Research shows efficacy of malarial drug Chloroquine in treating Zika infection

Zika virus remains a major global health risk. In most adults, Zika causes mild flu-like symptoms. But in pregnant women, the virus can cause serious birth defects in babies including microcephaly a neurological condition in which newborns have unusually small heads and fail to develop properly. There is no treatment or way to reverse the condition.

A new research study led by researchers at Sanford Burnham Prebys Medical Discovery Institute (SBP) and UC San Diego School of Medicine has found that chloroquine, a medication used to prevent and treat malaria may also be effective for Zika virus. The drug has a long history of safe use during pregnancy, and is relatively inexpensive. The research was published today in Scientific Reports.

Terskikh is co-senior author of a new study that examined the effect of chloroquine in human brain organoids and pregnant mice infected with the virus, and found the drug markedly reduced the amount of Zika virus in maternal blood and neural progenitor cells in the fetal brain. Pregnant mice received chloroquine through drinking water in dosages equivalent to acceptable levels used in humans.

Citation: Shiryaev, Sergey A., Pinar Mesci, Antonella Pinto, Isabella Fernandes, Nicholas Sheets, Sujan Shresta, Chen Farhy, Chun-Teng Huang, Alex Y. Strongin, Alysson R. Muotri, and Alexey V. Terskikh. “Repurposing of the anti-malaria drug chloroquine for Zika Virus treatment and prophylaxis.” Scientific Reports 7, no. 1 (2017).
Funding: California Institute for Regenerative Medicine, National Institutes of Health, NARSAD Independent Investigator Grant, International Rett Syndrome Foundation.
Adapted from press release by Sanford-Burnham Prebys Medical Discovery Institute.

Malaria drug Chloroquine helps fight treatment resistant brain cancer

After her brain cancer became resistant to chemotherapy and then to targeted treatments, 26-year-old Lisa Rosendahl’s doctors gave her only a few months to live. Now a paper published in the journal eLife describes a new drug combination that has stabilized Rosendahl’s disease and increased both the quantity and quality of her life: Adding the anti-malaria drug chloroquine to her treatment stopped an essential process that Rosendahl’s cancer cells had been using to resist therapy, re-sensitizing her cancer to the targeted treatment that had previously stopped working. Along with Rosendahl, two other brain cancer patients were treated with the combination and both showed similar, dramatic improvement.

The science behind the innovative, off-label use of this malaria drug, chloroquine, was in large part built in the lab of Andrew Thorburn, PhD, deputy director of the CU Cancer Center, where Mulcahy-Levy worked as a postdoctoral fellow, starting in 2009. Thorburn’s lab studies a cellular process called autophagy. Autophagy is a process of cellular recycling in which cell organelles called autophagosomes encapsulate extra or dangerous material and transport it to the cell’s lysosomes for disposal. In fact, the first description of autophagy earned the 2016 Nobel Prize in Medicine or Physiology for its discoverer, Yoshinori Ohsumi.

Mulcahy-Levy’s work with Thorburn (among others), showed that cancers with mutations in the gene BRAF, and specifically those with a mutation called BRAFV600E, were especially dependent on autophagy. In addition to melanoma, in which this mutation was first described, epithelioid glioblastomas are especially likely to carry BRAFV600E mutation.

With this new understanding, Mulcahy-Levy became an essential link between Thorburn’s basic science laboratory and the clinical practice of oncologist, Nicholas Foreman, MD, CU Cancer Center investigator and creator of the pediatric neuro-oncology at Children’s Hospital Colorado, who had been overseeing Lisa’s care.

After many surgeries, radiation treatments and chemotherapy, Lisa had started the drug vermurafenib, which was originally developed to treat BRAF+ melanoma and is now being tested in pediatric brain tumors. Lisa’s experience on the drug was typical of patients with BRAF+ cancers who are treated with BRAF inhibitors such as vemurafenib – after a period of control, cancer develops additional genetic mechanisms to drive its growth and survival and is able to progress past the initial drug.

