Immunity and Pathogenesis Program Archives - Sanford Burnham Prebys
Institute News

Common gut bacteria have a taste for tungsten

AuthorGreg Calhoun
Date

January 9, 2025

A bacteria linked to longevity was found to feast on lactate only when the meal contains the metallic side dish

In a new paper published December 30, 2024, in PNAS, study coauthor Dmitry A. Rodionov, PhD, research assistant professor in the Immunity and Pathogenesis Program at Sanford Burnham Prebys, and colleagues, studied how Eubacterium limosum contribute to a healthy human gastrointestinal microbiome by metabolizing lactate.

Lactate or lactic acid is a normal byproduct that is created as our cells generate energy. Lactate can be found in the guts of healthy adults at low concentrations because microbes such as E. limosum make a meal of much of it, preventing the abnormal accumulation sometimes found in patients suffering from ulcerative colitis and other gut-related disorders.

Rodionov and his colleagues examined how E. limosum bacteria break down lactate into short-chain fatty acids (SCFAs) and were surprised to find that the metabolic process depends on two tungsten-containing enzymes.

The authors suggest that their findings are a tipoff that tungsten might be an overlooked micronutrient in the human gut microbiome and may contribute in unappreciated ways to overall human health.

Institute News

Jamey Marth interviewed by The Scientist

AuthorGreg Calhoun
Date

October 31, 2024

The Sanford Burnham Prebys scientist discussed the Cre-loxP recombination system, which continues to be a mainstay genetic engineering technology.

“Techniques come and go with new technology, it’s just like night and day.” said Jamey Marth, PhD, professor and director of the Immunity and Pathogenesis Program at Sanford Burnham Prebys during his interview with The Scientist regarding his lab’s contributions to a genetic engineering technique that has stood the test of time.

“So, when you have a technique that’s lasted 30 years with no replacement technology, I think that’s kind of remarkable.”

Marth was interviewed about the Cre-loxP recombination system, which acts as a molecular genetic editor for controlling mutations in the genome. It was initially investigated by Drs. Nat Sternberg and Brian Sauer in the 1980s in tests to manipulate the genes of yeast and mammalian cells.

Marth wanted to use the technique for conditional mutagenesis in animal studies that would enable temporal and cell-type specific genetic models to better investigate biological systems and more effectively model human diseases. He and his team advanced the Cre-loxP system for use in laboratory mice and demonstrated the ability to efficiently delete DNA sequences in specific T cells in 1992.

The Cre-loxP recombination system continues to be a mainstay technology today and some scientists are exploring ways to combine it with the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease, Cas9, to gain the advantages of both genetic engineering techniques.

Institute News

A potential new weapon against a deadly, drug-resistant bacterial pathogen

AuthorScott LaFee
Date

January 8, 2024

Carbapenems are a class of highly effective antibiotics that are often used to treat severe bacterial infections. They are usually reserved for known or suspected bacterial infections resistant to other drugs.

Carbapenem-resistant Acinetobacter baumannii (CRAB) is, as the name suggests, impervious to carbapenems; and it has become a major global pathogen, particularly in hospital settings and conflict zones. No new antibiotic chemical class with activity against A. baumannii has successfully emerged in more than 50 years.

In a paper published January 3, 2024, in Nature, a multi-institutional team including Andrei Osterman, PhD, at Sanford Burnham Prebys, with colleagues at Roche—the Swiss-based pharmaceutical/healthcare company—and others, describe a novel class of small-molecule tethered macrocyclic peptide (MCP) antibiotics with potent antibacterial activity against CRAB. Osterman’s lab provided critical data and discoveries related to the drug target and mapping of drug-resistant mutations.

Developing a new class of antibiotics effective against CRAB is critical. The bacterium is resistant to nearly all antibiotics and is difficult to remove from the environment. It poses a particular health threat to hospitalized patients and nursing home residents, with an estimated mortality rate in invasive cases of 40–60%.

The World Health Organization and the Centers for Disease Control (CDC) have both categorized multidrug-resistant A. baumannii as a top-priority pathogen and public health threat.

In the new study, Osterman and colleagues applied an experimental evolution approach to help identify the drug target (the LPS transporter complex) of a new class of antibiotics—a macrocyclic peptide called Zosurabalpin—and elucidate the dynamics and mechanisms of acquired drug resistance in four distinct strains of A. baumannii.

