ubiquitin

A doctoral thesis has identified a component in the immune system that acts as a molecular switch.

Researchers at the University identified the component that is a novel regulator and is able to deactivate the innante immune system, and can also prevent many diseases that are caused by the activation of the immune system.

“It is an important milestone in the understanding of how our immune system works and how its response can be controlled to prevent inflammatory diseases,” said Swarupa Panda, PhD Student at the Department of Molecular Biology at UmeÃ¥ University.

Panda identified the key component of the ubiquitin system in her doctoral thesis, and described how it regulated the immune system and prevented the development of various inflammatory conditions and cancer.

Despite the immune system being vital for our health, it can overreact, causing cancer and other chronic inflammatory diseases such as rheumatoid arthritis, multiple sclerosis and systemic lupus erythematosus.

Under the supervision of Dr Nelson O. Gekara, Panda identified MYSM1, a component of the ubiquitin system, that stops excessive inflammation. The team found that this molecule acts as a ‘rheostat’, and turns ‘on and off’ in response to an innate immune stimuli in order to restore immune homeostasis.

Previously, MYSM1 was known for its function within the cell nucleus. This doctoral thesis described MYSM1’s cytoplasmic function, where in response to inflammation and infection, it accumulates rapidly in the cytoplasm. Here, it inactivates the major immune signalling pathways, preventing the immune system from attacking its own tissue. 

The research team also found that after it had completed the task at hand, MYSM1 is rapidly degraded from the cytosol, thus preventing immune suppression.

Other studies have indicated that this component of the ubiquitin signalling system may also be a tumour suppressor, with further studies elucidating upon this and how it could be applied.

“This emphasises the importance of MYSM1 as a high value molecular target for future anti-inflammatory and anti-tumor therapies,” added Panda.

The discovery was published in the journals Immunity and Nature Communications.

Researchers have identified an innovative and promising therapeutic option to treat multiple sclerosis. They discovered that the protein prohibitin occurs in high concentrations on the surface of certain T-cells in MS patients and that its presence is associated with stimulation of the member of the mitogen-activated protein kinase (MAPK) pathway called CRAF. The researchers were able to show in a model that the interaction between prohibitin and CRAF could be interrupted by a polysaccharide vaccine, blocking the Th17 production in pathogenic Th17 cells and promoting the proliferation of anti-inflammatory regulatory T-cells. In this experimental model of MS, this led to alleviation of the severity of the condition. 

In an experimental model of MS, the team led by Professor Frauke Zipp and Professor Krishnaraj Rajalingam of the Mainz University Medical Center found that there was significant upregulation of the proteins prohibitin 1 and 2 on the surfaces of interleukin-17 (IL-17) producing Th17 cells, a subpopulation of T-cells. IL-17 is a protein secreted by a unique population of immune cells. “The increased surface expression of prohibitin 1 and 2 was associated with a similarly elevated activity of the MAP kinase CRAF and downstream MAP-kinase signal transduction. We were not only able to observe this in healthy individuals but also in Th17 cells of patients suffering from MS,” Professor Frauke Zipp, Director of the Department of Neurology at the Mainz University Medical Center, pointed out. MAP kinases are activated by growth factors. They initiate a multi-stage signalling cascade, which, as a signalling pathway, regulates fundamental biological processes such as cell growth. In many cancer-related disorders, components of this signalling pathway are modified, which, among other things, can promote a greater proliferation of tumour cells.

Based on these findings, the Prof Mainz-based team hoped to discover whether and, if so, how the interaction between prohibitin and CRAF might not only be interrupted but also prevented. One approach they employed in their study was to test Vi polysaccharide, a vaccine approved by the World Health Organization (WHO) for the treatment of typhoid. This vaccine blocks the interaction between CRAF and prohibitin and thus represents a new type of kinase inhibitor. It was found that this vaccine significantly inhibits CRAF activity in treated cells. “Further investigations using this disease model allowed us to show that the number of anti-inflammatory regulatory T-cells increased and, as a result, the severity of MS was significantly alleviated,” explained cell biologist Professor Krishnaraj Rajalingam, head of the Cell Biology Unit at the Mainz University Medical Center. “Developing novel kinase inhibitors that target protein-protein interactions are of special interest especially in treating immune disorders. Our next goal is to apply these findings to other autoimmune diseases such as rheumatoid arthritis,” added Rajalingam, who is also a Heisenberg Professor of Cell Biology and a Fellow of the JGU Gutenberg Research College.