At that point, one promising strategy is to predict and/or test for new genetic dependencies and then treat any new dependency with another targeted therapy. For example, many BRAF+ cancers treated with BRAF inhibitors develop KRAS, NRAS, EGFR or PTEN changes that drive their resistance, and treatments exist targeting many of these “escape pathways”. However, some cancers develop multiple resistance mechanisms and others evolve so quickly that it can be difficult to stay ahead of these changes with the correct, next targeted treatment.

“Pre-clinical and clinical experience invariably shows that tumor cells rapidly evolve ways around inhibition of mutated kinase pathways like the BRAF pathway targeted here,” the paper writes.

“However, based on our results, we hypothesize that by targeting an entirely different cellular process, i.e. autophagy, upon which these same tumor cells rely, it may be feasible to overcome such resistance and thus re-establish effective tumor control.”

In other words, knowing that Lisa Rosendahl’s tumor was positive for BRAFV600E mutation, and that this marked the tumor as especially dependent on autophagy – and also knowing that traditional options and even clinical trials were nonexistent – the group worked with Rosendahl and her father, Greg, to add the autophagy-inhibiting drug chloroquine to her treatment.

“In September 2015, the previous targeted drugs weren’t working anymore,” says Greg Rosendahl. “Doctors gave Lisa less than 12 months to live. We took all our cousins up to Alaska for a final trip kind of thing. Then they came up with this new combination including chloroquine.”

Vemurafenib had initially pushed Lisa’s cancer past the tipping point of survival. Then the cancer had learned to use autophagy to pull itself back from the brink. Now with chloroquine nixing autophagy, vemurafenib started working again.

“We have treated three patients with the combination and all three have had a clinical benefit. It’s really exciting – sometimes you don’t see that kind of response with an experimental treatment. In addition to Lisa, another patient was on the combination two-and-a-half years. She’s in college, excelling, and growing into a wonderful young adult, which wouldn’t have happened if we hadn’t put her on this combination,” Mulcahy-Levy says.

Research accompanying these results in patients implies that the addition of autophagy inhibition to targeted treatments may have benefits beyond glioblastoma and beyond only BRAF+ cancers.

Because chloroquine has already earned FDA approval as a safe and effective (and inexpensive) treatment for malaria, the paper points out that it should be possible to “quickly test” the effectiveness of adding autophagy inhibition to a larger sample of BRAF+ glioblastoma and other brain tumor patients, and also to possibly expand this treatment to other likely mutations and disease sites.

As Mulcahy-Levy’s early studies show, many cancers do not depend on autophagy. But at the same time, many do. Because a safe and simple drug already exists to inhibit autophagy, the time between discovering an autophagy-dependent cancer and the ability to add autophagy-inhibiting chloroquine to a treatment regimen against this cancer may be short.

Citation: Jean M Mulcahy Levy , Shadi Zahedi, Andrea M Griesinger, Andrew Morin, Kurtis D Davies, Dara L Aisner, BK Kleinschmidt-DeMasters, Brent E Fitzwalter, Megan L Goodall, Jacqueline Thorburn, Vladimir Amani, Andrew M Donson, Diane K Birks, David M Mirsky, Todd C Hankinson, Michael H Handler, Adam L Green, Rajeev Vibhakar, Nicholas K Foreman and Andrew Thorburn. “Autophagy inhibition overcomes multiple mechanisms of resistance to BRAF inhibition in brain tumors.” eLife  2017; 6:e19671.
DOI: 10.7554/eLife.19671
Research funding: National Institutes of Health, US Department of Defense, St. Baldrick’s Foundation.
Adapted from press release by University of Colorado.

Novel diagnostic test for malaria using holographic imaging and artificial intelligence using deep learning

Duke researchers have devised a computerized method to autonomously and quickly diagnose malaria with clinically relevant accuracy — a crucial step to successfully treating the disease and halting its spread.

In 2015 alone, malaria infected 214 million people worldwide, killing an estimated 438,000.
While Western medicine can spot malaria with near-perfect accuracy, it can be difficult to diagnose in resource-limited areas where infection rates are highest.

Malaria’s symptoms can look like many other diseases, and there are simply not enough well-trained field workers and functioning microscopes to keep pace with the parasite. While rapid diagnostic tests do exist, it is expensive to continuously purchase new tests. These tests also cannot tell how severe the infection is by tallying the number of infected cells, which is important for managing a patient’s recovery.