They used an integrative workflow that employs continuous bacterial culturing in an “evolution machine” (morbidostat) followed by time-resolved, whole-genome sequencing and bioinformatics analysis to map resistance-inducing mutations.

In addition to a mechanistic understanding (crucial from a regulatory perspective), the new information also helped reveal the drug-binding site. A related paper in the same issue experimentally verified the findings.

“This comprehensive mapping of the drug-resistance landscape yields valuable insights for a variety of practical applications,” says Osterman, “from therapy optimization via genomics-based assessment of drug resistance/susceptibility of bacterial pathogens to a rational development of novel drugs with minimized resistibility potential.”

A commentary in Nature said the research was “cause for cautious celebration” and urged further development.

Institute News

New COVID-19 drug passes phase 2 clinical trial

AuthorMiles Martin
Date

January 20, 2022

The new treatment, developed by Avalo Therapeutics with Sanford Burnham Prebys researchers, can mitigate lung damage and improve survival in COVID patients.

In a phase 2 clinical trial conducted by Avalo and supported by Sanford Burnham Prebys, a significantly higher proportion of hospitalized patients with COVID-19 remained alive and free of respiratory failure for 28 days after receiving treatment with the new antibody, called CERC-002. Unlike other experimental COVID therapies, CERC-002 does not target the virus itself, instead targeting the immune response associated with the virus to stop the disease from progressing before it becomes fatal.

“At the beginning of the pandemic we thought vaccines were going to be all we really needed. But with variants like omicron, we’re going to have more people that progress to serious illness even with the vaccine,” says study coauthor Carl F. Ware, PhD, director of the Infectious and Inflammatory Diseases Center at Sanford Burnham Prebys. “We need treatments to stop the progression to severe disease and death.”

The findings were published December 6 in the Journal of Clinical Investigation.

COVID-19: a continuing crisis
In the United States, over 840,000 people have died from COVID-19. A large proportion of these deaths have been among the elderly or those who are immunocompromised due to a preexisting condition. And while three quarters of the population has received at least one dose of the COVID-19 vaccine, many remain unvaccinated.

“A lot of us feel safer now that we’ve gotten our shots,” Ware says, “but the threat of the pandemic has not gone away, even for vaccinated people.”

Most people with COVID-19 experience few to no symptoms. However, elderly individuals, people with a concurrent health condition or those who are immunocompromised are susceptible to a condition called cytokine storm, in which their own immune molecules called cytokines flood the body in higher concentrations than usual.

Rather than helping fight the virus, these extra immune molecules wreak havoc, causing patients to develop the deadly respiratory failure characteristic of severe COVID disease.

“The COVID virus gets the immune system amped up by producing these molecules, which is normally how the immune system fights diseases,” says Ware. “But when there are too many cytokines and they’re not doing their job, it can lead to severe damage.” 

Neutralizing the cytokine storm
The new treatment, CERC-002, is a cytokine neutralizer—an immune molecule that recognizes and deactivates a cytokine known as LIGHT, which is elevated in patients with COVID-19. Cytokine neutralization drugs are currently being tested in the clinic, but they are mainly effective in severely ill patients who are already on a ventilator or other organ support.

“There is a critical need for drugs to stop milder cases from progressing to severe,” says Ware. “This treatment targets the cytokine immune response early enough to stop it in its tracks, which no other treatment does right now.”

83 COVID patients were enrolled in the study, half receiving the treatment, and half receiving a placebo. All patients were hospitalized with mild-to-moderate respiratory distress and were also receiving standard-of-care therapy during the trial.

They found that 83.9% of patients who received a dose of CERC-002 on top of standard of care remained alive and free from respiratory distress for 28 days. For patients receiving placebo, the number was only 64.5%.

Looking ahead
As a phase 2 clinical trial, the purpose of this study was to test whether the compound has therapeutic potential in a small number of patients. Now that the drug has proven successful at a small scale, it can be tested on a larger number of patients to ensure its benefits are consistent across the population.

Additionally, because CEC-002 targets the immune response in COVID cases rather than the virus itself, the compound may have applications that extend beyond COVID.