The speaker and coordinator of the Research Center for Immunotherapy (FZI), Professor Tobias Bopp, also considers the new approach to be promising, especially as active substances that can inhibit kinases are already being used to treat patients. “Targeted treatment of a tumour and autoimmune diseases with kinase inhibitors is a promising approach that is already being employed in a clinical setting.”

The team has published their findings in The EMBO Journal.

Novel classification can lead to new ways to diagnose and treat cancer

Researchers have identified elevated levels of a protein called ubiquilin-4 as a new biomarker for genome instability. Genome instability can lead to genetic disorders, chronic diseases and a predisposition to cancer. The study finds that ubiquilin-4 takes part in defending the genome from DNA damage, but too much ubiquilin-4 is harmful. When the amount of ubiquilin-4 rises in tumour cells, the cells become more prone to genome instability, accelerating the tumour’s progression and making it resistant to commonly used cancer treatments.

The study led by Professor Yossi Shiloh of the Department of Human Molecular Genetics and Biochemistry at TAU’s Sackler School of Medicine, in close collaboration with Professor Christian Reinhardt of University Hospital Cologne and the University of Cologne. Research for the study was carried out in Tel Aviv by Dr Ron Jachimowicz, now at the University Hospital of Cologne, and Dr. Yael Ziv and PhD student Bhavana Velpula, both of TAU. Dr Dave Hoon of the John Wayne Cancer Institute in Santa Monica, CA, also contributed to the research.

“This novel biomarker provides new, critical information about the tumour stage and grade, as well as the patient’s chances of responding to treatment,” says Prof. Shiloh. “Tumours with high levels of ubiquilin-4 may be more resistant to radiation and some chemotherapies than those with normal levels of this protein. But the good news is that they may also respond better to other types of cancer therapy. Obviously, this is vital information for clinicians and patients.

“The importance of maintaining genome stability and integrity has been demonstrated through the study of rare genetic disorders,” Prof Shiloh continues. “But genome stability has now become a public health issue. There are so many proteins involved in responding to DNA damage, and behind every protein is a different gene. There are infinite ways in which a gene can mutate. Various combinations of these mutations may lead to chronic diseases and a predisposition to cancer, premature ageing and other conditions. Genome stability is everyone’s problem.”

According to the new research, the body’s DNA damage response is key to maintaining genome stability in the face of the constant onslaught of damaging agents. The response is composed of a broad, fine-tuned signalling network involving a standing army of proteins fully dedicated to this mission, as well as reserve proteins recruited temporarily to help resolve genome integrity.

In 1995, the Shiloh lab discovered the gene encoding of one of the major sentries at the gate of genome stability — the protein ataxia-telangiectasia mutated (ATM). The finding was met with great fanfare. It concluded a long effort to identify the gene mutated in a severe genome instability syndrome, ataxia-telangiectasia (A-T).

But ATM also plays a critical role in the body’s DNA damage response, mobilising an extensive signalling network in response to tears in the long DNA molecule. It causes subtle chemical modifications in many proteins, which temporarily render them reserve proteins and recruits them away from their regular duties to carry out damage control.

“We are constantly searching for new reserve proteins that respond to ATM’s call,” Prof Shiloh says. “Our new study shows that, like many other proteins, ubiquilin-4 is modified by ATM, and for several hours it serves the ATM-governed system.”

The researchers, in collaboration with Prof. Dagmar Wieczorek of the Institute of Human Genetics at Heinrich-Heine-University in Düsseldorf, also discovered that the deficiency of ubiquilin-4 alone can lead to yet another rare genome instability syndrome.

“We hope our findings will provide a new tool for tumour classification, prognosis and treatment design,” Prof. Shiloh concludes. “The research highlights the broader implications of the importance of genome stability for our health.”

The study has been published in the journal Cell.

gene expression

A study has provided insight into the mechanism of controlling gene expression in living organisms.

The researchers mentioned how the finding could ultimately improve our understanding of how certain antibacterial drugs work against the enzyme RNA polymerase (RNAP) in treating conditions such as Clostridium difficile infections and tuberculosis.

