targets and removes the short form of BRD4, which then allows the virus to make copies of itself.
“Many people in the field don’t even know that a short form of BRD4 exists,” said Ryan Conrad, a postdoctoral scholar in Ott’s lab and first author of the study. “While uncovering the role of this protein in HIV, we discovered that it may also be involved in fighting other viruses related to HIV. Therefore, our findings could provide new insights into an ‘old’ cellular defense mechanism against invading viruses.”
The study could also impact a broader range of diseases, given that the drug JQ1 is already being tested as a way to target the BRD4 protein to treat cancer, heart failure, and inflammation.
A Holistic Approach to Curing HIV
Many scientists concentrate on the “shock and kill” strategy as a way to cure HIV, but more and more of them are shifting their focus to silencing the virus. The mechanism discovered at Gladstone can support both strategies—manipulating the BRD4 protein either to help HIV resurface or to strengthen the body’s capacity to suppress it.
“Silencing and reactivating HIV are often seen as competing approaches, but I think they could actually be combined to develop more effective therapies in the future,” added Ott, who is also a professor in the Department of Medicine at the University of California, San Francisco (UCSF). “You could start by shocking and killing the virus that’s easy to target, then use silencing mechanisms to slow the resurfacing of latent virus.”
This strategy could potentially allow patients to stop taking drugs, and for several years to elapse before the virus reactivates. By that time, the immune system could be strong enough to eliminate the virus as it surfaces.
“That’s how I see the future of HIV cure research,” said Ott.
Scientists may not completely eliminate HIV overnight, but Ott’s team is working to find a way to target the virus so people who are infected can stop continuously taking pills.
Publication: Conrad RJ, Fozouni P, Thomas S, Sy H, Zhang Q, Zhou MM, Ott M. The Short Isoform of BRD4 Promotes HIV-1 Latency by Engaging Repressive SWI/SNF Chromatin-Remodeling Complexes. Mol Cell. 2017 Aug 17. pii: S1097-2765(17)30549-X. doi: 10.1016/j.molcel.2017.07.025.
News and Highlights Community News Research News Media Coverage Videos For Journalists Study Reveals a New Method to Address a Major Barrier to Eradicating HIV
Scientists at the Gladstone Institutes discovered that an enzyme called SMYD2 could be a new therapeutic target for flushing out the HIV that hides in infected individuals. Overcoming this latent virus remains the most significant obstacle to a cure.
While drug therapy allows people living with HIV to lead a relatively normal life, it also comes with adverse effects. In addition, patients must stay on the drugs for life to prevent the virus hiding in their body from reactivating. In the early stages of infection, HIV hides in viral reservoirs in a type of immune cells called T cells. This dormant, or latent, virus can then spontaneously reactivate and rekindle infection if drug therapy is stopped.
To eliminate HIV latency, scientists are exploring a “shock and kill” strategy that would use a combination of drugs to wake up the dormant virus, then act with the body’s own immune system to eliminate the virus and kill infected cells. Previous research has had limited success in efficiently reactivating latent HIV, so scientists are working to find new, more effective drugs.
“Our study focused on a class of enzymes called methyltransferases, which have emerged as key regulators of HIV latency,” explained Melanie Ott, MD, PhD, a senior investigator at Gladstone and lead author of the study published in the scientific journal Cell Host & Microbe. “These enzymes have also become increasingly important in disease development, particularly cancer, and efforts have intensified to develop specific pharmacological inhibitors targeting them.”
“We systematically screened over 50 methyltransferases to determine which ones regulate latency in infected T cells,” said Daniela Boehm, postdoctoral scholar in the Ott laboratory and first author of the study. “We identified SMYD2 as a regulating enzyme, and found that inhibiting it reactivates, or wakes up, latent cells. SMYD2 could therefore be used as a therapeutic target in the shock and kill strategy.”
Although SMYD2 was not previously considered a target for HIV, pharmacological inhibitors are already being developed against this enzyme due to its effect on various cancer tumors.
