An artificial intelligence algorithm can parse gene expression data to predict patient outcomes by identifying signature genes that reveal the severity of viral infection immune response including COVID-19, according to a recent study published in eBiomedicine.
University of California San Diego School of Medicine researchers analyzed over 45,000 transcriptomic datasets from viral pandemics among humans, mice, and rats. They identified a 166-gene signature that sheds light on how the immune system reacts to viral infections. In addition, a signature of 20 genes can predict the severity of a patient’s condition.
“When the COVID-19 pandemic began, I wanted to use my computer science background to find something that all viral pandemics have in common—some universal truth we could use as a guide as we try to make sense of a novel virus,” said Debashis Sahoo, PhD, one of the study’s authors and an assistant professor of pediatrics at UC San Diego School of Medicine and of computer science and engineering at Jacobs School of Engineering, in a press release.
“This coronavirus may be new to us, but there are only so many ways our bodies can respond to an infection.”
The gene signatures “provide a quantitative and qualitative framework for titrating the immune response in viral pandemics and may serve as a powerful unbiased tool to rapidly assess disease severity and vet candidate drugs,” the study stated.
Researchers looked for patterns in viral respiratory infections including swine flu, MERS, and SARS, and validated the algorithm using lung tissues from deceased patients. The 166-gene signature also performed well with identifying and classifying bacterial and fungal infections, which shows promise for the AI model’s effectiveness outside of coronaviruses.
Researchers defined the severity of a disease by ranking the 166 genes. Intubation and medical ventilation were defined as elements of severe disease. With each new dataset that became available, researchers tested the model and found the same gene expression patterns in each case.
“These viral pandemic-associated signatures tell us how a person’s immune system responds to a viral infection and how severe it might get, and that gives us a map for this and future pandemics,” explained Pradipta Ghosh, MD, one of the study’s authors and a professor of cellular and molecular medicine at UC San Diego School of Medicine and Moores Cancer Center, in the press release.
The study’s primary finding is that viral pandemics, regardless of their differences, all share a fundamental host immune response. The 166-gene signature revealed a phenomenon called a cytokine storm, in which the body releases too many cytokines, causing the immune system to attack healthy tissue.
Researchers were also able to define the source of the cytokine storm and revealed that the storm can lead to lung airway cells being damaged, preventing the immune system from killing the cells infected by the virus.
“We could see and show the world that the alveolar cells in our lungs that are normally designed to allow gas exchange and oxygenation of our blood, are one of the major sources of the cytokine storm, and hence, serve as the eye of the cytokine storm,” explained Soumita Das, PhD, co-author and associate professor of pathology at UC San Diego School of Medicine.
Scientists from the Terasaki Institute for Biomedical Innovation (TIBI) have developed a contact lens that can capture and detect exosomes, nanometer-sized vesicles found in bodily secretions which have the potential for being diagnostic cancer [...]
Among the total number of deaths caused by different types of cancer, esophageal cancer is the sixth most significant. Several conventional treatments, such as radiotherapy, chemotherapy, and surgery have multiple side effects, including off-target [...]
Cell membrane-coated nanoparticles, applied in targeted drug delivery strategies, combine the intrinsic advantages of synthetic nanoparticles and cell membranes. Although stem cell-based delivery systems were highlighted for their targeting capability in tumor therapy, inappropriate [...]
When babies in the African countries of Guinea Bissau and Uganda were given the tuberculosis vaccine, something remarkable happened. Instead of the vaccine only protecting against the target bacteria – Myocbacterium tuberculosis – the tuberculosis vaccine offered broad protection against a [...]
Thousands of years ago, across the Eastern Mediterranean, multiple Bronze Age civilizations took a distinct turn for the worse at around the same time. The Old Kingdom of Egypt and the Akkadian Empire both collapsed, and there was [...]
IN OCTOBER 2014, virologist Edward Holmes took a tour of the Huanan Seafood Wholesale Market in Wuhan, a once relatively overlooked city of about 11 million people in the central Chinese province of Hubei. The market would [...]
Self-healable ionic sensing materials with fatigue resistance are imperative in robotics and soft electronics for extended service life. The existing artificial ionic skins with self-healing capacity were prepared by network reconfiguration, constituting low-energy amorphous [...]
As demand for solar energy rises around the world, scientists are working to improve the performance of solar devices—important if the technology is to compete with traditional fuels. But researchers face theoretical limits on [...]
When shrimp shell nanoparticles were mixed into cement paste, the material became substantially stronger — researchers propose an innovation that could lead to less seafood waste and fewer carbon dioxide emissions from concrete production. [...]
A black-and-white video shared on social media showed a microscopic corkscrew-shaped helix as it appeared to consume a sperm, transport it, and ultimately lead the little swimmer into the wall of an [...]
Polymers containing quantum dots (QDs) are considered crucial components of next-generation consumer items, but ambiguity remains regarding how these compounds may negatively affect public health and the environment. A pre-proof paper from the Journal of Hazardous [...]
A new copper coating that kills bacteria quicker and in greater amounts than current formulations could soon be available for hospitals and other high-traffic facilities. Although current formulations made of pure copper are antibacterial [...]
A vaccination as tumor therapy - with a vaccine individually created from a patient's tissue sample that " attaches" the body's own immune system to cancer cells: the basis for this long-term vision has [...]
Although retinoic acid (RA) can induce cell death, its weak anticancer efficacy limits its clinical applications. To this end, stimulus-responsive self-assembling prodrug-based nanomedicines are promising candidates that enable controlled drug delivery. In an article [...]
Graphene is a multifunctional carbon nanomaterial widely synthesized for its applications in composites, energy storage, and sensors. Although previous reviews mentioned that achieving an increased yield compromises graphene quality, limiting its commercialization, recent research [...]
A new COVID variant has recently been detected in several countries including the UK, US, India, Australia and Germany. Called BA.2.75, it’s a subvariant of omicron. You might have also heard it called “Centaurus”, the [...]