Gene expression occurs when DNA is used to produce functional products that the body is able to use, such as proteins. The process includes both transcription and translation.

During transcription, RNAP ‘reads’ the genetic DNA code on a single strand of DNA, which is then copied into a new mRNA molecule. Translation includes the processing of this information into the actual production of the molecule.

To control the levels of gene expression, transcriptional pausing by RNAP can occur between the two stages, providing a kind of ‘roadblock’ where transcription may be terminated or modulated.

“A consensus pause sequence that acts on RNAPs in all organisms, from bacteria to mammals, halts the enzyme in an elemental paused state from which longer-lived pauses can arise,” explained senior author Dr Robert Landick, Charles Yanofsky Professor of Biochemistry & Bacteriology at the University of Wisconsin-Madison, US. “As the fundamental mechanism of this elemental pause is not well defined, we decided to explore this using a variety of biochemical and biophysical approaches.”

The research team’s analyses revealed that the elemental pause process involves several biological players, which together create a barrier to prevent escape from paused states. The process also causes a modest conformational shift that makes RNAP ‘stumble’ in feeding DNA into its reaction centre, temporarily stopping it from making RNA.

“We also found that transcriptional pausing makes RNAP loosen its grip and backtrack on the DNA while paused,” said Prof Landick. “Together, these results provide a framework to understand how the process is controlled by certain conditions and regulators within cells.”

He added that these insights could aid future efforts to design synthetic genes, for example to direct the pausing behaviour of RNAP in a way that yields desired outputs from genes. It could also help our understanding of how certain drugs, known as RNAP inhibitors, target the enzyme.

“For now, we would like to try and generate structures of paused transcription complexes obtained at a series of time intervals,” Prof Landick concludes. “This would allow us to see exactly how parts of the enzyme move as it enters and leaves the paused state.”

The study was published in eLife.

heart failure

An international research team led by scientists at the University of Alberta have pinpointed a hidden culprit that leads to dilated cardiomyopathy – a dangerous condition that accounts for 20 percent of all cases of heart failure – which opens the door to potential new treatments that could help counter the threat.

The team identified a key molecule named PI3K alpha that binds to gelsolin – an enzyme that can destroy filaments that help make up the structure of the heart’s cells – and suppresses it.

The researchers, led by Dr Gavin Oudit, a Professor of Cardiology at the University of Alberta and Director of the Heart Function Clinic at the Mazankowski Alberta Heart Institute, believe the molecule holds great promise as a possible therapeutic target, offering a possible path forward to personalised and precision medicine for patients with dilated cardiomyopathy.

The condition decreases the heart’s ability to pump blood because its main pumping chamber, the left ventricle, is enlarged and weakened. Researchers studied the condition at the molecular level in animal models and in explanted human hearts, and found that the pathway leading to dilated cardiomyopathy is common in all species.

According to Prof Oudit, who holds the Canada Research Chair in Heart Failure, the condition is caused by biomechanical stress, which activates the gelsolin enzyme.

“You need some gelsolin, but when it gets out of control, it destroys things. The molecule chews up the filaments and you get really bad heart failure,” said Prof Oudit. “But we have also shown that when you suppress this molecule, you preserve your heart function. It’s intact.”

Prof Oudit said the potential impact on patient care is huge.

“By understanding these patients better, we’ll hopefully be able to develop specific therapies for them,” he said.

According to Prof Oudit, there are currently no specific treatments for patients with heart failure. The same medications are used for all patients.

“But if we can now identify patients that have problems with this type of remodelling (dilated cardiomyopathy), we can target them specifically,” he explained. “That’s where we’re heading down the road. And to take this research right from the molecule to our patients, it’s very rewarding.”

drug sponge

A ‘drug sponge’ could be used in future to soak up excess drugs in the hope that it would prevent debilitating and dangerous side effects of toxic treatments. It could even deliver higher doses to tumours that do not respond to more benign treatments.

The “drug sponge” is an absorbent polymer coating a cylinder that is 3D printed to fit precisely in a vein that carries the blood flowing out of the target organ – the liver in liver cancer, for example. There, it would absorb up any drug not absorbed by the tumour, preventing it from reaching and potentially poisoning other organs.

In early tests in pigs, the polymer-coated drug absorber took up, on average, 64 percent of a liver cancer drug – the chemotherapy agent doxorubicin – injected upstream.