“Our findings offer new biological and mechanistic insights into how latency functions,” added Ott, who is also a professor in the Department of Medicine at the University of California, San Francisco (UCSF). “They also suggest potential translational applications. Through a valuable collaboration with our industry partners, we obtained samples of small molecules in pre-clinical development that target SMYD2 and could potentially activate latent HIV.”
In collaboration with Warner C. Greene, MD, PhD, the researchers tested the small molecules that inhibit SMYD2 in human cells.
“We found that these small SMYD2 inhibitors were able to activate the virus in latently infected T cells isolated from HIV patients,” said Greene, senior investigator and director of the Gladstone Institute of Virology and Immunology.
“Our findings provide the basis for a new model of HIV latency wherein SMYD2 contributes to durably repressing the latent virus,” said Ott. “They also underscore the emerging ties between cancer and HIV treatment through shared pharmacological targets. Though we are still far from a human application, it is exciting to know that data from this study might readily connect with clinical efforts.”
Publication: Boehm D, Ott M. Flow Cytometric Analysis of Drug-induced HIV-1 Transcriptional Activity in A2 and A72 J-Lat Cell Lines. Bio Protoc. 2017 May 20;7(10). pii: e2290. doi: 10.21769/BioProtoc.2290.
Using Viruses to Find the Cellular Achilles Heel
SAN FRANCISCO, CA—January 22, 2015—A study from researchers at the Gladstone Institutes has exposed new battle tactics employed by the hepatitis C virus (HCV). Published in the January 22 issue of Molecular Cell, the investigators created full protein interaction maps—interactomes—of where the virus comes into contact with the host proteins during the course of infection. Through these protein interactions, the scientists not only gained insight into the virus, they also uncovered a common set of host proteins that are targeted by various infections. Their results suggest that these proteins and the cellular processes they govern are the most crucial—in effect, the collective Achilles heel—for both the human body and its viral invaders.
“Viruses are fantastic tools for shedding new light on human biology,” says Nevan Krogan, PhD, a senior investigator at the Gladstone Institutes and a corresponding author. “Viruses are relatively simple organisms—often they only have about 10-20 genes—but they wreak havoc on our system by targeting key proteins and essential functional pathways in every major biological process. This gives us great insight into what the critical mechanisms are that are being hijacked during infection, and it helps us to develop new strategies for preventing or stemming disease.”
Dr. Krogan, who is also a professor of cellular and molecular pharmacology at the University of California, San Francisco (UCSF) and director of the UCSF branch of QB3, partnered with Gladstone senior investigator Melanie Ott, MD, PhD, to map the interaction between the proteins in HCV and those in the human liver cells that HCV infects. This resulted in over 5,000 virus-host protein-to-protein interactions, which the investigators narrowed down to 139 key connections that are necessary for HCV infection, involving all 10 HCV proteins and 133 proteins in the host liver cells.
Although patients have benefited from numerous advancements in the treatment of HCV, how the virus damages the liver remains unknown. The HCV interactome map, led by first authors Holly Ramage, PhD, and G. Renuka Kumar, PhD, may help on this front.
“There’s a lot we still don’t know about HCV, like how it infects the cell, what processes it disrupts, and why it’s so harmful to the body,” explains Dr. Ott, who is also a professor of medicine at UCSF. “The protein interactome offers us an unbiased and global view of how the virus is affecting the infected cells, and this can help us to start answering a lot of the important questions. Ultimately, this information may direct us to new leads for preventative treatments for associated liver pathologies, like fibrosis and cancer.”
By removing the interacting host proteins from the cell one at a time, the researchers were able to determine what their functional contribution was in the infection process: whether the host proteins were hijacked by the virus and used to spread infection, or whether they were part of a defense mechanism against the virus. This revealed a new critical host mechanism that HCV inactivates and usurps to support its own survival and replication.
Publication: Ramage HR, Kumar GR, Verschueren E, Johnson JR, Dollen Von J, Johnson T, Newton B, Shah P, Horner J, Krogan NJ, Ott M (2015) A combined proteomics/genomics approach links hepatitis C virus infection with nonsense-mediated mRNA decay. Mol Cell 57:329–340.