Tag Archives: proteins

AI Detects Alzheimer’s Six Years In Advance

Using a common type of brain scan, researchers programmed a machine-learning algorithm to diagnose early-stage Alzheimer’s disease about six years before a clinical diagnosis is made – potentially giving doctors a chance to intervene with treatment. No cure exists for Alzheimer’s disease, but promising drugs have emerged in recent years that can help stem the condition’s progression. However, these treatments must be administered early in the course of the disease in order to do any good. This race against the clock has inspired scientists to search for ways to diagnose the condition earlier.

A PET scan of the brain of a person with Alzheimer’s disease

One of the difficulties with Alzheimer’s disease is that by the time all the clinical symptoms manifest and we can make a definitive diagnosis, too many neurons have died, making it essentially irreversible,” says Jae Ho Sohn, MD, MS, a resident in the Department of Radiology and Biomedical Imaging at UC San Francisco.

 

Positron emission tomography (PET) scans, which measure the levels of specific molecules, like glucose, in the brain, have been investigated as one tool to help diagnose Alzheimer’s disease before the symptoms become severe. Glucose is the primary source of fuel for brain cells, and the more active a cell is, the more glucose it uses. As brain cells become diseased and die, they use less and, eventually, no glucose.

Other types of PET scans look for proteins specifically related to Alzheimer’s disease, but glucose PET scans are much more common and cheaper, especially in smaller health care facilities and developing countries, because they’re also used for cancer staging.

Radiologists have used these scans to try to detect Alzheimer’s by looking for reduced glucose levels across the brain, especially in the frontal and parietal lobes of the brain. However, because the disease is a slow progressive disorder, the changes in glucose are very subtle and so difficult to spot with the naked eye. To solve this problem, Sohn applied a machine learning algorithm to PET scans to help diagnose early-stage Alzheimer’s disease more reliably.

This is an ideal application of deep learning because it is particularly strong at finding very subtle but diffuse processes. Human radiologists are really strong at identifying tiny focal finding like a brain tumor, but we struggle at detecting more slow, global changes,” says Sohn. “Given the strength of deep learning in this type of application, especially compared to humans, it seemed like a natural application.

To train the algorithm, Sohn fed it images from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), a massive public dataset of PET scans from patients who were eventually diagnosed with either Alzheimer’s disease, mild cognitive impairment or no disorder. Eventually, the algorithm began to learn on its own which features are important for predicting the diagnosis of Alzheimer’s disease and which are not.

Once the algorithm was trained on 1,921 scans, the scientists tested it on two novel datasets to evaluate its performance. The first were 188 images that came from the same ADNI database but had not been presented to the algorithm yet. The second was an entirely novel set of scans from 40 patients who had presented to the UCSF Memory and Aging Center with possible cognitive impairment.

The algorithm performed with flying colors. It correctly identified 92 percent of patients who developed Alzheimer’s disease in the first test set and 98 percent in the second test set. What’s more, it made these correct predictions on average 75.8 months – a little more than six yearsbefore the patient received their final diagnosis.

Source: https://www.ucsf.edu/

Sharpen Molecular Scissors And Expand The Gene Editing Toolbox

Wake Forest Institute for Regenerative Medicine (WFIRM) scientists have figured out a better way to deliver a DNA editing tool to shorten the presence of the editor proteins in the cells in what they describe as a “hit and run” approach.

CRISPR (clustered regularly interspaced short palindromic repeats) technology is used to alter DNA sequences and modify gene function. CRISPR/Cas9 is an enzyme that is used like a pair of scissors to cut two strands of DNA at a specific location to add, remove or repair bits of DNA. But CRISPR/Cas9 is not 100 percent accurate and could potentially cut unexpected locations, causing unwanted results.

One of the major challenges of CRISPR/Cas9 mRNA technologies is the possibility of off-targets which may cause tumors or mutations,” said Baisong Lu, Ph.D, assistant professor of regenerative medicine at WFIRM and one of the lead authors of the paper. Although other types of lentivirus-like bionanoparticles (LVLPs) have been described for delivering proteins or mRNAs, Lu said, “the LVLP we developed has unique features which will make it a useful tool in the expanding genome editing toolbox.

To address the inaccuracy issue, WFIRM researchers asked the question: Is there a way to efficiently deliver Cas9 activity but achieve transient expression of genome editing proteins? They tested various strategies and then took the best properties of two widely used delivery vehicles – lentivirus vector and nanoparticles – and combined them, creating a system that efficiently packages Cas9 mRNA into LVLPs, enabling transient expression and highly efficient editing.