“Surgeons snake a wire into the bloodstream and place the sponge like a stent, and just leave it in for the amount of time you give chemotherapy, perhaps a few hours,” said Dr Nitash Balsara, a Professor of Chemical and Biomolecular Engineering at the University of California, Berkeley, and a faculty scientist at Lawrence Berkeley National Laboratory.

“Because it is a temporary device, there is a lower bar in terms of approval by the FDA,” said Professor Steven Hetts, an interventional radiologist at UC San Francisco who first approached Prof Balsara in search of a way to remove drugs from the bloodstream. “I think this type of chemofilter is one of the shortest pathways to patients.”

Most anticancer drugs are poisonous, so doctors walk a delicate line when administering chemotherapy. A dose must be sufficient to kill or stop the growth of cancer cells, but not high enough to irreparably damage the patient’s other organs. Even so, chemotherapy is typically accompanied by major side effects, including nausea, vomiting, diarrhea and suppression of the immune system, not to mention hair loss and ulcers.

“We are developing this around liver cancer because it is a big public health threat – there are tens of thousands of new cases every year – and we already treat liver cancer using intra-arterial chemotherapy,” Prof Hetts said. “But if you think about it, you could use this sort of approach for any tumour or any disease that is confined to an organ, and you want to absorb the drug on the venous side before it can distribute and cause side effects elsewhere in the body. Ultimately we would like to use this technology in other organs to treat kidney tumours and brain tumours.”

Prof Hetts, the chief of interventional neuroradiology at the UCSF Mission Bay Hospitals, treats tumours of the eye and brain by threading catheters through the bloodstream to deliver chemotherapy drugs directly to the site of the tumour. This delivers the maximum dose to the tumour and the least dose to the rest of the body, minimising side effects. It is a vast improvement over injecting chemotherapy drugs straight into the bloodstream, which allows the drugs to reach and poison every part of the body and gambles on the tumour succumbing before the patient. Nevertheless, typically more than half of the dose injected into the body escapes the target organ.

Several years ago, he started thinking about a major improvement: filtering the blood coming out of the targeted organ to remove excess chemo so that much less of the drug reaches the body as a whole.

Prof Balsara, a chemical engineer who specialises in ionic polymers for batteries and fuel cells, is one of the people Prof Hetts approached to find a suitable absorber to put in the bloodstream. In 2016, former UC Berkeley and Berkeley Lab postdoctoral fellow Chelea Chen identified an ionic polymer, not unlike polymers used in fuel cells, that efficiently absorbed doxorubicin,

“An absorber is a standard chemical engineering concept,” Prof Balsara said. “Absorbers are used in petroleum refining to remove unwanted chemicals such as sulfur. Literally, we’ve taken the concept out of petroleum refining and applied it to chemotherapy.”

That polymer led Prof Balsara’s team to a commercial version of the absorbent polymer that was easier to obtain in large quantities, and Berkeley postdoc Hee Jeung Oh spent more than a year perfecting a way to adhere the polymer to a 3D-printed cylinder with crisscrossing struts that could be placed inside a person’s vein.

“Fitting the cylinder in the vein is important; if the fit is poor, then the blood with the dissolved drug will flow past the cylinder without interacting with the absorbent,” Prof Balsara said. Recognising the need for customising the device for individual patients, Prof Balsara solicited the help of a long-time collaborator, Joseph DeSimone, the CEO of Carbon, Inc., a 3D-printing company in Redwood City.

In the experiments Prof Hetts implanted the 3D-printed device into the vein of a pig and measured how much of the doxorubicin injected upstream remained downstream of the absorber. In a healthy pig, about 64 percent of the drug was removed.

They are currently in the midst of experiments to determine how much drug is absorbed when the device is implemented at the exit of a healthy pig liver, though the true test will be in humans, perhaps in a couple of years, Prof Hetts said.

“This is a first level in vivo validation that yes, this device will bind up drug in the bloodstream,” he said. “But extensive animal testing is not the next path; the next path is getting conditional approval from FDA to do first-in-human studies, because it is much more realistic to test these in people who have cancer as opposed to continuing to test in young pigs who have otherwise healthy livers.”

