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.

News
Tiny robots made from human cells heal damaged tissue
The ‘anthrobots’ were able to repair a scratch in a layer of neurons in the lab. Scientists have developed tiny robots made of human cells that are able to repair damaged neural tissue1. The [...]
Antimicrobial Resistance – A Global Concern
Key facts Antimicrobial resistance (AMR) is one of the top global public health and development threats. It is estimated that bacterial AMR was directly responsible for 1.27 million global deaths in 2019 and contributed to [...]
Advancing Pancreatic Cancer Treatment with Nanoparticle-Based Chemotherapy
Pancreatic cancer, a particularly lethal form of cancer and the fourth leading cause of cancer-related deaths in the western world, often remains undiagnosed until its advanced stages due to a lack of early symptoms. [...]
The ‘jigglings and wigglings of atoms’ reveal key aspects of COVID-19 virulence evolution
Richard Feynman famously stated, "Everything that living things do can be understood in terms of the jigglings and wigglings of atoms." This week, Nature Nanotechnology features a study that sheds new light on the evolution of the coronavirus [...]
AI system self-organizes to develop features of brains of complex organisms
Cambridge scientists have shown that placing physical constraints on an artificially-intelligent system—in much the same way that the human brain has to develop and operate within physical and biological constraints—allows it to develop features [...]
How Blind People Recognize Faces via Sound
Summary: A new study reveals that people who are blind can recognize faces using auditory patterns processed by the fusiform face area, a brain region crucial for face processing in sighted individuals. The study employed [...]
Treating tumors with engineered dendritic cells
Cancer biologists at EPFL, UNIGE, and the German Cancer Research Center (Heidelberg) have developed a novel immunotherapy that does not require knowledge of a tumor's antigenic makeup. The new results may pave the way [...]
Networking nano-biosensors for wireless communication in the blood
Biological computing machines, such as micro and nano-implants that can collect important information inside the human body, are transforming medicine. Yet, networking them for communication has proven challenging. Now, a global team, including EPFL [...]
Popular Hospital Disinfectant Ineffective Against Common Superbug
Research conducted during World Antimicrobial Awareness Week examines the effects of employing suggested chlorine-based chemicals to combat Clostridioides difficile, the leading cause of antibiotic-related illness in healthcare environments worldwide. A recent study reveals that a [...]
Subjectivity and the Evolution of AI Philosophy
An Historical Overview of the Philosophy of Artificial Intelligence by Anton Vokrug Many famous people in the philosophy of technology have tried to comprehend the essence of technology and link it to society and human [...]
How Lockdowns Shaped the Virus: AI Uncovers COVID-19’s Evolutionary Secrets
A new research study shows that human behavior, like lockdowns, influences the evolution of COVID-19, leading to strains that are more transmissible earlier in their lifecycle. Using artificial intelligence technology and mathematical modeling, a research [...]
Groundbreaking therapy approved: chances of cure for 7000 diseases:
Hereditary diseases are usually not curable. Now, however, an epochal turning point is taking place in medicine: For the first time ever, a therapy with the CRISPR/Cas9 gene scissors has received approval. According to [...]
Uncovering the Genetic Mystery: Why Some Never Show COVID-19 Symptoms
New study shows that common genetic variation among people is responsible for mediating SARS-CoV-2 asymptomatic infection. Have you ever wondered why some people never became sick from COVID-19? A study published recently in the journal Nature shows that common [...]
AI maps tumor geography for tailored treatments
Researchers have integrated AI approaches from satellite mapping and community ecology to develop a tool to interpret data obtained from tumor tissue imaging, with the aim of implementing a more individualized approach to cancer care. [...]
Lung cancer cells’ ‘memories’ suggest new strategy for improving treatment
A new understanding of lung cancer cells' "memories" suggests a new strategy for improving treatment, Memorial Sloan Kettering Cancer Center (MSK) researchers have found. Research from the lab of cancer biologist Tuomas Tammela, MD, Ph.D. [...]
Artificial sensor similar to a human fingerprint can recognize fine fabric textures
An artificial sensory system that is able to recognize fine textures—such as twill, corduroy and wool—with a high resolution, similar to a human finger, is reported in a Nature Communications paper. The findings may help improve the subtle [...]