In a new study, engineers from Duke University report a method that uses computer ‘deep learning’ and light-based, holographic scans to spot malaria-infected cells from a simple, untouched blood sample without any help from a human. The innovation could form the basis of a fast, reliable test that could be given by most anyone, anywhere in the field, which would be invaluable in the $2.7 billion-per-year global fight against the disease. The results were published online Sept. 16 in the journal PLOS ONE.

“With this technique, the path is there to be able to process thousands of cells per minute,” said Adam Wax, professor of biomedical engineering at Duke. “That’s a huge improvement to the 40 minutes it currently takes a field technician to stain, prepare and read a slide to personally look for infection.”

Cells in different stages of infection as analyzed by a new algorithm.

The new technique is based on a technology called quantitative phase spectroscopy. As a laser sweeps through the visible spectrum of light, sensors capture how each discrete light frequency interacts with a sample of blood. The resulting data captures a holographic image that provides a wide array of valuable information that can indicate a malarial infection.

“We identified 23 parameters that are statistically significant for spotting malaria,” said Han Sang Park, a doctoral student in Wax’s laboratory and first author on the paper. For example, as the disease progresses, red blood cells decrease in volume, lose hemoglobin and deform as the parasite within grows larger. This affects features such as cell volume, perimeter, shape and center of mass.
“However, none of the parameters were reliable more than 90 percent of the time on their own, so we decided to use them all,” said Park.

“To be adopted, any new diagnostic device has to be just as reliable as a trained field worker with a microscope,” said Wax. “Otherwise, even with a 90 percent success rate, you’d still miss more than 20 million cases a year.”

To get a more accurate reading, Wax and Park turned to deep learning — a method by which computers teach themselves how to distinguish between different objects. By feeding data on more than 1,000 healthy and diseased cells into a computer, the deep learning program determined which sets of measurements at which thresholds most clearly distinguished healthy from diseased cells.

When they put the resulting algorithm to the test with hundreds of cells, it was able to correctly spot malaria 97 to 100 percent of the time — a number the researchers believe will increase as more cells are used to train the program. Because the technique breaks data-rich holograms down to just 23 numbers, tests can be easily transmitted in bulk, which is important for locations that often do not have reliable, fast internet connections, and that, in turn, could eliminate the need for each location to have its own computer for processing.

Wax and Park are now looking to develop the technology into a diagnostic device through a startup company called M2 Photonics Innovations. They hope to show that a device based on this technology would be accurate and cost-efficient enough to be useful in the field. Wax has also received funding to begin exploring the use of the technique for spotting cancerous cells in blood samples.

Publication: Automated Detection of P. falciparum Using Machine Learning Algorithms with Quantitative Phase Images of Unstained Cells.
Adapted from press release by Duke University

New vaccine targets found for Plasmodium vivax Malaria

Thousands died and more than 13 million people fell ill with malaria caused by the parasite Plasmodium vivax last year. There is no vaccine for the disease, partly because multiple strains of P. vivax circulate globally, making it difficult to develop a vaccine. Now, researchers studying a protein crucial for the parasite’s survival have found two portions of that protein that do not vary across many strains. Antibodies against these portions of the protein protect against disease, according to researchers at Washington University School of Medicine in St. Louis. The study is available online in the Proceedings of the National Academy of Sciences.

“This protein – called Duffy binding protein – is the most promising target for vaccine development because it is almost impossible for the parasite to cause infection without it,” said Niraj Tolia, associate professor of molecular microbiology and the study’s senior author.

If the parasite does not bind to the human protein – either because antibodies block the binding site or because the human protein is missing – the parasite is unable to cause disease. P. vivax is found all over the world, but it causes relatively little disease in Africa, where many people lack this specific protein on their red blood cells.

Tolia and colleagues studied three antibodies that are known to prevent a range of binding proteins from latching on to the human protein, and identified the portion of the binding protein to which the antibodies were bound. Two antibodies bound to the same portion, or epitope, while the third bound at another spot. “Our study helps define what we should be targeting to get universal protection,” Tolia said.

Press release: Vaccine targets identified for deadly form of malaria