Lentiviral vector is a widely used gene delivery vehicle in research labs and is already widely used for delivering the CRISPR/Cas9 mRNA technology for efficient genome editing. Nanoparticles are also being used but they are not as efficient in delivery of CRISPR/Cas9.

By combining the transient expression feature of nanoparticle-delivery strategies while retaining the transduction efficiency of lentiviral vectors, we have created a system that may be used for packaging various editor protein mRNA for genome editing in a ‘hit and run’ manner,” said Anthony Atala, M.D., director of WFIRM and co-lead author of the paper. “This system will not only improve safety but also avoid possible immune response to the editor proteins, which could improve in vivo gene editing efficiency which will be useful in research and clinical applications.

The WFIRM team published its findings in a paper published recently in the journal  Nucleic Acids Research.

Source: https://school.wakehealth.edu/

 

Potential Revolutionnary Treatment For Alzheimer’s

Leaky capillaries in the brain portend early onset of Alzheimer’s disease as they signal cognitive impairment before hallmark toxic proteins appear, new USC research shows. The findings, which appear in Nature Medicine, could help with earlier diagnosis and suggest new targets for drugs that could slow or prevent the onset of the disease.

The number of Americans with Alzheimer’s is expected to more than double to about 14 million in 40 years, according to the Centers for Disease Control and Prevention. Five Alzheimer’s drugs are approved by the U.S. Food and Drug Administration to temporarily help with memory and thinking problems, but none treats the underlying cause of the disease or slow its progression. Researchers believe that successful treatment will eventually involve a combination of drugs aimed at multiple targets.

USC’s five-year study, which involved 161 older adults, showed that people with the worst memory problems also had the most leakage in their brain’s blood vessels — regardless of whether abnormal proteins amyloid and tau were present.

This image depicts a blood vessel in the brain that has become leaky, or permeable.

The fact that we’re seeing the blood vessels leaking, independent of tau and independent of amyloid, when people have cognitive impairment on a mild level, suggests it could be a totally separate process or a very early process,” said senior author Berislav Zlokovic, director of the Zilkha Neurogenetic Institute at the Keck School of Medicine of USC. “That was surprising that this blood-brain barrier breakdown is occurring independently.”

In healthy brains, the cells that make up blood vessels fit together so tightly they form a barrier that keeps stray cells, pathogens, metals and other unhealthy substances from reaching brain tissue. Scientists call this the blood-brain barrier. In some aging brains, the seams between cells loosen, and the blood vessels become permeable.

If the blood-brain barrier is not working properly, then there is the potential for damage,” said co-author Arthur Toga, director of the USC Mark and Mary Stevens Neuroimaging and Informatics Institute at the Keck School of Medicine. “It suggests the vessels aren’t properly providing the nutrients and blood flow that the neurons need. And you have the possibility of toxic proteins getting in.

Participants in the study had their memory and thinking ability assessed through a series of tasks and tests, resulting in measures of cognitive function and a “clinical dementia rating score.” Individuals diagnosed with disorders that might account for cognitive impairment were excluded. The researchers used neuroimaging and cerebral spinal fluid analysis to measure the permeability, or leakiness, of capillaries serving the brain’s hippocampus, and found a strong correlation between impairment and leakage.

“The results were really kind of eye-opening,” said first author Daniel Nation, an assistant professor of psychology at the USC Dornsife College of Letters, Arts and Sciences. “It didn’t matter whether people had amyloid or tau pathology; they still had cognitive impairment.”

Source: https://news.usc.edu/

How To Use The Body’s Inbuilt Healing System

Imperial researchers have developed a new bioinspired material that interacts with surrounding tissues to promote healing. Materials are widely used to help heal wounds: Collagen sponges help treat burns and pressure sores, and scaffold-like implants are used to repair broken bones. However, the process of tissue repair changes over time, so scientists are looking to biomaterials that interact with tissues as healing takes place.

Now, Dr Ben Almquist and his team at Imperial College London have created a new molecule that could change the way traditional materials work with the body. Known as traction force-activated payloads (TrAPs), their method lets materials talk to the body’s natural repair systems to drive healing.

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The researchers say incorporating TrAPs into existing medical materials could revolutionise the way injuries are treated.

Our technology could help launch a new generation of materials that actively work with tissues to drive healing,” said Dr Almquist, from mperial’s Department of Bioengineering.
After an injury, cells ‘crawl’ through the collagen ‘scaffolds’ found in wounds, like spiders navigating webs. As they move, they pull on the scaffold, which activates hidden healing proteins that begin to repair injured tissue. The researchers in the study designed TrAPs as a way to recreate this natural healing method. They folded the DNA segments into three-dimensional shapes known as aptamers that cling tightly to proteins. Then, they attached a customisable ‘handle’ that cells can grab onto on one end, before attaching the opposite end to a scaffold such as collagen.
During laboratory testing of their technique, they found that cells pulled on the TrAPs as they crawled through the collagen scaffolds. The researchers tailor TrAPs to release specific therapeutic proteins based on which cells are present at a given point in time.