Prof Hetts says that the technique is superior to another liver cancer treatment now undergoing testing, which requires major endovascular surgery to completely block the outputs from the liver with balloons and divert the outflowing blood to an external dialysis machine, where the drug is removed and the blood returned to the body.

“There is a lot of opportunity to develop less-invasive devices that will bind up the drug in a gentler manner,” he said.

Drug sponges could be applied to many types of tumours and chemotherapy drugs, Prof Hetts said, and could potentially be used to sop up other dangerous drugs, such as high-powered antibiotics that are toxic to the kidneys but required to kill a pathogen.

“We think this is a generally applicable concept,” he said.

Prof Hetts, Prof Balsara and their colleagues at UC Berkeley, UCSF and the University of North Carolina, Chapel Hill, published their results in the journal ACS Central Science.

diabetes

Artificial Intelligence has been used to support the early diagnosis of diabetes-related eye diseases, one of the main causes of blindness.

Researchers led by RMIT University have developed an algorithm that processes images and can automatically detect fluid on the retina of the eye – one of the key signs of the disease. It has an accuracy rate of 98 percent.

With 191 million people set to be affected by 2030, diabetic retinopathy is the leading cause of vision loss in adults. Its impact is growing worldwide.

Professor Dinesh Kant Kumar, at RMIT University, said that the method was cost-effective and instantaneous.

We know that only half of those with diabetes have regular eye exams and one-third have never been checked,” Prof Kumar said.

“But the gold standard methods of diagnosing diabetic retinopathy are invasive or expensive, and often unavailable in remote or developing parts of the world.

“Our AI-driven approach delivers results that are just as accurate as clinical scans but relies on retinal images that can be generated with ordinary optometry equipment.

“Making it quicker and cheaper to detect this incurable disease could be life changing for the millions of people who are currently undiagnosed and risk losing their sight.”

Currently, optical coherence tomography and fluorescein angiography are the most accurate method of diagnosing diabetic retinopathy. A cheaper method uses inexpensive equipment called fundus cameras, however this process is time-consuming and manual.

The researchers used the fundus images, and developed a method of automating the analysis of the images. The team collaborated with researchers in Brazil and used deep learning and artificial intelligence techniques.

The algorithm the team developed accurately and reliably identifies the presence of fluid from damaged blood vessels inside the retina.

The researchers hope that the method could be used for widespread screening of at-risk populations.

“Undiagnosed diabetes is a massive health problem here and around the globe,” Prof Kumar said.

“For every single person in Australia who knows they have diabetes, another is living with diabetes but isn’t diagnosed. In developing countries, the ratio is one diagnosed to four undiagnosed.

“This results in millions of people developing preventable and treatable complications from diabetes-related diseases. With further development, our technology has the potential to reduce that burden.”

The research is published in the journal Computers in Biology and Medicine.

mRNA

Cells can be induced to produce therapeutic proteins by messenger RNA (mRNA), which can then be used to treat numerous diseases. 

Researchers at Massachusettes Institute of Technology (MIT) have designed an inhalable form of mRNA, to overcome the biggest obstacle in this approach – the method of delivery.

The developed aerosol could be administered directly to the lungs to help treat diseases such as cystic fibrosis.

“We think the ability to deliver mRNA via inhalation could allow us to treat a range of different disease of the lung,” said Dr Daniel Anderson, an Associate Professor in MIT’s Department of Chemical Engineering, a member of MIT’s Koch Institute for Integrative Cancer Research and Institute for Medical Engineering and Science (IMES), and the senior author of the study.

During the study, the researchers showed they could induce lung cells in mice to produce a target bioluminescent protein. The team mentioned that should the same success rate be achieved with therapeutic proteins, it could be enough to treat many lung diseases.

Numerous researchers have worked on developing mRNA to treat genetic disorders or cancer, using the patients’ own cells and turning them into tiny drug factories.

Messenger RNA can be easily broken down in the body, and so needs to be transported with some form of protection.

During the study, the team wanted to develop a material that could stabilise the RNA during the process of aerosol delivery. 

Hyperbranched poly (beta amino esters), positively charged biodegradable polymers were used by the researchers to help stabilise the RNA.

The created particles were approximately 150 nanometres in diameter, including a mixture of the polymer and mRNA molecules that encode luciferase, a bioluminescent protein. 