“Cytokine storm is not unique to COVID. It occurs in other infections—even in autoimmune diseases with no active infection, so this treatment may have some utility in these other diseases as well.” 
While there is more work to be done before CERC-002 becomes widely available, it does offer a glimmer of hope during a pandemic that seems never-ending.

“We have made a lot of progress in controlling the pandemic with vaccines and other new therapies, but it’s not over yet,” says Ware. “Treatments like this may bring physicians an option to protect infected people from severe illness.

Institute News

HIV and METH: An unpredictable storm

Authorsgammon
Date

January 6, 2016

 

Research has shown that methamphetamine (METH) use among HIV-positive individuals may be as high as 25%, compared with a national average of less than one percent. On its own, METH can cause irreparable physical, psychological, and social damage to individuals who abuse or become dependent on the drug. For HIV-positive patients, particularly individuals undergoing treatment with antivirals, the combined effects of METH and HIV infection on the central nervous system are particularly concerning.

A new study by SBP researchers evaluates the neuronal damage caused by HIV proteins, METH, and combinations of antiretroviral drugs (ARVs). Combinations of ARVs are the most common treatment for HIV-positive individuals, and are credited for increasing the survival of patients to near normal life spans. The results, published in Antimicrobial Agents and Chemotherapy, are surprising.

  • The overall positive effect of ARVs—keeping patients alive—comes with a downside. Certain ARV drug combinations are neurotoxic.
  • Some combinations of HIV, ARVs and METH increase neuronal impairment, while others have no additive effect. And the results are unpredictable.

“Our finding that ARVs can be neurotoxic is concerning,” said Marcus Kaul, PhD, associate professor in the Immunity and Pathogenesis Program at SBP. “We already know the virus on its own can cause a condition called HAND, which stands for HIV-associated neurocognitive disorders. That’s a fancy way of describing changes in memory, concentration, attention, and motor skills that affect up to 50% of HIV-positive patients.”

“Since the goal is to keep HIV-positive patients alive and healthy, it’s important to learn if the treatments we use to prolong life have unwanted side effects. Our research suggests that some ARV combination therapies aggravate neurocognitive decline. ”

Adding methamphetamine to the mix further complicates matters.

“We found that even though METH on its own is toxic to neurons, with some combinations of ARVs, we observe increased neuronal impairment, but in other combinations there is no additive affect. This means that the neurocognitive effects of METH may depend on the ARV combination prescribed to the patient.”

The study tested four of the most commonly used ARTs in the presence and absence of METH and gp120, a neurotoxic HIV protein that sits on the surface of the virus but can also be released from infected cells. The researchers used an in vitro system to assess neuronal damage produced by various combinations of the drugs and virus protein. Damage was measured by assessing the number of neurons and quantifying components of their processes and synapses. The analysis also included measurement of neuronal ATP levels—the main energy source of cells. Measuring ATP levels is a well-established method for evaluating toxicity. A reduction in ATP levels is indicative of cell damage.

“In a perfect world we would be able to predict which ARV therapy combinations are best suited to HIV-positive individuals prone to recreational drug use. While we are probably a few years from this degree of personalizing HIV treatment, in the short term the information adds to our understanding of the pathways and mechanisms that lead to neurocognitive decline and dementia, so the lessons we learn may ultimately be applied more broadly to neurological disorders,” Kaul added.

 

Institute News

Sanford-Burnham presents at the 2014 Society for Neurosience Meeting

Authorsgammon
Date

November 13, 2014

The Society for Neuroscience’s 44th annual meeting is the premier venue for neuroscientists to present emerging science, learn from experts, forge collaborations, and learn about new technologies and tools. Sanford-Burnham has several dynamic research programs in neuroscience, and below are our presentations scheduled for this year’s event. Continue reading “Sanford-Burnham presents at the 2014 Society for Neurosience Meeting”

Institute News

A new way to generate insulin-producing cells in type 1 diabetes

Authorsgammon
Date

July 31, 2014

A new study by researchers at Sanford-Burnham Medical Research Institute (Sanford-Burnham) has found that a peptide called caerulein can convert existing cells in the pancreas into those cells destroyed in type 1 diabetesinsulin-producing beta cells. The study, published online July 31 in Cell Death and Disease, suggests a new approach to treating the estimated 3 million people in the U.S., and over 300 million worldwide, living with type 1 diabetes. Continue reading “A new way to generate insulin-producing cells in type 1 diabetes”