This is the first time scientists have activated healing proteins using differing cell types in man-made materials. The technique mimics healing methods found in nature. “Creatures from sea sponges to humans use cell movement to activate healing. Our approach mimics this by using the different cell varieties in wounds to drive healing,” explains Dr Almquist.”

This approach is adaptable to different cell types, so could be used in a variety of injuries such as fractured bones, scar tissue after heart attacks, and damaged nerves. New techniques are also desperately needed for patients whose wounds won’t heal despite current interventions, like diabetic foot ulcers, which are the leading cause of non-traumatic lower leg amputationsTrAPs are relatively straightforward to create and are fully man-made, meaning they are easily recreated in different labs and can be scaled up to industrial quantities.

TrAPs could harness the body’s natural healing powers to repair bone

TrAPs provide a flexible method of actively communicating with wounds, as well as key instructions when and where they are needed. This intelligent healing is useful during every phase of the healing process, has the potential to increase the body’s chance to recover, and has far-reaching uses on many different types of wounds. This technology could serve as a conductor of wound repair, orchestrating different cells over time to work together to heal damaged tissues,” said Dr Almquist.

The findings are published in Advanced Materials.

Source: https://www.imperial.ac.uk/

 

The Immune System’s Fountain of Youth

If only we could keep our bodies young, healthy and energetic, even as we attain the wisdom of our years. New research at the Weizmann Institute of Science in Israel suggests this dream could be at least partly obtainable in the future. The results of this research, led by Prof. Valery Krizhanovsky and Dr. Yossi Ovadya in the Molecular Cell Biology Department, were recently published in Nature Communications.

The research began with an investigation into the way that the immune system is involved in a crucial activity: clearing away old, senescent cells that spell trouble for the body when they hang around. Senescent cells – not completely dead but suffering loss of function or irreparable damage – have been implicated in diseases of aging by promoting inflammation. The researchers used mice in which a crucial gene for this immune activity was missing. At two years (elderly, for mice), the bodies of these mice had a greater accumulation of senescent cells compared with the mice in which the gene for removing these cells was intact. The mice missing the gene suffered from chronic inflammation, and various functions in their bodies appeared to be diminished. They also looked older – and died earlier – than their normal counterparts.

Drug treatment eliminates senescent cells from tissues of old mice. The blue staining shows senescent cells in lung and liver tissue. The amount of the staining is significantly reduced following the drug treatment

Next, the researchers gave the mice a drug that inhibits the function of certain proteins that help the aging cells survive in their senescent state, to see if this would contribute to the removal of these cells from the body. The drugs were administered to mice whose aging was a result of the malfunctions the group had uncovered in the immune system as well as those suffering premature aging from a different genetic error. The treated mice responded exceptionally well to the drug: Their blood tests and activity tests showed improvement, and their tissues appeared to be much closer to those of young mice. The scientists counted senescent cells, finding many fewer of them remaining in the treated mice’s bodies; and when they looked for signs of inflammation, they found that this, too, was significantly lower. The mice treated with the drug were more active and their median lifespan rose.

Source: https://wis-wander.weizmann.ac.il/

How To Nullify Proteins That Allow Cancer Cells To Grow

A physicist in the College of Arts and Sciences at Syracuse University hopes to improve cancer detection with a new and novel class of nanomaterials. Liviu Movileanu, professor of physics, creates tiny sensors that detect, characterize and analyze protein-protein interactions (PPIs) in blood serum. Information from PPIs could be a boon to the biomedical industry, as researchers seek to nullify proteins that allow cancer cells to grow and spread.

Movileanu’s findings are the subject of a paper in Nature Biotechnology (Springer Nature, 2018), co-authored by Ph.D. student Avinash Kumar Thakur. The National Institutes of Health (NIH) has supported their work with a four-year, $1.17 million grant award.

 

A digital illustration of a cancer cell undergoing mitosis

Detailed knowledge of the human genome has opened up a new frontier for the identification of many functional proteins involved in brief physical associations with other proteins,” Movileanu says. “Major perturbations in the strength of these PPIs lead to disease conditions. Because of the transient nature of these interactions, new methods are needed to assess them.”

Enter Movileanu’s lab, which designs, creates and optimizes a unique class of biophysical tools called nanobiosensors. These highly sensitive, pore-based tools detect mechanistic processes, such as PPIs, at the single-molecule level.

Source: https://news.syr.edu/