These tiny particles were suspended in droplets and delivered to mice as an inhalable mist, using a nebuliser. 

“Breathing is used as a simple but effective delivery route to the lungs. Once the aerosol droplets are inhaled, the nanoparticles contained within each droplet enter the cells and instruct it to make a particular protein from mRNA,” Assisstant Professor Asha Patel. lead author of the study, said.

The mice produced the protein 24 hours after inhalation, with repeated doses maintaining protein production.

The study was published in the journal Advanced Materials.

cancer

A mechanism for activating the immune system against cancer cells allows immune cells to detect and destroy cancer cells better than before.

The study was led by Professor Nick Haining, at Harvard Medical School, and was co-authored by Professor Erez Levanon, doctoral student Ilana Buchumansky, of the Mina and Everard Goodman Faculty of Life Sciences at Bar-Ilan University, and an international team.

The focus of the study was to develop a mechanism that routinely serves the cell by marking human virus-like genes in order to avoid identifying them as viruses. 

Prof Levanon, together with the Harvard team, discovered during the study that when inhibiting this mechanism, the immune system can be harnessed to fight cancer cells in a particularly efficient manner, and also more effectively in both lung cancer and melanoma.

“We found that if the mechanism is blocked, the immune system is much more sensitive. When the mechanism is deactivated, the immune system becomes much more aggressive against the tumor cells,” said Prof Levanon.

In recent years, a new generation of cancer drugs has been developed which blocks proteins that inhibit immune activity against malignant tumors. These drugs have shown remarkably poisitve success in several tumor types, in some.

This year’s Nobel Prize in Medicine was awarded to James Allison and Tasuku Honjo, who discovered the key genes of this mechanism.

Despite this achievement, the current generation of drugs helps only a small number of patients, while most of the drugs fail to cause the immune system to attack the tumor.

The research team hope that the new discovery will allow enhanced activity of the immune system to attack cancer cells. A number of companies have already begun research to screen for drugs that will operate on the basis of this discovery.

The study was published in the journal Nature.

bladder

Researchers have developed a tiny device that can be implanted to help those with bladder problems.

The team of engineers and neuroscientists, from Washington University School of Medicine in St. Louis, the University of Illinois at Urbana-Champaign, and the Feinberg School of Medicine at Northwestern University in Chicago, developed the soft device in order to help people bypass the need for medication or electronic stimulators. 

The soft, implantable device can detect overactivity in the bladder and then use light from tiny, biointegrated LEDs to tamp down the urge to urinate. The team conducted in vivo investigations in  laboratory rats, and found the device worked, and could be used to help those who suffer from incontinence, or feel the need to frequently urinate. 

“There definitely is benefit to that sort of nerve stimulation,” said Dr Robert W. Gereau IV, the Dr Seymour and Rose T. Brown Professor of Anesthesiology at Washington University School of Medicine, and one of the study’s senior investigators.

Previously, severe bladder problems have been treated using stimulators that send an electric current to the nerve that controls the bladder. These implants improve incontinence, however also disrupted ordinary nerve signalling to other organs.

“But there also are some off-target side effects that result from a lack of specificity with those older devices.”

Prof Gereau and his team developed the new device with the hope to eliminate the side effects of the previous devices.

The team used a minor surgical procedure to implant the soft, stretchy, belt-like device around the bladder. As the bladder fills and empties, the belt expands and contracts. The team also injected proteins called opsins into the bladders of the animals. These proteins are carried by a virus that binds to nerve cells in the bladder, which makes the cells sensitive to light signals.

The researchers then used optogenetics to control and activate the cells, using bluetooth communication.

“When the bladder is emptying too often, the external device sends a signal that activates micro-LEDs on the bladder band device, and the lights then shine on sensory neurons in the bladder. This reduces the activity of the sensory neurons and restores normal bladder function,” Prof Gereau said.

“We’re excited about these results,” said Dr John A. Rogers, the study’s other senior investigator and a Professor of Materials Science and Engineering at Northwestern. “This example brings together the key elements of an autonomous, implantable system that can operate in synchrony with the body to improve health: a precision biophysical sensor of organ activity; a noninvasive means to modulate that activity; a soft, battery-free module for wireless communication and control; and data analytics algorithms for closed-loop operation.”

The article was published in the journal Nature.